Allyson Lister Andy Brown Duncan Hull Helen Parkinson James Malone Jon Ison Nandini Badarinarayan Robert Stevens The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. https://creativecommons.org/licenses/by/4.0/ Software Ontology The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licensing, provenance and associated data. It contains SWO-specific classes and axioms as well as imports from: 1. BFO 2. IAO 3. OBI 4. EDAM 2023-03-05 editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not. A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO example of usage example of usage definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor description Mark Miller 2018-05-11T13:47:29Z license title The version in which a class or property has been made obsolete EFO Development Team obsoleted in version is defined by is defined by This is an experimental annotation label label deprecated Allyson Lister 14.9.22: Added as a temporary workaround with issues relating to equivalentClass axioms between IAO software and SWO software. 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. IAO James Malone Alan Ruttenberg is about is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer OBI is manufactured by is_manufactured_by objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in Andy Brown Please see the official RO definition for the inverse of this property, 'has participant.' participates in participates in has participant The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant Andy Brown has participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B. inverse of has input Allyson Lister input of input of A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software. An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B. inverse of has output Allyson Lister output of output of inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Replaced by rdfs:comment as no longer within the EFO release files. obsolete reason_for_obsolescence true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete is developed by true The relationship between software and a software publisher. Marked as obsolete by Allyson Lister. 0.5 This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead. obsolete_is_published_by true Marked as obsolete by Allyson Lister. 1.4 This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage. has legal status true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete implements true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete is encoded in true 'is version of' provides a link between a 'version name' and the entity with that version. Allyson Lister For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ is version of Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use. Allyson Lister uses software is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. James Malone is implemented by The relationship between input data which is permitted to a piece of software. James Malone AL 2.9.22: This cannot be a child of 'has specified input' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ has specified data input The relationship between a piece of software and the data that it is possible to output. James Malone AL 2.9.22: This cannot be a child of 'has specified output' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ has specified data output The relationship between a data and the software which can possibly take this data as input. James Malone AL 2.9.22: This cannot be a child of 'is specified input of' or 'input of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. is specified data input of The relationship between a data and the software which can possibly produce this data as output. James Malone AL 2.9.22: This cannot be a child of 'is specified output of' or 'output of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. is specified data output of Microsoft version 2007 is directly preceded by Microsoft version 2003. Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. Allyson Lister OBO Foundry directly preceded by 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. Allyson Lister directly followed by 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. Allyson Lister This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations. uses platform is software for AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' (which was the original parent for 'directly followed by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class that performs a similar function to BFO 'precedes' but without the domain/range restrictions. followed by AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' and 'preceded by' (which was the original parent for 'directly preceded by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class (and this, its inverse) that performs a similar function to BFO 'precedes' but without the domain/range restrictions. follows The relationship between a software and software developer. is developed by implements is the relationship between software and an algorithm that is defined for use within that software when executed. James Malone implements Linking a type of software to its particular programming language. Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class. Allyson Lister is encoded in relationship between an entity and a version name or number For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ has version Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. Allyson Lister Andy Brown Andy Brown has interface Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. Allyson Lister has format specification Marked as obsolete by Allyson Lister. James Malone 0.3 is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead. obsolete_is developed by true 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. Allyson Lister James Malone is published by Stores those object properties which are no longer appropriate for use within SWO. Marked as obsolete by Allyson Lister Allyson Lister obsolete object property is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, Allyson Lister Allyson Lister OBI is executed in Marked as obsolete by Allyson Lister. 0.3 There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead. obsolete_is specified output of true Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied. Allyson Lister has clause The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license. has license The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. is license for The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format. With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data. Allyson Lister is alternative format of 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program. http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013. Allyson Lister is compatible license of 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information. Allyson Lister has declared status 1.4 Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class. obsolete_has_participant true Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". OBO Foundry RO part of Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. Allyson Lister has documentation The location from where the software can be downloaded. Allyson Lister Allyson Lister has download location The URL of the homepage for the resource this property is associated with. Allyson Lister has website homepage Andy Brown The official date of release of software has release date Andy Brown A URL for a source of support information about software has support URL An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. Ontologies Ontology A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. Heat map Heatmap Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification. Gene product profile Gene product quantification data Gene transcription profile Gene transcription quantification data Microarray data Non-coding RNA profile Non-coding RNA quantification data RNA profile RNA quantification data RNA-seq data Transcriptome profile Transcriptome quantification data mRNA profile mRNA quantification data Gene expression data Microarray data Biological or biomedical data has been rendered into an image, typically for display on screen. Image data Image Groupings of gene expression profiles according to a clustering algorithm. Clustered gene expression profiles PDBML Format of Taverna workflows. Taverna workflow format newick FASTA format Genbank entry format. GenBank GenBank format GFF Textual format html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. http://www.w3.org/TR/html401/ James Malone HTML Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C. James Malone XML binary format OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. OBO flat file format OBO Flat File Format Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. Systems Biology Markup Language http://sbml.org SBML BED format The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools. PSI-MI format PSI-MIF Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012. Allyson Lister MAGE-ML MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. http://www.mged.org/mage-tab/ A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. MAGE-TAB CopasiML, the native format of COPASI. CopasiML Search or query a data resource and retrieve entries and / or annotation. Database retrieval Query Query and retrieval Annotate a genome sequence with terms from a controlled vocabulary. Metagenome annotation Genome annotation Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. Mathematical modelling Modelling and simulation data visualization algorithm data cleaning algorithm data selection algorithm data integration algorithm A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset. data processing task data construction algorithm Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed. OntoDM generalization specification Allyson Lister A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output. data processing algorithm http://purl.obolibrary.org/obo/OBI_0200111 1.7 AL 25.9.19: Already obsoleted in originating ontology (OntoDM) so added here so people could see the history of the term. data visualization task is information processing objective achieved by a data visualization algorithm execution process. data visualization task true APOLLO_SV:00000008 A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development APOLLO_SV:00000796 creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000040 material MaterialEntity material entity material entity Collection of random bacteria, a chair, dorsal surface of the body. a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. BFO A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function GO:0003674 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process biological process physiological process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process GO:0008150 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000005 objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000007 Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO:0000009 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label IAO:0000010 software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software http://www.ebi.ac.uk/swo/SWO_0000001 IAO:0000025 programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert IAO OBI_0000058 group:OBI programming language programming language IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item http://www.ontobee.org/browser/rdf.php?o=IAO&iri=http://purl.obolibrary.org/obo/IAO_0000027 IAO:0000028 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert IAO OBI_0000142 information content entity information content entity IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000037 dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot IAO:0000038 graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph IAO:0000064 algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch IAO OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm algorithm IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000096 source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module IAO:0000098 data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 IAO:0000129 version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version name version number IAO:0000178 material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer IAO:0000179 histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram IAO:0000180 heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap IAO:0000183 dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram IAO:0000184 scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure IAO:0000309 diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000409 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type NCBITaxon:10239 Viruses Viruses NCBITaxon:117571 Euteleostomi bony vertebrates Euteleostomi NCBITaxon:2 Bacteria eubacteria Bacteria NCBITaxon:2157 Archaea Archaea NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eukaryota NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:32523 Tetrapoda tetrapods Tetrapoda NCBITaxon:32524 Amniota amniotes Amniota NCBITaxon:33154 Opisthokonta Opisthokonta NCBITaxon:33208 Metazoa metazoans multicellular animals Metazoa NCBITaxon:33213 Bilateria Bilateria NCBITaxon:40674 Mammalia mammals Mammalia NCBITaxon:7742 Vertebrata <vertebrates> Vertebrata vertebrates Vertebrata <vertebrates> NCBITaxon:9606 Homo sapiens human human being Homo sapiens OBI:0000011 planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000014 regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role OBI:0000017 regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role OBI:0000018 material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role OBI:0000023 classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set OBI:0000047 processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000094 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization organization OBI:0000450 regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency OBI:0000456 material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective OBI:0000457 manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing OBI:0000458 manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective OBI:0000571 manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role OBI:0000648 clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set OBI:0000659 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000663 class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation OBI:0000684 specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0000700 support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine OBI:0000704 decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective OBI:0000707 decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation OBI:0000713 GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software OBI:0000726 peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching OBI:0000727 k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors OBI:0000749 CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART OBI:0000792 statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation OBI:0000835 manufacturer A person or organization that has a manufacturer role manufacturer OBI:0000947 service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role OBI:0000953 processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen OBI:0000963 categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label OBI:0001000 questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire OBI:0001930 categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification OBI:0001933 value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification OBI:0002076 collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens OBI:0002205 histologic grade according to AJCC 7th edition G1:Well differentiated G4: Undifferentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition OBI:0002210 histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System OBI:0002215 histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor OBI:0002216 histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system OBI:0002219 histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization OBI:0002224 pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition OBI:0002232 pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition OBI:0002243 pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition OBI:0002256 pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition OBI:0002270 pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition OBI:0002279 pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition OBI:0002284 pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition OBI:0002287 pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition OBI:0002290 pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition OBI:0002298 pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition OBI:0002306 pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition OBI:0002310 pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition OBI:0002314 clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition OBI:0002326 International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification OBI:0002341 International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification OBI:0002356 performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification OBI:0002357 Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification OBI:0002363 Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification OBI:0002989 material supplier A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:0200033 leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method OBI:0200041 k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering OBI:0200042 hierarchical clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering OBI:0200050 dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction OBI:0200051 principal components analysis dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction OBI:0200111 data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization OBI:0200166 data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective OBI:0200171 partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation OBI:0200172 partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective OBI:0200175 class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation OBI:0200178 class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective OBI:0200179 class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective OBI:0200188 cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective OBI:0200190 clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality PATO:0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG UO:0000001 length unit A unit which is a standard measure of the distance between two points. length unit UO:0000002 mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit UO:0000003 time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit UO:0000005 temperature unit temperature unit UO:0000006 substance unit substance unit UO:0000051 concentration unit concentration unit UO:0000095 volume unit volume unit UO:0000105 frequency unit frequency unit UO:0000270 volumetric flow rate unit volumetric flow rate unit UO:0000280 rate unit rate unit http://www.ebi.ac.uk/swo/data/SWO_3000069 1.7 AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/16 obsolete sequence feature format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete matlab software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 2-sample pooled t-test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 50-50 MANOVA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ABarray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ACME' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Algorithms for Calculating Microarray Enrichment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix Expression Console true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AIDA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Average log expression across arrays (ALE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ALL/AML data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AMDIS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ANCOVA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ANOVA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AP-MS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ARACNE algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ARR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AWS algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Absolute Expression Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Absolute Expression Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AffyCompatible' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AffyExpress' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix GCOS v1.2 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix GeneChip Operating Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agi4x44PreProcess true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction 5.1.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version 7.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version 7.5 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version A.5.1.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Scan Control true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Technologies Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AnnotationDbi' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Applied Biosystems 1700 Expression Array System Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayGauge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ArrayTools' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayVision true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayVision 6.0 (Imaging Research Inc.) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Array_vision_(Interfocus) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AtlasImage true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Axon GenePix Pro 3 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BAC true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Binning clustering method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BCRANK' true Marked as obsolete by Allyson Lister. After 0.4 release. Equivalence with EDAM term "BED" (format_3003). obsolete_BED format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BGL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BGmix' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BLAST true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iterative Bayesian Model Averaging (BMA) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Base-Pair-Distance Kernel true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BPMAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BRB-ArrayTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BSgenome' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BZScan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BaldiLongT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BasReader 3.01 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bayesian Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Beadstudio true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BicARE' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BioMVCClass' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Biobase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BiocCaseStudies' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BioConductor Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Biostrings' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BlueFuse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BufferedMatrix' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BufferedMatrixMethods' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CALIB' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CAMERA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CBS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CBS algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CDF binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CEL binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHbase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHcall' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHregions' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CHP binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CLR algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CMA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CORREP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CRLMM algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CARMAweb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Category analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Category true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ChemmineR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipReader 3.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipSkipper true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipSkipper V0.99 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete multiscan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affycomp true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PCMG true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Feature Extraction Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Chi-square true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Annotation-Driven Clustering true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete distance calculation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BCRANK true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Cosmo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete F test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAGE-TAB inputting software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Text data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CSV data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Non-linear functional regression model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CoCiteStats' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CodeLink Expression Analysis Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CodeLink Expression Scanning Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Complex Estimation Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Cyber-T true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DEDS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DFP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Discriminant Fuzzy Pattern Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete DFW true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Digital gene expression (DGE) datasets true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DNAcopy' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DynDoc' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'EBImage' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'EBarrays' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Expectation-Maximization(EM) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Empirical Bayes rule true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Expert 2100 true Marked as obsolete by Allyson Lister. 0.5 This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method. obsolete_FACS ( fluorescence-activated cell sorter) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FACS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FARMS true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM term format_1929. Please use this term instead. obsolete_FASTA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FC true Marked as obsolete by Allyson Lister 0.5 Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class. obsolete_FCS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'FDR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Fixed effect model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Firth's bias reduction procedure true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Fischer's Exact Test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FoxDimmicT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GACK true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GASSCO method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GC-RMA Quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEMTools 2.4 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEO data type true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEO Matrix Series format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEOmetadb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEOquery true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GGBase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gamma Gamma Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GGtools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GLAD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GLEAMS software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GMS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GOstats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene Recommender algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GSEABase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GSEAlm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gamma-Gamma hierarchical model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gaussian locally weighted regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene-Set Enrichment Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneData Expressionist Analyst v4.0.5 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene Pix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 3.0.6 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 4.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 4100A true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 5.0.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 3 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 5.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 6.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 6 [Axon Instruments] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro [Axon Instruments] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneRegionScan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneRfold true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSelectMMD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSelector true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSpring true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSpringGX true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneTac Analyser true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneTraffic true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 3.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsBase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsPed true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenomeGraphs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GlobalAncova true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GOSemSim true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GraphAT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GraphAlignment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GridGrinder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hexagon binning algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HELP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HEM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Heterogeneous Error Model (HEM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hubert’s gamma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hidden Markov Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hidden Variable Dynamic Modelling HVDM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HaarSeg algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hardy-Weinberg equilibrium true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Harshlight true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Heatplus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HilbertVis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HilbertVisGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hypergeometric probability true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ICS-501 (version 2.3) Image Capture System true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iteratively ReWeighted Least Squares true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete IRanges true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ITALICS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ILLUMINA data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene4.1 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene 3.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImageQuant true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImageReader true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Imagene v4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Initial microarray data processing (data filtering, local normalisation and quality control) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Jaccard’s index true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Jaguar true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KCsmart true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KEGGSOAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KEGGgraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KGML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'KLD' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Kolmogorov Smirnov rank-sum based algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LBE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LC-MS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LMGene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Locally Moderated Weighted-t (LMW) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Lognormal Normal Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Lognormal Normal with Modied Variance Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LPE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LPEadj true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete publisher role true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Langmuir Isotherm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Laplace mixture model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Library Search Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Loess algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Logic regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAANOVA v1.2 package for MATLAB true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Median Average Difference Algorithm true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM format_3161. obsolete_MAGE-ML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MANOR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAQC data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MIcroarray Analysis Suite true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MicroArraySuite 5.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MATLAB language true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAVI Pro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multivariate correlation estimator true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Markov Chain Monte Carlo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MCR algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MCRestimate true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MEDME true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'MI' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mutual information matrix (MIM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MLInterfaces true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MMD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MVCClass true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mahalanobis distance true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MantelCorr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MassSpecWavelet true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MeasurementError.cor true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MergeMaid true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mfuzz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MiPP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Misclassification-Penalized Posteriors (MiPP) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MicroArraySuite 4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mixed model equations true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Needleman-Wunsch' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Nested Effects Models true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Nonlinear Estimation by Iterative Partial Least Squares true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OCplus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OLIN true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OLINgui true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Optiquant true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OrderedList true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OutlierD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Presence-Absence calls with Negative Probesets (PANP) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PAnnBuilder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Pearson correlation estimator true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PCpheno true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PGSEA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'PLM' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PLPE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Probe level Locally moderated Weighted median-t (PLW) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PPC algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PROcess true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Propagation of uncertainty in microarray analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Pathways 2.01 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Power Law Global Error Model (PLGEM) analysis method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Probe Cell Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray scanner software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray, PackaardBiochip technologies true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray version 2 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Radial basis function true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RBGL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R interface to boost graph library algorithm (RBGL) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RBioinf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Random effects model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Recursive Feature Elimination (RFE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RLMM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Regression model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA+ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA++ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress 2.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAGEML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RNAither true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ROC true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RWebServices true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RankProd true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RbcBook1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rdbi true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RdbiPgSQL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rdisop true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RefPlus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Resourcerer true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rgraphviz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Ringo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rintact true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rmagpie true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rnw true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Robust likelihood-based survival modeling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rosetta Resolver true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RpsiXML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rredland true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rtreemix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Ruuid true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete S-Score algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Serial Analysis of Gene Expression (SAGE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAGx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAS/STAT Software, Version 8 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SBMLR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SBMLR format true Marked as obsolete by Allyson Lister 0.4 Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037 obsolete_SBML file true Marked as obsolete by Allyson Lister. 0.5 'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'. obsolete_SBML model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SDF format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SIM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SLGI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SLqPCR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SMAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SNPRMA algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SNPchip true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SPIA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Semantic Similarity Measures true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SSPA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SVDimpute algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software developer role true Information processing is a process in which input information is analysed or transformed in order to produce information as output. James Malone Marked as obsolete by Allyson Lister. 0.4 Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead. obsolete_Information processing true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software developer organization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software publisher organization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 50-50 MANOVA algorithm true Marked as obsolete by Allyson Lister. 0.4 There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead. obsolete_html true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayExpress Bioconductor true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene list true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Clustered data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R data frame true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R language true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScISI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanAlyze true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanArray v3.1 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete scanning software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Scanning software G2565AA version A6.3.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ShortRead true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Signaling Pathway Impact Analysis (SPIA) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Silicon Genetics Genespring true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Similarity score true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Smith-Waterman' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spot quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spotfinder [TIGR] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spotfire true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TAS Software true Marked as obsolete by Allyson Lister. 0.4 SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead. obsolete_TIFF image true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TargetSearch true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Theodore Ts’o’s true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TypeInfo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Variance-stabilizing transformation (VST) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete VanillaICE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete WilcEbam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Wilcoxon true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete XDE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete XDotsReader true Marked as obsolete by Allyson Lister. 0.4 5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead. obsolete_XML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Xba.CQV and Xba.regions true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Array Comparative Genomic Hybridization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Acuity true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affxparser true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyContam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyImGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'affyPLM' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyPara true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyQCReport true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyTiling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'affycoretools' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyio true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affypdnn true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete altcdfenvs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete annaffy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'annotate' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete data annotation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete annotationTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Annotation data packages true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'apComplex' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete aroma.light true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayMvout true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayQuality true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayQualityMetrics true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayWoRx 2.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayWoRx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Associative T method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AvgNRRs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'beadarray' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'beadarraySNP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'betr' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bgafun true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bgx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bitmap object true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bioDist true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocDatasets' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocGraph' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocViews' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete biomaRT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bootstrap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'bridge' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cdt true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'cellHTS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'cellHTS2' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cghMCR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete chamber slide format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cls true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'clusterStab' true Marked as obsolete by Allyson Lister. 0.4 The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead. obsolete_Clustering algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'codelink' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dataset comparison true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Concordance true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete convert true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete copa true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cosmo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cosmoGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete covdesc file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete database creation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete crlmm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ctc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dChip true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete daMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dcf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete design file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'diffGeneAnalysis' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'domainsignatures' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'dualKS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dyebias true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Dynamic programming algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ecolitk true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete edd true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'edgeR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete exonmap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'explorase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'externalVector' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete f-test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete factDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete fbat true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete fdrame true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flagme true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowClust true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowCore true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowFlowJo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowQ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowStats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowUtils true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowViz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gaga true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'gaggle' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gcRMA quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gcrma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gct true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'genArise' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gene2pathway true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete geneRecommender true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene array analysis algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gene expression analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene expression dataset true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genefilter true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genemeta true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete geneplotter true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genomeIntervals true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM format_2305. obsolete_gff format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Global test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete globaltest true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gmt format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete goProfiles true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete goTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gpls true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gpr format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete graph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gtr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gxl format true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM data_1636. obsolete_Heatmap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hexbin true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hierarchical clustering true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hopach true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HTML report true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hypergeometric enrichment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hypergraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Icens true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete idiogram true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM data_2968 obsolete_Image true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete impute true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete iterativeBMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete iterativeBMAsurv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iterative local regression and model selection true Marked as obsolete by Allyson Lister. 0.4 The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead. obsolete_.java file true Marked as obsolete by Allyson Lister. 0.4 SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead. obsolete_jpeg true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-cores true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-means true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-nearest neighbour classification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete keggorth true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lapmix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Likelihood method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete limma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete limmaGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Linear modelling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Local-pooled-error true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete log file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logicFS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logicFS dataset true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logitT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Logit-t algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lumi true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maCorrPlot true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maDB true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maSigPro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maanova true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete macat true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete made4 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maigesPack true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete makePlatformDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete makecdfenv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete marray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'MAS5' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mas5 format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete matchprobes true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mdqc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete M-estimation regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete metaArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Meta data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete metahdep true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete miRNApath true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete microRNA true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalent to EDAM class data_2603. obsolete_Microarray data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete minet true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mrnet algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multinomial probit regression with Gaussian Process priors true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multiple testing true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multivariate t mixture models true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete multtest true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Negative binomial distribution true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nem true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Neural networks models true Marked as obsolete by Allyson Lister Obsoleted after the 0.4 release. Equivalence with EDAM format_1910. obsolete_newick true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nnNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nudge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete occugene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oligo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oligoClasses true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OMICS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oneChannelGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ontoTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pair file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pamr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete panp true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete parody true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete parse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pathRender true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pcaMethods true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pcot2 true Marked as obsolete by Allyson Lister. 0.4 SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead. obsolete_pdf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pdInfoBuilder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pdmclass true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pedigree data file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pgUtils true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pickgene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pkgDepTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plgem true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plier true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Graph plot true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plw true Marked as obsolete by Allyson Lister. 0.4 SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead. obsolete_png true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Position weight matrix (PWM ) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ppiStats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete prada true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete preprocessCore true Marked as obsolete by Allyson Lister. 0.4 An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead. obsolete_ps true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete puma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qPCR data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qpcrNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qpgraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Quantile normalization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Quantile regression techniques true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete quantsmooth true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qvalue true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rHVDM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rMAT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rama true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rank-invariant set normalization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rank product non-parametric method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .raw files true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rbsurv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rda true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete reb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rflowcyt true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .rma format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rsbml true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rtracklayer true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete safe true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sagenhaft true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete seqLogo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sigPathway true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete siggenes true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Sim method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete simpleaffy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete simulatorAPMS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sizepower true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xmapbridge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete snapCGH true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete snpMatrix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spikeLI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spkTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete splicegear true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete splots true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spotSegmentation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sproc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sqlite true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sscore true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ssize true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete stam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Statistical tests true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete stepNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 't-test' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tilingArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete timecourse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tkWidgets true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete topGO true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tspair true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete twilight true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Two-stage measurement error model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete vbmp true http://purl.obolibrary.org/obo/OBI_0200111 1.7 AL 25.9.19: Redundant with http://purl.obolibrary.org/obo/OBI_0200111 obsolete data visualization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete vsn true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete weaver true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete webbioc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete widgetTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xcms true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xps true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete yaqcaffy true swo:SWO_0000001 Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations. James Malone Modified in parts from https://en.wikipedia.org/wiki/Software Robert Stevens AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship. software http://purl.obolibrary.org/obo/IAO_0000010 swo:SWO_0000002 A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence. Modified from http://en.wikipedia.org/wiki/Software_license James Malone licence software license swo:SWO_0000003 Information processing is a process in which input information is analysed or transformed in order to produce information as output. James Malone http://purl.obolibrary.org/obo/OBI_0200000 1.7 AL 18.9.2019: This class is identical (based on its definition) with OBI 'data transformation' and is no longer required. obsolete information processing true http://office.microsoft.com/ 2007-01-30T0:00:00 swo:SWO_0000004 Microsoft Excel 2007 is a spreadsheet editing and viewing tool. Microsoft Excel 2007 http://www.mathworks.com/products/matlab/ swo:SWO_0000005 MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB Nandini Badarinarayan MATLAB http://protege.stanford.edu/ swo:SWO_0000006 Protege 4 http://www.omnigroup.com/products/omnioutliner/ swo:SWO_0000007 OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group OmniOutliner swo:SWO_0000008 Racket is a Scheme-based language interpreter and programming environment Racket http://www.kakadusoftware.com swo:SWO_0000009 Kakadu swo:SWO_0000010 WordStar http://www.jetbrains.com/idea/ swo:SWO_0000011 IntelliJ IDEA is a commercial Java IDE for developing software. IntelliJ IntelliJ IDEA http://www.java.com swo:SWO_0000012 Java http://www.copasi.org swo:SWO_0000013 COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 24 March 2015. COPASI swo:SWO_0000014 Microsoft Excel 2003 is a spreadsheet editing and viewing tool. Microsoft Excel 2003 swo:SWO_0000015 Microsoft Excel 2002 swo:SWO_0000016 MATLAB 7 swo:SWO_0000017 MATLAB 6 swo:SWO_0000018 MATLAB 7.12 swo:SWO_0000019 STARLIMS swo:SWO_0000020 Unix swo:SWO_0000021 An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources. operating system swo:SWO_0000022 Linux swo:SWO_0000023 Microsoft Word 2001 swo:SWO_0000024 Adobe Illustrator is a graphics editor for creating and editing vector graphics. James Malone Adobe Illustrator 10 swo:SWO_0000025 Microsoft Word swo:SWO_0000026 software with image input http://oboedit.org/ swo:SWO_0000027 OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. OBO edit OBO-Edit swo:SWO_0000028 ontology engineering software swo:SWO_0000029 Microsoft developed software swo:SWO_0000030 software with command line interface http://www.peterborgapps.com/smultron/ swo:SWO_0000031 Smultron swo:SWO_0000032 Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions Scan Control Application software http://www.chem.agilent.com/ Nandini Badarinarayan Agilent Scan Control swo:SWO_0000034 Nandini Badarinarayan Agilent Technologies Software swo:SWO_0000035 This package provides user interface and database connection code for annotation data packages using SQLite data storage. http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html Nandini Badarinarayan 'AnnotationDbi' swo:SWO_0000037 Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results. http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp Nandini Badarinarayan Applied Biosystems 1700 Expression Array System Software swo:SWO_0000039 Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop. ArrayGauge [FUJIFILM] http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/ Nandini Badarinarayan ArrayGauge swo:SWO_0000040 ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis. http://bin.tugraz.at/Tools/ArrayNorm.html Nandini Badarinarayan ArrayNorm swo:SWO_0000041 This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html Nandini Badarinarayan 'ArrayTools' swo:SWO_0000042 This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting. Nandini Badarinarayan ArrayVision ftp://ftp.ncbi.nih.gov/blast/executables/ swo:SWO_0000044 The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763) Allyson Lister BLAST+ 2.2.26 swo:SWO_0000045 Nandini Badarinarayan Array_vision_(Interfocus) swo:SWO_0000047 Nandini Badarinarayan Axon GenePix Pro 3 swo:SWO_0000048 This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments http://bioconductor.org/packages/2.4/bioc/html/BAC.html Nandini Badarinarayan BAC swo:SWO_0000049 binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory eciency by avoiding the calculation of an all-against-all distance matrix. Binning clustering method swo:SWO_0000050 Ensembl swo:SWO_0000051 Multiple alignment program for nucleic acid or protein sequences. http://www.clustal.org/, Accessed 13 June 2012. Allyson Lister Clustal swo:SWO_0000052 Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. http://www.clustal.org/omega/, Accessed 13 June 2012 Allyson Lister Clustal Omega swo:SWO_0000053 Allyson Lister ClustalW swo:SWO_0000054 Allyson Lister ClustalX http://dx.doi.org/10.1038/msb.2011.75 swo:SWO_0000055 Allyson Lister Clustal Omega 1.1 http://dx.doi.org/10.1093/bioinformatics/btm404 swo:SWO_0000056 Allyson Lister ClustalW 2.1 http://dx.doi.org/10.1093/bioinformatics/btm404 swo:SWO_0000057 Allyson Lister ClustalX 2.1 swo:SWO_0000058 Allyson Lister EBI Clustal W2 Web Tool swo:SWO_0000059 Allyson Lister EBI Clustal Omega Web Tool swo:SWO_0000060 Allyson Lister MUSCLE swo:SWO_0000061 Allyson Lister EBI Muscle Web Tool http://dx.doi.org/10.1093/nar/gkh340 http://www.drive5.com/muscle/muscle_userguide3.8.html http://www.drive5.com/muscle/downloads.htm swo:SWO_0000062 Allyson Lister MUSCLE 3.8.31 swo:SWO_0000063 Allyson Lister Drive5 MUSCLE swo:SWO_0000064 Allyson Lister TCoffee http://dx.doi.org/10.1006/jmbi.2000.4042 swo:SWO_0000065 TCoffee is a multiple sequence alignment program with a number of different modes. Allyson Lister CRG TCoffee swo:SWO_0000066 Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL. Allyson Lister EBI TCoffee Web Tool http://dx.doi.org/10.1093/nar/gkn278 swo:SWO_0000067 Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software. http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 Allyson Lister CRG RCoffee Web Tool http://dx.doi.org/10.1093/nar/gkr245 swo:SWO_0000068 Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 Allyson Lister CRG TCoffee Web Tool http://dx.doi.org/10.1093/nar/gkm333 swo:SWO_0000069 Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software. http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 Allyson Lister CRG MCoffee Web Tool http://dx.doi.org/10.1093/nar/gkl092 swo:SWO_0000070 Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software. http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 Allyson Lister CRG Expresso Web Tool http://dx.doi.org/10.1093/nar/gkr245 swo:SWO_0000071 Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software. http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 Allyson Lister CRG PSICoffee Web Tool swo:SWO_0000072 The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface. Allyson Lister CRG TCoffee 9.02.r1228 http://xray.bmc.uu.se/~aqwww/q/ swo:SWO_0000073 Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities. Allyson Lister Q Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities. http://xray.bmc.uu.se/~aqwww/q swo:SWO_0000074 Q 4.2 swo:SWO_0000075 Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. Allyson Lister SPSS http://www-01.ibm.com/software/uk/analytics/spss/downloads.html swo:SWO_0000076 Allyson Lister SPSS 20.0 swo:SWO_0000077 Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. SAM http://bioinformatics.org/wiki/SAM, Accessed 19 June 2012. Allyson Lister Sequence Alignment and Modeling System swo:SWO_0000078 SAM 3.5 http://dx.doi.org/10.1101/gr.1239303 swo:SWO_0000079 Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. http://www.cytoscape.org/what_is_cytoscape.html, Accessed June 20, 2012. Allyson Lister Cytoscape http://www.cytoscape.org/download.html swo:SWO_0000080 Cytoscape 2.8 swo:SWO_0000083 This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as "ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)" Allyson Lister Plugin swo:SWO_0000084 CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. Allyson Lister It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CEL format. As such, this class has been renamed as the binary format, and a new class created (CEL ASCII format) to make both options available. (22/05/2013) CEL binary format https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R swo:SWO_0000090 R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R Gene Expression Atlas at EBI R statistics package swo:SWO_0000091 http://dbpedia.org/resource/ActionScript ActionScript swo:SWO_0000092 http://dbpedia.org/resource/Ada_(programming_language) Ada swo:SWO_0000093 http://dbpedia.org/resource/AppleScript AppleScript swo:SWO_0000094 Assembly swo:SWO_0000095 http://dbpedia.org/resource/C_(programming_language) C swo:SWO_0000096 http://dbpedia.org/resource/C_Sharp_(programming_language) C Sharp swo:SWO_0000097 http://dbpedia.org/resource/C++ C++ swo:SWO_0000098 http://dbpedia.org/resource/COBOL COBOL swo:SWO_0000099 http://dbpedia.org/resource/ColdFusion_Markup_Language ColdFusion swo:SWO_0000100 http://dbpedia.org/resource/D_(programming_language) D swo:SWO_0000101 Delphi swo:SWO_0000102 http://dbpedia.org/resource/Dylan_(programming_language) Dylan swo:SWO_0000103 http://dbpedia.org/resource/Eiffel_(programming_language) Eiffel swo:SWO_0000104 http://dbpedia.org/resource/Forth_(programming_language) Forth swo:SWO_0000105 http://dbpedia.org/resource/Fortran Fortran swo:SWO_0000106 http://dbpedia.org/resource/Groovy_(programming_language) Groovy swo:SWO_0000107 http://dbpedia.org/resource/Haskell_(programming_language) Haskell swo:SWO_0000108 http://dbpedia.org/resource/JavaScript JavaScript swo:SWO_0000109 LabVIEW swo:SWO_0000110 http://dbpedia.org/resource/Lisp_(programming_language) Lisp swo:SWO_0000111 http://dbpedia.org/resource/Lua_(programming_language) Lua swo:SWO_0000112 Maple swo:SWO_0000113 Mathematica swo:SWO_0000114 http://dbpedia.org/resource/Pascal_(programming_language) Pascal swo:SWO_0000115 http://dbpedia.org/resource/Perl Perl swo:SWO_0000116 http://dbpedia.org/resource/PHP PHP swo:SWO_0000117 http://dbpedia.org/resource/Prolog Prolog swo:SWO_0000118 Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles. http://dbpedia.org/resource/Python_(programming_language), accessed 27 November 2014. Python swo:SWO_0000119 http://dbpedia.org/resource/REXX REXX swo:SWO_0000120 http://dbpedia.org/resource/Ruby_(programming_language) Ruby swo:SWO_0000121 SAS swo:SWO_0000122 http://dbpedia.org/resource/Scala_(programming_language) Scala swo:SWO_0000123 http://dbpedia.org/resource/Scheme_(programming_language) Scheme swo:SWO_0000124 Shell swo:SWO_0000125 http://dbpedia.org/resource/Smalltalk Smalltalk swo:SWO_0000126 http://dbpedia.org/resource/SQL SQL swo:SWO_0000127 http://dbpedia.org/resource/Turing_(programming_language) Turing swo:SWO_0000128 http://dbpedia.org/resource/Verilog Verilog swo:SWO_0000129 http://dbpedia.org/resource/VHDL VHDL swo:SWO_0000130 http://dbpedia.org/resource/Visual_Basic Visual Basic http://david.abcc.ncifcrf.gov/ swo:SWO_0000133 DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. DAVID Bioinformatics resource Database for Annotation, Visualization and Integrated Discovery http://david.abcc.ncifcrf.gov/ James Malone DAVID swo:SWO_0000134 MLXTRAN swo:SWO_0000135 Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...". Position-Specific Iterative NIH BLAST homepage PSI-BLAST swo:SWO_0000136 NMTRAN swo:SWO_0000137 NONMEM swo:SWO_0000138 The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez Global Query Cross-Database Search System Ncbi Resource, C. (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20. doi:10.1093/nar/gks1189. PMC 3531099. Entrez swo:SWO_0000139 Web content search is the searching for information on the World Wide Web. website content search web content search swo:SWO_0000140 A search engine is a software system that is designed to search for information on the World Wide Web. web search engine search engine http://www.cs.waikato.ac.nz/~ml/weka/ swo:SWO_0000141 Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand. Waikato Environment for Knowledge Analysis Weka http://www.postgresql.org/ swo:SWO_0000142 PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance. Postgres PostgreSQL swo:SWO_0000143 The storing of digital information. Often this is done for archiving and retrieval purposes. data storage swo:SWO_0000145 The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014. Segway 1.2 swo:SWO_0000146 Version 2.6 of the Python programming language. Allyson Lister Allyson Lister Python 2.6 swo:SWO_0000147 Version 2.7 of the Python programming language. Allyson Lister Allyson Lister Python 2.7 swo:SWO_0000148 Firth's bias reduction procedure swo:SWO_0000149 Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc. http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015. Allyson Lister Mac OS swo:SWO_0000151 OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system. http://en.wikipedia.org/wiki/History_of_Mac_OS#OS_X, accessed 25 March 2015. Allyson Lister OS X swo:SWO_0000152 iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. http://www.async.ece.utah.edu/iBioSim/, accessed 25 March 2015. Allyson Lister iBioSim swo:SWO_0000153 VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. Virtual Cell http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 26 March 2015. Allyson Lister The licensing issue is not clear. On the VCell wikipedia page, the source is described as having an MIT license (see http://en.wikipedia.org/wiki/Virtual_Cell, accessed 26 March 2015). However, the exact type of license is not mentioned on the VCell homepage (http://www.vcell.org), therefore I have not added the statement that the MIT license is the *only* license for VCell. VCell swo:SWO_0000154 COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models. COnstraints Based Reconstruction and Analysis Allyson Lister COBRA swo:SWO_0000155 COBRA Toolbox is the version of the COBRA software for Python. COnstraints Based Reconstruction and Analysis for Python Allyson Lister COBRApy swo:SWO_0000156 COBRA Toolbox is the version of the COBRA software for Matlab. COnstraints Based Reconstruction and Analysis Toolbox for MATLAB Allyson Lister COBRA Toolbox swo:SWO_0000158 LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux. http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 27 March 2015. Allyson Lister libSBML swo:SWO_0000159 GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. https://www.gnu.org/software/octave/, accessed 27 March 2015. Allyson Lister GNU Octave swo:SWO_0000160 GWT swo:SWO_0000161 S language swo:SWO_0000162 Excel swo:SWO_0000163 This package deals with hapmap SNP reports, GWAS, etc. http://bioconductor.org/packages/2.4/bioc/html/GGtools.html Nandini Badarinarayan GGtools swo:SWO_0000164 Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified. http://bioconductor.org/packages/2.4/bioc/html/GLAD.html Nandini Badarinarayan GLAD swo:SWO_0000165 Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) swo:SWO_0000166 Microarray image quantification is performed using GLEAMS software http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf Nandini Badarinarayan GLEAMS software swo:SWO_0000167 Nandini Badarinarayan GMS swo:SWO_0000168 A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations http://bioconductor.org/packages/2.4/bioc/html/GOstats.html Nandini Badarinarayan GOstats swo:SWO_0000169 Gene Recommender algorithm swo:SWO_0000170 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html Nandini Badarinarayan GSEABase swo:SWO_0000171 Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html Nandini Badarinarayan GSEAlm swo:SWO_0000172 Gamma-Gamma hierarchical model swo:SWO_0000173 Gaussian locally weighted regression swo:SWO_0000174 Gene-Set Enrichment Analysis swo:SWO_0000175 Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data. http://www.genedata.com/products/expressionist/overview.html Nandini Badarinarayan GeneData Expressionist Analyst v4.0.5 swo:SWO_0000176 GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use. Gene Pix Genepix http://www.moleculardevices.com/pages/software/gn_genepix_pro.html Nandini Badarinarayan Gene Pix swo:SWO_0000177 Nandini Badarinarayan GenePix 3.0.6 swo:SWO_0000178 Nandini Badarinarayan GenePix 4.1 swo:SWO_0000179 GenePix 4100A [Axon Instruments] Nandini Badarinarayan GenePix 4100A swo:SWO_0000180 Nandini Badarinarayan GenePix 5.0.1 swo:SWO_0000181 GenePix [Axon Instruments] Nandini Badarinarayan GenePix swo:SWO_0000182 Nandini Badarinarayan GenePix Pro swo:SWO_0000183 Nandini Badarinarayan GenePix Pro 3 swo:SWO_0000184 Nandini Badarinarayan GenePix Pro 5.0 swo:SWO_0000185 Nandini Badarinarayan GenePix Pro 6.0 swo:SWO_0000186 Nandini Badarinarayan GenePix Pro 6 [Axon Instruments] swo:SWO_0000187 Axon GenePix Pro Nandini Badarinarayan GenePix Pro [Axon Instruments] swo:SWO_0000188 Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) http://bioconductor.org/packages/2.4/bioc/html/GeneR.html Nandini Badarinarayan GeneR swo:SWO_0000189 A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html Nandini Badarinarayan GeneRegionScan swo:SWO_0000190 Package manipulating sequences with fold routines http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html Nandini Badarinarayan GeneRfold swo:SWO_0000191 Gene selection based on a mixture of marginal distributions http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html Nandini Badarinarayan GeneSelectMMD swo:SWO_0000192 The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html Nandini Badarinarayan GeneSelector swo:SWO_0000193 Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html Nandini Badarinarayan GeneSpring swo:SWO_0000194 Nandini Badarinarayan GeneSpringGX swo:SWO_0000195 Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600530 Nandini Badarinarayan GeneTac Analyser swo:SWO_0000196 Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw) http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html Nandini Badarinarayan GeneTraffic swo:SWO_0000199 GenePix Pro v4.0 scanning software Genepix Pro 4.0 Nandini Badarinarayan GenePix Pro 4.0 swo:SWO_0000200 Genepix pro 3.0 Nandini Badarinarayan GenePix Pro 3.0 swo:SWO_0000201 This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html Nandini Badarinarayan GeneticsBase swo:SWO_0000202 This package contains functions useful for designing genetics studies, including power and sample-size calculations. http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html Nandini Badarinarayan GeneticsDesign swo:SWO_0000203 Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable http://bioconductor.org/packages/2.4/bioc/html/GeneticsPed.html Nandini Badarinarayan GeneticsPed swo:SWO_0000205 Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html Nandini Badarinarayan GenomeGraphs swo:SWO_0000206 GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. http://bioconductor.org/packages/2.4/bioc/html/GlobalAncova.html Nandini Badarinarayan GlobalAncova swo:SWO_0000207 Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast. http://bioconductor.org/packages/2.4/bioc/html/GOSemSim.html Nandini Badarinarayan GOSemSim swo:SWO_0000208 Functions and data used in Balasubramanian, et al. (2004) http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html Nandini Badarinarayan GraphAT swo:SWO_0000209 Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html Nandini Badarinarayan GraphAlignment swo:SWO_0000210 Software for microarray image analysis. http://www.oxfordjournals.org/nar/webserver/summary/825 Nandini Badarinarayan GridGrinder swo:SWO_0000212 Hexagon binning algorithm swo:SWO_0000213 The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications http://bioconductor.org/packages/2.4/bioc/html/HELP.html Nandini Badarinarayan HELP swo:SWO_0000214 This package fits heterogeneous error models for analysis of microarray data http://bioconductor.org/packages/2.4/bioc/html/HEM.html Nandini Badarinarayan HEM swo:SWO_0000215 Heterogeneous Error Model (HEM) swo:SWO_0000216 Hubert’s gamma swo:SWO_0000217 Hidden Markov Model swo:SWO_0000218 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm swo:SWO_0000219 Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets. Hidden Variable Dynamic Modelling HVDM) swo:SWO_0000220 HaarSeg algorithm swo:SWO_0000221 Hardy-Weinberg equilibrium swo:SWO_0000222 The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem. http://bioconductor.org/packages/2.4/bioc/html/Harshlight.html Nandini Badarinarayan Harshlight swo:SWO_0000224 Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. http://bioconductor.org/packages/2.4/bioc/html/Heatplus.html Nandini Badarinarayan Heatplus swo:SWO_0000225 Functions to visualize long vectors of integer data by means of Hilbert curves http://bioconductor.org/packages/2.4/bioc/html/HilbertVis.html Nandini Badarinarayan HilbertVis swo:SWO_0000226 An interactive tool to visualize long vectors of integer data by means of Hilbert curves http://bioconductor.org/packages/2.4/bioc/html/HilbertVisGUI.html Nandini Badarinarayan HilbertVisGUI swo:SWO_0000227 Hypergeometric probability swo:SWO_0000228 Nandini Badarinarayan ICS-501 (version 2.3) Image Capture System swo:SWO_0000229 Iteratively ReWeighted Least Squares swo:SWO_0000230 The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions. http://bioconductor.org/packages/2.4/bioc/html/IRanges.html Nandini Badarinarayan IRanges swo:SWO_0000231 A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set http://bioconductor.org/packages/2.4/bioc/html/ITALICS.html Nandini Badarinarayan ITALICS swo:SWO_0000233 ILLUMINA data swo:SWO_0000234 Nandini Badarinarayan ImaGene4.1 software swo:SWO_0000235 Nandini Badarinarayan ImaGene 3.0 swo:SWO_0000236 This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes. ImageQuant (Molecular Dynamics) http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp Nandini Badarinarayan ImageQuant swo:SWO_0000237 Nandini Badarinarayan ImageReader swo:SWO_0000238 ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis. ImaGene [BioDiscovery] Imagene http://www.biodiscovery.com/index/imagene Nandini Badarinarayan ImaGene swo:SWO_0000239 Nandini Badarinarayan Imagene v4.0 swo:SWO_0000241 These scripts are for primer design and initial microarray data processing and are available as .zip files: http://www.bahlerlab.info/resources/ Nandini Badarinarayan Initial microarray data processing (data filtering, local normalisation and quality control) swo:SWO_0000243 Jaccard’s index swo:SWO_0000245 Image analysis software Nandini Badarinarayan Jaguar swo:SWO_0000246 Multi sample aCGH analysis package using kernel convolution http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html Nandini Badarinarayan KCsmart swo:SWO_0000247 A package that provides a client interface to the KEGG SOAP server http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html Nandini Badarinarayan KEGGSOAP swo:SWO_0000248 KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. http://bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html Nandini Badarinarayan KEGGgraph swo:SWO_0000249 KGML swo:SWO_0000250 'KLD' swo:SWO_0000251 KS measures how biased the ranks of a subset of items are among the ranks of the entire set Kolmogorov Smirnov rank-sum based algorithm swo:SWO_0000252 LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. http://bioconductor.org/packages/2.4/bioc/html/LBE.html Nandini Badarinarayan LBE swo:SWO_0000253 LC-MS data swo:SWO_0000254 LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package http://bioconductor.org/packages/2.4/bioc/html/LMGene.html Nandini Badarinarayan LMGene swo:SWO_0000255 Locally Moderated Weighted-t (LMW) method swo:SWO_0000256 Lognormal Normal Model swo:SWO_0000257 Lognormal Normal with Modied Variance Model swo:SWO_0000258 This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. http://bioconductor.org/packages/2.4/bioc/html/LPE.html Nandini Badarinarayan LPE swo:SWO_0000259 Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. http://bioconductor.org/packages/2.4/bioc/html/LPEadj.html Nandini Badarinarayan LPEadj swo:SWO_0000260 A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software. James Malone publisher role swo:SWO_0000261 Langmuir Isotherm swo:SWO_0000262 Laplace mixture model swo:SWO_0000263 Library Search Algorithm swo:SWO_0000264 Loess algorithm swo:SWO_0000265 Logic regression swo:SWO_0000266 Tools for analyzing Micro Array experiments http://cran.r-project.org/web/packages/maanova/index.html Nandini Badarinarayan MAANOVA v1.2 package for MATLAB swo:SWO_0000267 Median Average Difference Algorithm swo:SWO_0000269 We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. http://bioconductor.org/packages/2.4/bioc/html/MANOR.html Nandini Badarinarayan MANOR swo:SWO_0000270 MAQC data swo:SWO_0000271 Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform. Affymetrix MicroArraySuite MAS http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf Nandini Badarinarayan MIcroarray Analysis Suite swo:SWO_0000272 MAS 5.0 software Nandini Badarinarayan MicroArraySuite 5.0 swo:SWO_0000274 MATLAB language swo:SWO_0000275 Nandini Badarinarayan MAVI Pro swo:SWO_0000276 Multivariate correlation estimator swo:SWO_0000277 Markov Chain Monte Carlo swo:SWO_0000278 minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples. MCR algorithm swo:SWO_0000279 This package includes a function for combining preprocessing and classification methods to calculate misclassification errors http://bioconductor.org/packages/2.4/bioc/html/MCRestimate.html Nandini Badarinarayan MCRestimate swo:SWO_0000280 MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments http://bioconductor.org/packages/2.4/bioc/html/MEDME.html Nandini Badarinarayan MEDME swo:SWO_0000281 'MI' swo:SWO_0000282 Mutual information matrix (MIM) swo:SWO_0000283 Uniform interfaces to machine learning code for data in Bioconductor containers http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html Nandini Badarinarayan MLInterfaces swo:SWO_0000284 MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes), MMD swo:SWO_0000285 Creates classes used in model-view-controller (MVC) design http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html Nandini Badarinarayan MVCClass swo:SWO_0000287 Mahalanobis distance swo:SWO_0000288 Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data) http://bioconductor.org/packages/2.4/bioc/html/MantelCorr.html Nandini Badarinarayan MantelCorr swo:SWO_0000289 Processing Mass Spectrometry spectrum by using wavelet based algorithm http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html Nandini Badarinarayan MassSpecWavelet swo:SWO_0000292 Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation http://bioconductor.org/packages/2.4/bioc/html/MeasurementError.cor.html Nandini Badarinarayan MeasurementError.cor swo:SWO_0000293 The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. http://bioconductor.org/packages/2.4/bioc/html/MergeMaid.html Nandini Badarinarayan MergeMaid swo:SWO_0000294 Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) http://bioconductor.org/packages/2.4/bioc/html/Mfuzz.html Nandini Badarinarayan Mfuzz swo:SWO_0000295 This package finds optimal sets of genes that seperate samples into two or more classes. http://bioconductor.org/packages/2.4/bioc/html/MiPP.html Nandini Badarinarayan MiPP swo:SWO_0000296 Misclassification-Penalized Posteriors (MiPP) swo:SWO_0000297 Nandini Badarinarayan MicroArraySuite 4.0 swo:SWO_0000298 Mixed model equations swo:SWO_0000304 'Needleman-Wunsch' swo:SWO_0000305 This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing Nested Effects Models swo:SWO_0000306 Nonlinear Estimation by Iterative Partial Least Squares swo:SWO_0000307 This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). http://bioconductor.org/packages/2.4/bioc/html/OCplus.html Nandini Badarinarayan OCplus swo:SWO_0000308 Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data http://bioconductor.org/packages/2.4/bioc/html/OLIN.html Nandini Badarinarayan OLIN swo:SWO_0000309 Graphical user interface for the OLIN package http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html Nandini Badarinarayan OLINgui swo:SWO_0000310 Computer software for image acquisition, analysis and reporting, for use in the life sciences http://www.findownersearch.com/optiquant/7766418/ Nandini Badarinarayan Optiquant swo:SWO_0000311 Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. http://bioconductor.org/packages/2.4/bioc/html/OrderedList.html Nandini Badarinarayan OrderedList swo:SWO_0000312 This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. http://bioconductor.org/packages/2.4/bioc/html/OutlierD.html Nandini Badarinarayan OutlierD swo:SWO_0000313 Presence-Absence calls with Negative Probesets (PANP) swo:SWO_0000314 Processing annotation data from public data repositories and building annoation data packages. http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html Nandini Badarinarayan PAnnBuilder swo:SWO_0000315 Pearson correlation estimator swo:SWO_0000316 Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html Nandini Badarinarayan PCpheno swo:SWO_0000317 Parametric Analysis of Gene Set Enrichment http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html Nandini Badarinarayan PGSEA swo:SWO_0000318 it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis 'PLM' swo:SWO_0000319 This package performs tests for paired high-throughput data. http://bioconductor.org/packages/2.4/bioc/html/PLPE.html Nandini Badarinarayan PLPE swo:SWO_0000320 Probe level Locally moderated Weighted median-t (PLW) method swo:SWO_0000321 PPC algorithm swo:SWO_0000322 A package for processing protein mass spectrometry data. http://bioconductor.org/packages/2.4/bioc/html/PROcess.html Nandini Badarinarayan PROcess swo:SWO_0000323 Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions Propagation of uncertainty in microarray analysis swo:SWO_0000324 The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background). http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html Nandini Badarinarayan Pathways 2.01 software swo:SWO_0000326 Power Law Global Error Model (PLGEM) analysis method swo:SWO_0000327 Nandini Badarinarayan Probe Cell Analysis swo:SWO_0000328 PLIER (Probe Logarithmic Error Intensity Estimate) method swo:SWO_0000329 QuantArray® is a powerful microarray analysis software that enables researchers to easily and accurately visualize and quantitate gene expression data. QuantArray http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf Nandini Badarinarayan QuantArray scanner software swo:SWO_0000330 Nandini Badarinarayan QuantArray, PackaardBiochip technologies swo:SWO_0000331 Nandini Badarinarayan QuantArray version 2 swo:SWO_0000332 Radial basis function swo:SWO_0000333 A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. http://bioconductor.org/packages/2.4/bioc/html/RBGL.html Nandini Badarinarayan RBGL swo:SWO_0000334 R interface to boost graph library algorithm (RBGL) swo:SWO_0000335 Functions and datasets and examples to accompany the monograph R For Bioinformatics. http://bioconductor.org/packages/2.4/bioc/html/RBioinf.html Nandini Badarinarayan RBioinf swo:SWO_0000336 Random effects model swo:SWO_0000337 for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC) Recursive Feature Elimination (RFE) swo:SWO_0000338 A Genotype Calling Algorithm for Affymetrix SNP Arrays http://bioconductor.org/packages/2.4/bioc/html/RLMM.html Nandini Badarinarayan RLMM swo:SWO_0000339 Regression model swo:SWO_0000340 RMA swo:SWO_0000341 RMA+ swo:SWO_0000342 RMA++ swo:SWO_0000343 RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays. http://rmaexpress.bmbolstad.com/ Nandini Badarinarayan RMAExpress swo:SWO_0000344 Nandini Badarinarayan RMAExpress 2.0 swo:SWO_0000345 Nandini Badarinarayan RMAExpress quantification swo:SWO_0000346 This package can be used to handle MAGEML documents in Bioconductor http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html Nandini Badarinarayan RMAGEML swo:SWO_0000347 RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes http://bioconductor.org/packages/2.4/bioc/html/RNAither.html Nandini Badarinarayan RNAither swo:SWO_0000348 utilities for ROC, with uarray focus http://bioconductor.org/packages/2.4/bioc/html/ROC.html Nandini Badarinarayan ROC swo:SWO_0000349 This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html Nandini Badarinarayan RWebServices swo:SWO_0000350 Rank Product method for identifying differentially expressed genes with application in meta-analysis http://bioconductor.org/packages/2.4/bioc/html/RankProd.html Nandini Badarinarayan RankProd swo:SWO_0000352 Support for Springer monograph on Bioconductor http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html Nandini Badarinarayan RbcBook1 swo:SWO_0000353 Generic database methods http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html Nandini Badarinarayan Rdbi swo:SWO_0000354 Provides methods for accessing data stored in PostgreSQL tables. http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html Nandini Badarinarayan RdbiPgSQL swo:SWO_0000355 Decomposition of Isotopic Patterns http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html Nandini Badarinarayan Rdisop swo:SWO_0000356 The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. http://bioconductor.org/packages/2.4/bioc/html/RefPlus.html Nandini Badarinarayan RefPlus swo:SWO_0000358 This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html Nandini Badarinarayan Resourcerer swo:SWO_0000359 Provides plotting capabilities for R graph objects http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html Nandini Badarinarayan Rgraphviz 2 swo:SWO_0000360 The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects http://bioconductor.org/packages/2.4/bioc/html/Ringo.html Nandini Badarinarayan Ringo swo:SWO_0000361 Queries and data structures for protein interactions http://bioconductor.org/packages/2.4/bioc/html/Rintact.html Nandini Badarinarayan Rintact swo:SWO_0000362 Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. http://bioconductor.org/packages/2.4/bioc/html/Rmagpie.html Nandini Badarinarayan Rmagpie swo:SWO_0000363 Rnw swo:SWO_0000364 Robust likelihood-based survival modeling swo:SWO_0000365 The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies. http://www.rosettabio.com/products/resolver Nandini Badarinarayan Rosetta Resolver swo:SWO_0000367 Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. http://bioconductor.org/packages/2.4/bioc/html/RpsiXML.html Nandini Badarinarayan RpsiXML swo:SWO_0000368 interface to redland RDF utilities http://bioconductor.org/packages/2.4/bioc/html/Rredland.html Nandini Badarinarayan Rredland swo:SWO_0000369 Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. http://bioconductor.org/packages/2.4/bioc/html/Rtreemix.html Nandini Badarinarayan Rtreemix swo:SWO_0000370 A package to provide UUID values in R http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html Nandini Badarinarayan Ruuid swo:SWO_0000371 S-Score algorithm swo:SWO_0000372 Serial Analysis of Gene Expression (SAGE) swo:SWO_0000373 A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. http://bioconductor.org/packages/2.4/bioc/html/SAGx.html Nandini Badarinarayan SAGx swo:SWO_0000374 Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister) SAM swo:SWO_0000375 Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis. http://en.wikipedia.org/wiki/SAS_System Nandini Badarinarayan SAS/STAT Software, Version 8 swo:SWO_0000377 This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. http://bioconductor.org/packages/2.4/bioc/html/SBMLR.html Nandini Badarinarayan SBMLR swo:SWO_0000378 SBMLR format swo:SWO_0000381 SDF format swo:SWO_0000382 Finds associations between DNA copy number and gene expression. http://bioconductor.org/packages/2.4/bioc/html/SIM.html Nandini Badarinarayan SIM swo:SWO_0000383 A variety of data files and functions for the analysis of genetic interactions http://bioconductor.org/packages/2.4/bioc/html/SLGI.html Nandini Badarinarayan SLGI swo:SWO_0000384 Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH http://bioconductor.org/packages/2.4/bioc/html/SLqPCR.html Nandini Badarinarayan SLqPCR swo:SWO_0000385 Functions and classes for DNA copy number profiling of array-CGH data http://bioconductor.org/packages/2.4/bioc/html/SMAP.html Nandini Badarinarayan SMAP swo:SWO_0000386 SNPRMA algorithm swo:SWO_0000387 This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing. http://bioconductor.org/packages/2.4/bioc/html/SNPchip.html Nandini Badarinarayan SNPchip swo:SWO_0000388 This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. http://bioconductor.org/packages/2.4/bioc/html/SPIA.html Nandini Badarinarayan SPIA swo:SWO_0000389 Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, 1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have presented to determine the semantic similarities of two GO terms based on the annotation statistics of their common ancestor terms. Wang [Wang et al., 2007] proposed a new method to measure the similarities based on the graph structure of GO. Semantic Similarity Measures swo:SWO_0000390 Sample size and power analysis for microarray data, where two groups are analysed. http://bioconductor.org/packages/2.4/bioc/html/SSPA.html Nandini Badarinarayan SSPA swo:SWO_0000391 SVDimpute algorithm swo:SWO_0000392 Software developer role is a role borne by an organization or individual in which they are responsible for authoring software. James Malone software developer role swo:SWO_0000396 An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing. software developer organization swo:SWO_0000397 An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing. software publisher organization swo:SWO_0000398 Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components. Langsrud, &Oslash. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317. 50-50 MANOVA algorithm swo:SWO_0000405 ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects. http://bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html Nandini Badarinarayan ArrayExpress Bioconductor swo:SWO_0000406 Gene list swo:SWO_0000408 Clustered data set swo:SWO_0000409 R data frame swo:SWO_0000415 R language swo:SWO_0000416 Package to create In Silico Interactomes http://bioconductor.org/packages/2.4/bioc/html/ScISI.html Nandini Badarinarayan ScISI swo:SWO_0000417 Processes fluorescent images of microarrays http://smd.stanford.edu/resources/restech.shtml Nandini Badarinarayan ScanAlyze swo:SWO_0000418 ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance. ScanArray Express ScanArray Express [PerkinElmer] http://las.perkinelmer.com/Catalog/ProductInfoPage.htm?ProductID=7000060 Nandini Badarinarayan ScanArray swo:SWO_0000419 ScanArray version 3.1 Nandini Badarinarayan ScanArray v3.1 software swo:SWO_0000420 Nandini Badarinarayan scanning software swo:SWO_0000421 High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx Nandini Badarinarayan Scanning software G2565AA version A6.3.1 swo:SWO_0000422 Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html Nandini Badarinarayan ShortRead swo:SWO_0000423 Signaling Pathway Impact Analysis (SPIA) algorithm swo:SWO_0000424 The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment SiliconGenetics GeneSpring http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf Nandini Badarinarayan Silicon Genetics Genespring swo:SWO_0000425 Similarity score swo:SWO_0000426 'Smith-Waterman' swo:SWO_0000428 Nandini Badarinarayan Spot quantification swo:SWO_0000429 TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression http://www.tm4.org/contributors.html Nandini Badarinarayan Spotfinder [TIGR] swo:SWO_0000430 Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability. http://spotfire.tibco.com/Products/Info.aspx Nandini Badarinarayan Spotfire swo:SWO_0000432 Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics. http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html Nandini Badarinarayan TAS Software swo:SWO_0000435 This packages provides a targeted pre-processing method for GC-MS data. http://bioconductor.org/packages/2.4/bioc/html/TargetSearch.html Nandini Badarinarayan TargetSearch swo:SWO_0000437 Theodore Ts’o’s swo:SWO_0000438 A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html Nandini Badarinarayan TypeInfo swo:SWO_0000441 Variance-stabilizing transformation (VST) algorithm swo:SWO_0000442 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays http://bioconductor.org/packages/2.4/bioc/html/VanillaICE.html Nandini Badarinarayan VanillaICE swo:SWO_0000444 WilcEbam swo:SWO_0000445 Wilcoxon swo:SWO_0000446 XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression http://bioconductor.org/packages/2.4/bioc/html/XDE.html Nandini Badarinarayan XDE swo:SWO_0000447 Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification http://www.cose.fr/us_dots.html Nandini Badarinarayan XDotsReader swo:SWO_0000449 Xba.CQV and Xba.regions swo:SWO_0000450 The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. http://bioconductor.org/packages/2.4/bioc/html/aCGH.html Nandini Badarinarayan Array Comparative Genomic Hybridization swo:SWO_0000451 Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security. http://www.bio-medicine.org/ Nandini Badarinarayan Acuity swo:SWO_0000452 affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. http://bioconductor.org/packages/2.4/bioc/html/affxparser.html Nandini Badarinarayan affxparser swo:SWO_0000453 affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness. http://bioconductor.org/packages/2.4/bioc/html/affyContam.html (access unknown); http://www.bioconductor.org/packages/2.12/bioc/vignettes/affyContam/inst/doc/affyContam.pdf, accessed 22 May 2013. Allyson Lister Nandini Badarinarayan affyContam swo:SWO_0000454 A Graphical User Interface for affy analysis using the limma Microarray package http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html Nandini Badarinarayan Removed the links to specified data inputs, as this software is a GUI wrapper for another package, and it is this package which takes the inputs. (Allyson Lister 22/05/2013) affyImGUI swo:SWO_0000455 A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html Nandini Badarinarayan 'affyPLM' swo:SWO_0000456 The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. http://bioconductor.org/packages/2.4/bioc/html/affyPara.html Nandini Badarinarayan affyPara swo:SWO_0000457 This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. http://bioconductor.org/packages/2.4/bioc/html/affyQCReport.html Nandini Badarinarayan affyQCReport swo:SWO_0000458 This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. http://bioconductor.org/packages/2.4/bioc/html/AffyTiling.html Nandini Badarinarayan affyTiling swo:SWO_0000459 Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html Nandini Badarinarayan 'affycoretools' swo:SWO_0000460 Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. http://bioconductor.org/packages/2.4/bioc/html/affyio.html Nandini Badarinarayan affyio swo:SWO_0000461 The package contains functions to perform the PDNN method described by Li Zhang et al. http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html Nandini Badarinarayan affypdnn swo:SWO_0000463 altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs. http://www.bioconductor.org/packages/release/bioc/html/altcdfenvs.html, accessed May 28 2013. Allyson Lister Nandini Badarinarayan altcdfenvs swo:SWO_0000465 This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria. http://bioconductor.org/packages/2.4/bioc/html/annaffy.html Nandini Badarinarayan annaffy swo:SWO_0000466 Using R enviroments for annotation. http://bioconductor.org/packages/2.4/bioc/html/annotate.html Nandini Badarinarayan 'annotate' swo:SWO_0000467 data annotation swo:SWO_0000468 This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). http://bioconductor.org/packages/2.4/bioc/html/annotationTools.html Nandini Badarinarayan annotationTools swo:SWO_0000469 Annotation data packages swo:SWO_0000470 This package functions to estimate a bipartite graph of protein complex membership using AP-MS data. http://bioconductor.org/packages/2.4/bioc/html/apComplex.html Nandini Badarinarayan 'apComplex' swo:SWO_0000471 This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. http://bioconductor.org/packages/2.4/bioc/html/aroma.light.html Nandini Badarinarayan aroma.light swo:SWO_0000472 This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html Nandini Badarinarayan arrayMvout swo:SWO_0000473 This package functions for performing print-run and array level quality assessment. http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html Nandini Badarinarayan arrayQuality swo:SWO_0000474 This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels. http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html Nandini Badarinarayan arrayQualityMetrics swo:SWO_0000475 Nandini Badarinarayan arrayWoRx 2.0 swo:SWO_0000476 Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data. http://www.hitechtrader.com/detail.cfm?autonumber=64022 Nandini Badarinarayan arrayWoRx swo:SWO_0000477 Associative T method swo:SWO_0000478 AvgNRRs swo:SWO_0000479 The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. http://bioconductor.org/packages/2.4/bioc/html/beadarray.html Nandini Badarinarayan 'beadarray' swo:SWO_0000480 Importing data from Illumina SNP experiments and performing copy number calculations and reports. http://bioconductor.org/packages/2.4/bioc/html/beadarraySNP.html Nandini Badarinarayan 'beadarraySNP' swo:SWO_0000481 betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. http://www.bioconductor.org/packages/2.12/bioc/html/betr.html, accessed 28 May 2013. Allyson Lister Nandini Badarinarayan 'betr' swo:SWO_0000482 BGAfun is a method to identify specifity determining residues in protein families http://bioconductor.org/packages/2.4/bioc/html/bgafun.html Nandini Badarinarayan bgafun swo:SWO_0000483 Bayesian integrated analysis of Affymetrix GeneChips http://bioconductor.org/packages/2.4/bioc/html/bgx.html Nandini Badarinarayan bgx swo:SWO_0000484 Bitmap object swo:SWO_0000485 The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist. http://bioconductor.org/packages/2.4/bioc/html/bioDist.html Nandini Badarinarayan bioDist swo:SWO_0000486 Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal. http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html Nandini Badarinarayan 'biocDatasets' swo:SWO_0000487 This package provides examples and code that make use of the different graph related packages produced by Bioconductor. http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html Nandini Badarinarayan 'biocGraph' swo:SWO_0000488 Categorized views of R package repositories http://bioconductor.org/packages/2.4/bioc/html/biocViews.html Nandini Badarinarayan 'biocViews' swo:SWO_0000489 The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html Nandini Badarinarayan biomaRT swo:SWO_0000490 Bootstrap swo:SWO_0000491 The bridge package consists of several functions for testing for dierential expression among mul- tiple samples http://bioconductor.org/packages/2.4/bioc/html/bridge.html Nandini Badarinarayan 'bridge' swo:SWO_0000493 cdt swo:SWO_0000494 Bioconductor package concerned with analysis of cell-based RNA interference screens Nandini Badarinarayan 'cellHTS' Bioconductor package concerned with analysis of cell-based RNA interference screens http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html swo:SWO_0000495 Analysis of cell-based RNA interference screens http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html Nandini Badarinarayan 'cellHTS2' swo:SWO_0000496 Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. http://bioconductor.org/packages/2.4/bioc/html/cghMCR.html Nandini Badarinarayan cghMCR swo:SWO_0000497 chamber slide format swo:SWO_0000498 Categorical (e.g tumor vs normal) class file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29 cls swo:SWO_0000499 This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. http://bioconductor.org/packages/2.4/bioc/html/clusterStab.html Nandini Badarinarayan 'clusterStab' swo:SWO_0000501 This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. http://bioconductor.org/packages/2.4/bioc/html/codelink.html Nandini Badarinarayan 'codelink' swo:SWO_0000502 dataset comparison swo:SWO_0000503 Concordance swo:SWO_0000504 Define coerce methods for microarray data objects. http://bioconductor.org/packages/2.4/bioc/html/convert.html Nandini Badarinarayan convert swo:SWO_0000505 COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. http://bioconductor.org/packages/2.4/bioc/html/copa.html Nandini Badarinarayan copa swo:SWO_0000506 cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. http://bioconductor.org/packages/2.4/bioc/html/cosmo.html Nandini Badarinarayan cosmo swo:SWO_0000507 cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. http://bioconductor.org/packages/2.4/bioc/html/cosmoGUI.html Nandini Badarinarayan cosmoGUI swo:SWO_0000508 covdesc file swo:SWO_0000509 An objective in which the aim is to create a new database instance. PERSON: James Malone James Malone database creation swo:SWO_0000510 Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0. http://bioconductor.org/packages/2.4/bioc/html/crlmm.html Nandini Badarinarayan crlmm swo:SWO_0000512 Tools for export and import classification trees and clusters to other programs http://bioconductor.org/packages/2.4/bioc/html/ctc.html Nandini Badarinarayan ctc swo:SWO_0000513 Analysis and visualization of gene expression and SNP microarrays http://www.bioinformatics.org/dchip/ Nandini Badarinarayan dChip swo:SWO_0000514 This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. http://bioconductor.org/packages/2.4/bioc/html/daMA.html Nandini Badarinarayan daMA swo:SWO_0000516 .data swo:SWO_0000518 debian control file format dcf swo:SWO_0000519 design file swo:SWO_0000520 Analyze microarray data http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html Nandini Badarinarayan 'diffGeneAnalysis' swo:SWO_0000521 Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. http://bioconductor.org/packages/2.4/bioc/html/domainsignatures.html Nandini Badarinarayan 'domainsignatures' swo:SWO_0000522 This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. http://bioconductor.org/packages/2.4/bioc/html/dualKS.html Nandini Badarinarayan 'dualKS' swo:SWO_0000523 Gene-specific dye-bias correction of two-color microarray data using the GASSCO method http://bioconductor.org/packages/2.4/bioc/html/dyebias.html Nandini Badarinarayan dyebias swo:SWO_0000524 Dynamic programming algorithm swo:SWO_0000525 Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. http://bioconductor.org/packages/2.4/bioc/html/ecolitk.html Nandini Badarinarayan ecolitk swo:SWO_0000526 This package provides tools for evaluating cohort distributions of gene expression levels http://bioconductor.org/packages/2.4/bioc/html/edd.html Nandini Badarinarayan edd swo:SWO_0000527 Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries. http://bioconductor.org/packages/2.4/bioc/html/edgeR.html Nandini Badarinarayan 'edgeR' swo:SWO_0000528 This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target. http://bioconductor.org/packages/2.4/bioc/html/exonmap.html Nandini Badarinarayan exonmap swo:SWO_0000529 This package explores and analyzes *omics data with R and GGobi http://bioconductor.org/packages/2.4/bioc/html/explorase.html Nandini Badarinarayan 'explorase' swo:SWO_0000530 Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided http://bioconductor.org/packages/2.4/bioc/html/externalVector.html Nandini Badarinarayan 'externalVector' swo:SWO_0000531 f-test swo:SWO_0000532 This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. http://bioconductor.org/packages/2.4/bioc/html/factDesign.html Nandini Badarinarayan factDesign swo:SWO_0000533 This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program http://bioconductor.org/packages/2.4/bioc/html/fbat.html Nandini Badarinarayan fbat swo:SWO_0000534 This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma http://bioconductor.org/packages/2.4/bioc/html/fdrame.html Nandini Badarinarayan fdrame swo:SWO_0000536 Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data http://bioconductor.org/packages/2.4/bioc/html/flagme.html Nandini Badarinarayan flagme swo:SWO_0000537 Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed http://bioconductor.org/packages/2.4/bioc/html/flowClust.html Nandini Badarinarayan flowClust swo:SWO_0000538 This package provides S4 data structures and basic functions to deal with flow cytometry data. http://bioconductor.org/packages/2.4/bioc/html/flowCore.html Nandini Badarinarayan flowCore swo:SWO_0000539 FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. http://bioconductor.org/packages/2.4/bioc/html/flowFlowJo.html Nandini Badarinarayan flowFlowJo swo:SWO_0000540 This package provides quality control and quality assessment tools for flow cytometry data. http://bioconductor.org/packages/2.4/bioc/html/flowQ.html Nandini Badarinarayan flowQ swo:SWO_0000541 This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. http://bioconductor.org/packages/2.4/bioc/html/flowStats.html Nandini Badarinarayan flowStats swo:SWO_0000542 This package provides utilities for flow cytometry data. http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html Nandini Badarinarayan flowUtils swo:SWO_0000543 Provides visualization tools for flow cytometry data http://bioconductor.org/packages/2.4/bioc/html/flowViz.html Nandini Badarinarayan flowViz swo:SWO_0000544 This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). http://bioconductor.org/packages/2.4/bioc/html/gaga.html Nandini Badarinarayan gaga swo:SWO_0000545 This package contains functions connecting R with the Gaggle http://bioconductor.org/packages/2.4/bioc/html/gaggle.html Nandini Badarinarayan 'gaggle' swo:SWO_0000546 Bioconductor package concerned with background adjustment using sequence information Allyson Lister Nandini Badarinarayan gcRMA quantification Bioconductor package concerned with background adjustment using sequence information http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html swo:SWO_0000547 Background adjustment using sequence information http://bioconductor.org/packages/2.4/bioc/html/gcrma.html Nandini Badarinarayan gcrma swo:SWO_0000548 Gene Cluster Text file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29 gct swo:SWO_0000549 genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. http://bioconductor.org/packages/2.4/bioc/html/genArise.html Nandini Badarinarayan 'genArise' swo:SWO_0000550 The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. http://bioconductor.org/packages/2.4/bioc/html/gene2pathway.html Nandini Badarinarayan gene2pathway swo:SWO_0000551 This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. http://bioconductor.org/packages/2.4/bioc/html/geneRecommender.html Nandini Badarinarayan geneRecommender swo:SWO_0000552 Gene array analysis algorithm swo:SWO_0000553 gene expression analysis swo:SWO_0000554 Gene expression dataset swo:SWO_0000555 Some basic functions for filtering genes http://bioconductor.org/packages/2.4/bioc/html/genefilter.html Nandini Badarinarayan genefilter swo:SWO_0000556 A collection of meta-analysis tools for analysing high throughput experimental data http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html Nandini Badarinarayan genemeta swo:SWO_0000557 Some basic functions for plotting genetic data http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html Nandini Badarinarayan geneplotter swo:SWO_0000558 Tools for operation on genomic intervals. http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.html Nandini Badarinarayan genomeIntervals swo:SWO_0000560 global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments. Global test swo:SWO_0000561 Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. http://bioconductor.org/packages/2.4/bioc/html/globaltest.html Nandini Badarinarayan globaltest swo:SWO_0000562 gmt format swo:SWO_0000563 The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. http://bioconductor.org/packages/2.4/bioc/html/goProfiles.html Nandini Badarinarayan goProfiles swo:SWO_0000564 Wraper functions for description/comparison of oligo ID list using Gene Ontology database http://bioconductor.org/packages/2.4/bioc/html/goTools.html Nandini Badarinarayan goTools swo:SWO_0000565 Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. http://bioconductor.org/packages/2.4/bioc/html/gpls.html Nandini Badarinarayan gpls swo:SWO_0000566 GenePix Pro Results file format gpr format swo:SWO_0000567 A package that implements some simple graph handling capabilities. http://bioconductor.org/packages/2.4/bioc/html/graph.html Nandini Badarinarayan graph swo:SWO_0000569 gtr swo:SWO_0000570 gxl format swo:SWO_0000572 Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. http://bioconductor.org/packages/2.4/bioc/html/hexbin.html Nandini Badarinarayan hexbin swo:SWO_0000573 Hierarchical clustering swo:SWO_0000574 The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). http://bioconductor.org/packages/2.4/bioc/html/hopach.html Nandini Badarinarayan hopach swo:SWO_0000575 HTML report swo:SWO_0000576 Hypergeometric enrichment swo:SWO_0000577 A package that implements some simple capabilities for representing and manipulating hypergraphs. http://bioconductor.org/packages/2.4/bioc/html/hypergraph.html Nandini Badarinarayan hypergraph swo:SWO_0000578 Many functions for computing the NPMLE for censored and truncated data. http://bioconductor.org/packages/2.4/bioc/html/Icens.html Nandini Badarinarayan Icens swo:SWO_0000579 A package for plotting genomic data by chromosomal location http://bioconductor.org/packages/2.4/bioc/html/idiogram.html Nandini Badarinarayan idiogram swo:SWO_0000581 Imputation for microarray data (currently KNN only) http://bioconductor.org/packages/2.4/bioc/html/impute.html Nandini Badarinarayan impute swo:SWO_0000582 The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). http://bioconductor.org/packages/2.4/bioc/html/iterativeBMA.html Nandini Badarinarayan iterativeBMA swo:SWO_0000583 The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. http://bioconductor.org/packages/2.4/bioc/html/iterativeBMAsurv.html Nandini Badarinarayan iterativeBMAsurv swo:SWO_0000584 Iterative local regression and model selection swo:SWO_0000587 k-cores swo:SWO_0000588 k-means swo:SWO_0000589 k-nearest neighbour classification swo:SWO_0000590 Test package for a pathway 'ontology' http://bioconductor.org/packages/2.4/bioc/html/keggorth.html Nandini Badarinarayan keggorth swo:SWO_0000591 lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. http://bioconductor.org/packages/2.4/bioc/html/lapmix.html Allyson Lister Nandini Badarinarayan lapmix swo:SWO_0000592 Likelihood method swo:SWO_0000593 Data analysis, linear models and differential expression for microarray data. http://bioconductor.org/packages/2.4/bioc/html/limma.html Nandini Badarinarayan limma swo:SWO_0000594 A Graphical User Interface for the limma Microarray package http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html Nandini Badarinarayan limmaGUI swo:SWO_0000595 Linear modelling swo:SWO_0000596 lma swo:SWO_0000597 Local-pooled-error swo:SWO_0000598 log file swo:SWO_0000599 Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. http://bioconductor.org/packages/2.4/bioc/html/logicFS.html Nandini Badarinarayan logicFS swo:SWO_0000600 logicFS dataset swo:SWO_0000601 The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. http://bioconductor.org/packages/2.4/bioc/html/logitT.html Nandini Badarinarayan logitT swo:SWO_0000602 Logit-t algorithm swo:SWO_0000603 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. http://bioconductor.org/packages/2.4/bioc/html/lumi.html Nandini Badarinarayan lumi swo:SWO_0000604 Graphically displays correlation in microarray data that is due to insufficient normalization http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html Nandini Badarinarayan maCorrPlot swo:SWO_0000605 maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. http://bioconductor.org/packages/2.4/bioc/html/maDB.html Nandini Badarinarayan maDB swo:SWO_0000606 maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html Nandini Badarinarayan maSigPro swo:SWO_0000607 Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree. http://bioconductor.org/packages/2.4/bioc/html/maanova.html Nandini Badarinarayan maanova swo:SWO_0000608 This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. Nandini Badarinarayan macat swo:SWO_0000609 Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. http://bioconductor.org/packages/2.4/bioc/html/made4.html Nandini Badarinarayan made4 swo:SWO_0000610 This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data http://bioconductor.org/packages/2.4/bioc/html/maigesPack.html Nandini Badarinarayan maigesPack swo:SWO_0000611 makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html Nandini Badarinarayan makePlatformDesign swo:SWO_0000612 This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html Nandini Badarinarayan makecdfenv swo:SWO_0000613 Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. http://bioconductor.org/packages/2.4/bioc/html/marray.html Nandini Badarinarayan marray swo:SWO_0000614 'MAS5' swo:SWO_0000615 mas5 format swo:SWO_0000616 Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that. http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html Nandini Badarinarayan matchprobes swo:SWO_0000617 MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. http://bioconductor.org/packages/2.4/bioc/html/mdqc.html Nandini Badarinarayan mdqc swo:SWO_0000618 M-estimation regression swo:SWO_0000619 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform http://bioconductor.org/packages/2.4/bioc/html/metaArray.html Nandini Badarinarayan metaArray swo:SWO_0000620 Meta data swo:SWO_0000621 Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies http://bioconductor.org/packages/2.4/bioc/html/metahdep.html Nandini Badarinarayan metahdep swo:SWO_0000622 This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. http://bioconductor.org/packages/2.4/bioc/html/miRNApath.html Nandini Badarinarayan miRNApath swo:SWO_0000623 microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them. http://bioconductor.org/packages/2.4/bioc/html/microRNA.html, accessed 28 May 2013. Allyson Lister Nandini Badarinarayan microRNA swo:SWO_0000625 This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented. http://bioconductor.org/packages/2.4/bioc/html/minet.html Nandini Badarinarayan minet swo:SWO_0000626 mrnet algorithm swo:SWO_0000627 Multinomial probit regression with Gaussian Process priors swo:SWO_0000628 multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. Multiple testing swo:SWO_0000629 Multivariate t mixture models swo:SWO_0000630 Resampling-based multiple hypothesis testing http://bioconductor.org/packages/2.4/bioc/html/multtest.html Nandini Badarinarayan multtest swo:SWO_0000631 Negative binomial distribution swo:SWO_0000632 Nested Effects Models to reconstruct phenotypic hierarchies http://bioconductor.org/packages/2.4/bioc/html/nem.html Nandini Badarinarayan nem swo:SWO_0000633 Neural networks models swo:SWO_0000635 This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. http://bioconductor.org/packages/2.4/bioc/html/nnNorm.html Nandini Badarinarayan nnNorm swo:SWO_0000636 Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) http://bioconductor.org/packages/2.4/bioc/html/nudge.html Nandini Badarinarayan nudge swo:SWO_0000637 Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. http://bioconductor.org/packages/2.4/bioc/html/occugene.html Nandini Badarinarayan occugene swo:SWO_0000638 A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. http://bioconductor.org/packages/2.4/bioc/html/oligo.html Nandini Badarinarayan oligo swo:SWO_0000639 This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package. http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html Nandini Badarinarayan oligoClasses swo:SWO_0000640 OMICS data swo:SWO_0000641 This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis. http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html Nandini Badarinarayan oneChannelGUI swo:SWO_0000642 tools for working with ontologies and graphs http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html Nandini Badarinarayan ontoTools swo:SWO_0000644 pair file swo:SWO_0000645 Some functions for sample classification in microarrays http://bioconductor.org/packages/2.4/bioc/html/pamr.html Nandini Badarinarayan pamr swo:SWO_0000646 A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. http://bioconductor.org/packages/2.4/bioc/html/panp.html Nandini Badarinarayan panp swo:SWO_0000647 Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics http://bioconductor.org/packages/2.4/bioc/html/parody.html Nandini Badarinarayan parody swo:SWO_0000648 parse swo:SWO_0000649 build graphs from pathway databases, render them by Rgraphviz http://bioconductor.org/packages/2.4/bioc/html/pathRender.html Nandini Badarinarayan pathRender swo:SWO_0000650 A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. http://bioconductor.org/packages/2.4/bioc/html/pcaMethods.html Nandini Badarinarayan pcaMethods swo:SWO_0000651 PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. http://bioconductor.org/packages/2.4/bioc/html/pcot2.html Nandini Badarinarayan pcot2 swo:SWO_0000653 Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. http://bioconductor.org/packages/2.4/bioc/html/pdInfoBuilder.html Nandini Badarinarayan pdInfoBuilder swo:SWO_0000654 This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. http://bioconductor.org/packages/2.4/bioc/html/pdmclass.html Nandini Badarinarayan pdmclass swo:SWO_0000655 pedigree data file swo:SWO_0000656 Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. http://bioconductor.org/packages/2.4/bioc/html/pgUtils.html Nandini Badarinarayan pgUtils swo:SWO_0000657 Functions to Analyze Microarray (Gene Expression) Data. http://bioconductor.org/packages/2.4/bioc/html/pickgene.html Nandini Badarinarayan pickgene swo:SWO_0000658 This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html Nandini Badarinarayan pkgDepTools swo:SWO_0000659 PLGEM is useful for detecting differential expression in microarray and proteomics datasets. http://bioconductor.org/packages/2.4/bioc/html/plgem.html Nandini Badarinarayan plgem swo:SWO_0000660 The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. http://bioconductor.org/packages/2.4/bioc/html/plier.html Nandini Badarinarayan plier swo:SWO_0000661 Graph plot swo:SWO_0000662 Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). http://bioconductor.org/packages/2.4/bioc/html/plw.html Nandini Badarinarayan plw swo:SWO_0000664 Position weight matrix (PWM ) swo:SWO_0000665 Tools for the analysis of protein interaction data. http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html Nandini Badarinarayan ppiStats swo:SWO_0000666 Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). http://bioconductor.org/packages/2.4/bioc/html/prada.html Nandini Badarinarayan prada swo:SWO_0000667 A library of core preprocessing routines http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html Nandini Badarinarayan preprocessCore swo:SWO_0000669 Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. http://bioconductor.org/packages/2.4/bioc/html/puma.html Nandini Badarinarayan puma swo:SWO_0000670 qPCR data swo:SWO_0000671 The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. http://bioconductor.org/packages/2.4/bioc/html/qpcrNorm.html Nandini Badarinarayan qpcrNorm swo:SWO_0000672 Reverse engineering of molecular regulatory networks with qp-graphs http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html Nandini Badarinarayan qpgraph swo:SWO_0000673 Quantile normalization swo:SWO_0000674 Quantile regression techniques swo:SWO_0000675 Quantile smoothing and genomic visualization of array data http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html Nandini Badarinarayan quantsmooth swo:SWO_0000676 This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. http://bioconductor.org/packages/2.4/bioc/html/qvalue.html Nandini Badarinarayan qvalue swo:SWO_0000677 Hidden Variable Dynamic Modeling http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html Nandini Badarinarayan rHVDM swo:SWO_0000678 R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. http://bioconductor.org/packages/2.4/bioc/html/rMAT.html Nandini Badarinarayan rMAT 2 swo:SWO_0000679 The rama package consists of several functions for robust estimation of two color microarray intensities with replicates http://bioconductor.org/packages/2.4/bioc/html/rama.html Nandini Badarinarayan rama swo:SWO_0000680 Rank-invariant set normalization swo:SWO_0000681 Rank product non-parametric method swo:SWO_0000682 .raw files swo:SWO_0000683 This package selects genes associated with survival. http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html Nandini Badarinarayan rbsurv swo:SWO_0000684 rda swo:SWO_0000685 A set of functions to dentify regional expression biases http://bioconductor.org/packages/2.4/bioc/html/reb.html Nandini Badarinarayan reb swo:SWO_0000686 Statistical tools and data structures for analytic flow cytometry http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html Nandini Badarinarayan rflowcyt swo:SWO_0000687 .rma format swo:SWO_0000688 R support for SBML, using libsbml http://bioconductor.org/packages/2.4/bioc/html/rsbml.html Nandini Badarinarayan rsbml swo:SWO_0000689 R interface to genome browsers and their annotation tracks http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html Nandini Badarinarayan rtracklayer 3 swo:SWO_0000690 SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. http://bioconductor.org/packages/2.4/bioc/html/safe.html Nandini Badarinarayan safe swo:SWO_0000691 This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison http://bioconductor.org/packages/2.4/bioc/html/sagenhaft.html Nandini Badarinarayan sagenhaft swo:SWO_0000692 seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo http://bioconductor.org/packages/2.4/bioc/html/seqLogo.html Nandini Badarinarayan seqLogo swo:SWO_0000693 Conducts pathway analysis by calculating the NT_k and NE_k statistics http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html Nandini Badarinarayan sigPathway swo:SWO_0000694 Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). http://bioconductor.org/packages/2.4/bioc/html/siggenes.html Nandini Badarinarayan siggenes swo:SWO_0000695 Sim method swo:SWO_0000696 Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html Nandini Badarinarayan simpleaffy swo:SWO_0000697 Functions to computationally simulate the AP-MS technology based on wet-lab data. http://bioconductor.org/packages/2.4/bioc/html/simulatorAPMS.html Nandini Badarinarayan simulatorAPMS swo:SWO_0000698 This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. http://bioconductor.org/packages/2.4/bioc/html/sizepower.html Nandini Badarinarayan sizepower swo:SWO_0000699 xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html Nandini Badarinarayan xmapbridge swo:SWO_0000700 Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. http://bioconductor.org/packages/2.4/bioc/html/snapCGH.html Nandini Badarinarayan snapCGH swo:SWO_0000701 Implements classes and methods for large-scale SNP association studies http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html Nandini Badarinarayan snpMatrix swo:SWO_0000703 Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html Nandini Badarinarayan spikeLI swo:SWO_0000704 The package contains functions that can be used to compare expression measures on different array platforms. http://bioconductor.org/packages/2.4/bioc/html/spkTools.html Nandini Badarinarayan spkTools swo:SWO_0000705 A set of tools to work with alternative splicing http://bioconductor.org/packages/2.4/bioc/html/splicegear.html Nandini Badarinarayan splicegear swo:SWO_0000706 The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format. http://bioconductor.org/packages/2.4/bioc/html/splots.html Nandini Badarinarayan splots swo:SWO_0000707 Spot segmentation via model-based clustering and gridding for blocks within microarray slides http://bioconductor.org/packages/2.4/bioc/html/spotSegmentation.html Nandini Badarinarayan spotSegmentation swo:SWO_0000708 sproc swo:SWO_0000709 sqlite swo:SWO_0000710 This package contains an implementation of the S-Score algorithm http://bioconductor.org/packages/2.4/bioc/html/sscore.html Nandini Badarinarayan sscore swo:SWO_0000711 Functions for computing and displaying sample size information for gene expression arrays. http://bioconductor.org/packages/2.4/bioc/html/ssize.html Nandini Badarinarayan ssize swo:SWO_0000712 The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects. http://bioconductor.org/packages/2.4/bioc/html/stam.html Nandini Badarinarayan stam swo:SWO_0000713 A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance. Modified from http://en.wikipedia.org/wiki/Statistical_test, accessed 9 May 2013; http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm, accessed 9 May 2013. Statistical tests swo:SWO_0000714 Stepwise normalization functions for cDNA microarray data. http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html Nandini Badarinarayan stepNorm swo:SWO_0000715 't-test' swo:SWO_0000716 Transcript mapping with high-density oligonucleotide tiling arrays http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html Nandini Badarinarayan tilingArray swo:SWO_0000717 Functions for data analysis and graphical displays for developmental microarray time course data. http://bioconductor.org/packages/2.4/bioc/html/timecourse.html Nandini Badarinarayan timecourse swo:SWO_0000718 Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. http://bioconductor.org/packages/2.4/bioc/html/tkWidgets.html Nandini Badarinarayan tkWidgets swo:SWO_0000719 topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. http://bioconductor.org/packages/2.4/bioc/html/topGO.html Nandini Badarinarayan topGO swo:SWO_0000720 Top Scoring Pairs for Microarray Classification http://bioconductor.org/packages/2.4/bioc/html/tspair.html Nandini Badarinarayan tspair swo:SWO_0000721 Estimation of local false discovery rate http://bioconductor.org/packages/2.4/bioc/html/twilight.html Nandini Badarinarayan twilight swo:SWO_0000722 Two-stage measurement error model swo:SWO_0000723 Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. http://bioconductor.org/packages/2.4/bioc/html/vbmp.html Nandini Badarinarayan vbmp swo:SWO_0000725 The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references http://bioconductor.org/packages/2.4/bioc/html/vsn.html Nandini Badarinarayan vsn swo:SWO_0000726 This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. http://bioconductor.org/packages/2.4/bioc/html/weaver.html Nandini Badarinarayan weaver swo:SWO_0000727 An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. http://bioconductor.org/packages/2.4/bioc/html/webbioc.html Nandini Badarinarayan webbioc swo:SWO_0000728 This packages contains tools to support the construction of tcltk widgets http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html Nandini Badarinarayan widgetTools swo:SWO_0000729 Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. http://bioconductor.org/packages/2.4/bioc/html/xcms.html Nandini Badarinarayan xcms swo:SWO_0000730 Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays http://bioconductor.org/packages/2.4/bioc/html/xps.html Nandini Badarinarayan xps swo:SWO_0000731 Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. http://bioconductor.org/packages/2.4/bioc/html/yaqcaffy.html Nandini Badarinarayan yaqcaffy swo:SWO_1100000 2-sample pooled t-test swo:SWO_1100001 50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented. General linear modeling of fixed-effects models with multiple responses is performed. The function calculates 50-50 MANOVA p-values, ordinary univariate p-values and adjusted p-values using rotation testing. http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html Nandini Badarinarayan 50-50 MANOVA swo:SWO_1100002 The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix. http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html Nandini Badarinarayan ABarray swo:SWO_1100003 The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe. 'ACME' swo:SWO_1100004 ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. http://bioconductor.org/packages/2.4/bioc/html/ACME.html Nandini Badarinarayan Algorithms for Calculating Microarray Enrichment swo:SWO_1100005 Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms http://www.affymetrix.com/ Nandini Badarinarayan Affymetrix Expression Console swo:SWO_1100006 AIDA is a modular software package for evaluation and documentation of images that were obtained with digital devices such as CCD cameras, flat bed scanners, or BAS / FLA- scanners from Fuji. Additionally, AIDA allows the loading of loading a variety of images in other image formats (e.g.: TIFF, JPEG, Bmp, gel). AIDA can control all scanning devices offering a TWAIN compatible driver. http://www.raytest.de/index2.html Nandini Badarinarayan AIDA swo:SWO_1100007 Average log expression across arrays (ALE) swo:SWO_1100008 ALL/AML data set swo:SWO_1100009 AMDIS swo:SWO_1100010 The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR ANCOVA swo:SWO_1100011 ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation. ANNOVA 'ANOVA' swo:SWO_1100012 AP-MS data swo:SWO_1100013 ARACNE algorithm swo:SWO_1100014 ARR swo:SWO_1100015 AWS algorithm swo:SWO_1100016 Nandini Badarinarayan Absolute Expression Analysis swo:SWO_1100017 Nandini Badarinarayan Absolute Expression Analysis swo:SWO_1100018 The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. http://bioconductor.org/packages/2.4/bioc/html/AffyCompatible.html Nandini Badarinarayan 'AffyCompatible' swo:SWO_1100019 The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. http://bioconductor.org/packages/2.4/bioc/html/AffyExpress.html Nandini Badarinarayan 'AffyExpress' swo:SWO_1100020 Nandini Badarinarayan Affymetrix GCOS v1.2 swo:SWO_1100021 The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. Affymetrix GCOS software GCOS software GeneChip Operating Software http://www.affymetrix.com Nandini Badarinarayan Affymetrix GeneChip Operating Software swo:SWO_1100022 Nandini Badarinarayan Affymetrix Software swo:SWO_1100023 Preprocessing of Agilent 4x44 array data http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html Nandini Badarinarayan Agi4x44PreProcess swo:SWO_1100024 Nandini Badarinarayan Agilent Feature Extraction 5.1.1 swo:SWO_1100025 Nandini Badarinarayan Agilent Feature Extraction software version 7.1 swo:SWO_1100026 Nandini Badarinarayan Agilent Feature Extraction software version 7.5 swo:SWO_1100027 Nandini Badarinarayan Agilent Feature Extraction software version A.5.1.1 swo:SWO_1100028 Nandini Badarinarayan ArrayVision 6.0 (Imaging Research Inc.) swo:SWO_1100029 Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search http://bioconductor.org/packages/2.4/bioc/html/BCRANK.html Nandini Badarinarayan 'BCRANK' swo:SWO_1100030 BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering BGL swo:SWO_1100031 Bayesian models for differential gene expression http://bioconductor.org/packages/2.4/bioc/html/BGmix.html Nandini Badarinarayan 'BGmix' swo:SWO_1100032 BLAST, or Basic Local Alignment Search Tool in full, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://blast.ncbi.nlm.nih.gov/Blast.cgi Allyson Lister: added 'achieves objective' axioms for pairwise and multiple sequence alignment classes. James Malone Nandini Badarinarayan BLAST swo:SWO_1100033 Iterative Bayesian Model Averaging (BMA) swo:SWO_1100034 Base-Pair-Distance Kernel swo:SWO_1100035 BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bpmap.html, accessed 22 May 2013. Allyson Lister BPMAP swo:SWO_1100036 BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis. http://linus.nci.nih.gov/BRB-ArrayTools.html Nandini Badarinarayan BRB-ArrayTools swo:SWO_1100037 This document describes the process of forging a BSgenome data package. It is intended for Bioconductor users who want to make a new BSgenome data package http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html Nandini Badarinarayan 'BSgenome' swo:SWO_1100038 BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation. http://tagc.univ-mrs.fr/bioinformatics/bzscan/ Nandini Badarinarayan BZScan swo:SWO_1100039 BaldiLongT swo:SWO_1100040 This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000). http://www.rubion.rub.de/labor/pdf/BASREAD.pdf Nandini Badarinarayan BasReader 3.01 swo:SWO_1100041 Bayesian Model swo:SWO_1100042 BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications http://www.illumina.com/pages.ilmn?ID=35 Nandini Badarinarayan Beadstudio swo:SWO_1100043 This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples http://bioconductor.org/packages/2.4/bioc/html/BicARE.html Nandini Badarinarayan 'BicARE' swo:SWO_1100044 Creates classes used in model-view-controller (MVC) design that uses Biobase Allyson Lister Nandini Badarinarayan 'BioMVCClass' Creates classes used in model-view-controller (MVC) design that uses Biobase http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html swo:SWO_1100045 Functions that are needed by many other packages or which replace R functions http://bioconductor.org/packages/2.4/bioc/html/Biobase.html Nandini Badarinarayan 'Biobase' swo:SWO_1100046 Software and data to support the case studies. http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html Nandini Badarinarayan 'BiocCaseStudies' swo:SWO_1100047 Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages. http://www.bioconductor.org/overview Bioconductor Nandini Badarinarayan This is a defined class which will be populated if a piece of software identifies itself as having the value 'Bioconductor' for the 'is published by' property. (Allyson Lister) BioConductor Software swo:SWO_1100048 Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences. http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html Nandini Badarinarayan 'Biostrings' swo:SWO_1100049 BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility. BlueFuse [BlueGnome] http://www.cambridgebluegnome.com/bluefuse.htm Nandini Badarinarayan BlueFuse swo:SWO_1100050 This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html Nandini Badarinarayan 'BufferedMatrix' swo:SWO_1100051 This package involves microarray Data related methods that utlize BufferedMatrix objects http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html Nandini Badarinarayan 'BufferedMatrixMethods' swo:SWO_1100052 This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes. http://bioconductor.org/packages/2.4/bioc/html/CALIB.html Nandini Badarinarayan 'CALIB' swo:SWO_1100053 Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments Nandini Badarinarayan 'CAMERA' swo:SWO_1100054 The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013. It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CDF format. As such, this class has been renamed as the binary format, and a new class created (CDF ASCII format) to make both options available. CDF binary format swo:SWO_1100055 This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. http://bioconductor.org/packages/2.4/bioc/html/CMA.html Nandini Badarinarayan 'CMA' swo:SWO_1100056 CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting) CMA swo:SWO_1100057 Multivariate correlation estimation and statistical inference. http://bioconductor.org/packages/2.4/bioc/html/CORREP.html Nandini Badarinarayan 'CORREP' swo:SWO_1100058 This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance. CRLMM algorithm swo:SWO_1100059 Continuous Wavelet Transform (CWT)-based peak detection algorithm swo:SWO_1100060 CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages. CarmaWEB https://carmaweb.genome.tugraz.at/carma/ Nandini Badarinarayan CARMAweb swo:SWO_1100061 Category analysis swo:SWO_1100062 A collection of tools for performing category analysis. http://bioconductor.org/packages/2.4/bioc/html/Category.html Nandini Badarinarayan Category swo:SWO_1100063 ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services. http://bioconductor.org/packages/2.4/bioc/html/ChemmineR.html Nandini Badarinarayan 'ChemmineR' swo:SWO_1100064 Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime. VersArray ChipReader http://www.bio-medicine.org/ Nandini Badarinarayan ChipReader 3.1 swo:SWO_1100065 ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data ChipSkipper Microarray Data Evaluation Software ChipSkipper [EMBL] http://angiogenesis.dkfz.de/software/chipskipper/index.htm Nandini Badarinarayan ChipSkipper swo:SWO_1100066 Nandini Badarinarayan ChipSkipper V0.99 swo:SWO_1100067 A multiscan is an R package for combining multiple scans http://bioconductor.org/packages/2.4/bioc/html/multiscan.html Nandini Badarinarayan multiscan swo:SWO_1100068 The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. http://bioconductor.org/packages/2.4/bioc/html/affy.html Nandini Badarinarayan affy swo:SWO_1100069 The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. http://bioconductor.org/packages/2.4/bioc/html/affycomp.html Nandini Badarinarayan affycomp swo:SWO_1100070 PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex. PCMG swo:SWO_1100071 Nandini Badarinarayan Feature Extraction Software swo:SWO_1100072 Chi-square swo:SWO_1100073 adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. http://bioconductor.org/packages/2.4/bioc/html/adSplit.html Nandini Badarinarayan Annotation-Driven Clustering swo:SWO_1100074 distance calculation swo:SWO_1100075 Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html Nandini Badarinarayan R software swo:SWO_1100076 BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. BCRANK swo:SWO_1100077 cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture Cosmo swo:SWO_1100078 F test swo:SWO_1100079 Nandini Badarinarayan MAGE-TAB inputting software swo:SWO_1100080 Text data set swo:SWO_1100081 CSV data set swo:SWO_1100082 non-linear functional regression model with both additive and multiplicative error terms Non-linear functional regression model swo:SWO_1100083 A collection of software tools for dealing with co-citation data. http://bioconductor.org/packages/2.4/bioc/html/CoCiteStats.html Nandini Badarinarayan 'CoCiteStats' swo:SWO_1100084 This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=101854 Nandini Badarinarayan CodeLink Expression Analysis Software swo:SWO_1100085 Slides are scanned using CodeLink Expression Scanning Software Nandini Badarinarayan CodeLink Expression Scanning Software swo:SWO_1100086 Complex Estimation Algorithm swo:SWO_1100087 Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic. http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html Nandini Badarinarayan Cyber-T swo:SWO_1100088 This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. http://bioconductor.org/packages/2.4/bioc/html/DEDS.html Nandini Badarinarayan 'DEDS' swo:SWO_1100089 This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. http://bioconductor.org/packages/2.4/bioc/html/DFP.html Nandini Badarinarayan 'DFP' swo:SWO_1100090 A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High' Discriminant Fuzzy Pattern Algorithm swo:SWO_1100091 DFW swo:SWO_1100092 Digital gene expression (DGE) datasets swo:SWO_1100093 Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html Nandini Badarinarayan 'DNAcopy' swo:SWO_1100094 EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. http://bioconductor.org/packages/2.4/bioc/html/EBImage.html Nandini Badarinarayan 'EBImage' swo:SWO_1100095 EBarrays provides tools for the analysis of replicated/unreplicated microarray data. http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html Nandini Badarinarayan 'EBarrays' swo:SWO_1100096 Expectation-Maximization(EM) algorithm swo:SWO_1100097 Empirical Bayes rule swo:SWO_1100098 Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools. http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx Nandini Badarinarayan Expert 2100 swo:SWO_1100099 FACS data is data which describes flow cytometry data sets. http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013. Allyson Lister FACS data swo:SWO_1100100 FARMS swo:SWO_1100101 FC swo:SWO_1100102 'FDR' swo:SWO_1100103 Fixed effect model swo:SWO_1100104 The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment Feature Extraction Software Feature Extraction Software [Agilent Technologies] Feature Extraction software http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx Nandini Badarinarayan Agilent Feature Extraction Software swo:SWO_1100105 Fischer's Exact Test swo:SWO_1100106 Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK. http://falkow.stanford.edu/whatwedo/software/software.html Nandini Badarinarayan GACK swo:SWO_1100107 GASSCO method swo:SWO_1100108 Single-user desktop software package for analyzing microarray data from multiple microarray platforms. GC-RMA Quantification (Stratagene ArrayAssist Expression Software) http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html Nandini Badarinarayan GC-RMA Quantification swo:SWO_1100109 Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery. http://www.baymedia.com/gemtools/ Nandini Badarinarayan GEMTools 2.4 swo:SWO_1100110 GEO data type swo:SWO_1100111 The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html Nandini Badarinarayan GEOmetadb swo:SWO_1100112 The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html Nandini Badarinarayan GEOquery swo:SWO_1100113 This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc. http://bioconductor.org/packages/2.4/bioc/html/GGBase.html Nandini Badarinarayan GGBase swo:SWO_1100114 Gamma Gamma Model swo:SWO_1100115 matlab software swo:SWO_1100116 Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays. http://www.clontech.com/images/pacs/634650-PA27475.pdf Nandini Badarinarayan AtlasImage swo:SWO_1100117 The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm. CBS swo:SWO_1100118 CBS algorithm swo:SWO_1100119 Contains functions and classes that are needed by arrayCGH packages. http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html Nandini Badarinarayan 'CGHbase' swo:SWO_1100120 Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. http://bioconductor.org/packages/2.4/bioc/html/CGHcall.html Nandini Badarinarayan 'CGHcall' swo:SWO_1100121 Dimension Reduction for Array CGH Data with Minimal Information Loss http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html Nandini Badarinarayan 'CGHregions' swo:SWO_1100122 CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html, http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp-xda.html, accessed 22 May 2013. Allyson Lister As this is a child of Binary format, it is assumed that this class is intended to represent the binary form of this format. As described in the definition sources, there are other formats for CHP available. CHP binary format swo:SWO_1100123 CLR algorithm swo:SWO_1100124 A set of functions to create and interact with dynamic documents and vignettes. http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html Nandini Badarinarayan 'DynDoc' swo:SWO_1100125 FoxDimmicT swo:SWO_1100126 GEO Matrix Series format swo:SWO_1100127 software before Microsoft 2007 https://github.com/bcbio/bcbio-nextgen swo:SWO_1100128 bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. https://github.com/drmarkreuter Allyson Lister AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15 bcbio bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. https://github.com/bcbio/bcbio-nextgen https://github.com/pinin4fjords/shinyngs swo:SWO_1100129 Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools. https://github.com/drmarkreuter Allyson Lister AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/12 shinyNGS Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools. https://github.com/pinin4fjords/shinyngs https://satijalab.org/seurat/ swo:SWO_1100130 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. https://github.com/drmarkreuter Allyson Lister AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/13 Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. https://satijalab.org/seurat/ https://www.graphpad.com/scientific-software/prism/ swo:SWO_1100131 GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers. https://github.com/drmarkreuter Allyson Lister AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/14 Graphpad Prism GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers. https://github.com/drmarkreuter https://combine-lab.github.io/salmon/ swo:SWO_1100132 Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data. https://github.com/drmarkreuter Allyson Lister AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15 Salmon Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data. https://combine-lab.github.io/salmon/ http://www.stavrox.com swo:SWO_1100133 StavroX software identifies cross-linked peptides. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/35 Stavrox StavroX software identifies cross-linked peptides. Mark Reuter https://github.com/shengqh/RCPA.Tools/wiki swo:SWO_1100134 ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/34 ProteomicsTools ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification. https://github.com/shengqh/RCPA.Tools https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7 swo:SWO_1100135 Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/32 Chromeleon Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments. https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7 https://www.spectralworks.com/products/analyzerpro/ swo:SWO_1100136 AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/31 AnalyzerPro AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform https://www.spectralworks.com/products/analyzerpro/ https://sciex.com/technology/swath-acquisition swo:SWO_1100137 SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/30 SWATH Software SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology. https://sciex.com/technology/swath-acquisition https://www.proteinmetrics.com/products/supernovo/ swo:SWO_1100138 SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/29 Supernovo SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery. https://www.proteinmetrics.com/products/supernovo/ http://www.bioinfor.com/peaksdb/ swo:SWO_1100139 Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/28 PEAKS DB Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions. Mark Reuter https://htseq.readthedocs.io/en/release_0.11.1/ swo:SWO_1100140 HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/27 HTSeq HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. https://htseq.readthedocs.io/en/release_0.11.1/overview.html https://github.com/broadinstitute/rnaseqc swo:SWO_1100141 RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/26 RNA-SeQC RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis. Mark Reuter http://rseqc.sourceforge.net/ swo:SWO_1100142 RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/25 RSeQC RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. http://rseqc.sourceforge.net/ https://github.com/samtools/samtools swo:SWO_1100143 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/24 SAMtools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Mark Reuter https://github.com/s-andrews/FastQC swo:SWO_1100144 FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/23 FastQC FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. Mark Reuter https://cutadapt.readthedocs.io/en/stable/ swo:SWO_1100145 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Allyson Lister Allyson Lister Mark Reuter Allyson Lister Mark Reuter AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/22 CutAdapt Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. https://cutadapt.readthedocs.io/en/stable/ swo:SWO_9000005 A licence clause is a component of a licence which defines some aspect of a restriction or conversely permission in how something corresponding to a licence may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way. James Malone clause licence clause swo:SWO_9000006 An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource. Modified by Allyson Lister from http://creativecommons.org/tag/attribution Attribution clause swo:SWO_9000007 Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways. Allyson Lister Derivatives clause swo:SWO_9000008 A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways. Allyson Lister Source code clause swo:SWO_9000009 A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways. Allyson Lister Platform clause swo:SWO_9000010 A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform. Allyson Lister Number of installations clause swo:SWO_9000011 A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource. Allyson Lister Number of users clause swo:SWO_9000012 A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways. Allyson Lister Time clause swo:SWO_9000013 A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways. Allyson Lister Usage clause swo:SWO_9000016 No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created. Allyson Lister No restrictions on derivatives swo:SWO_9000017 Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created. Allyson Lister Restrictions on derivative software swo:SWO_9000018 Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource. Allyson Lister Derivatives not allowed swo:SWO_9000019 Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license. Allyson Lister derivative code same license swo:SWO_9000020 A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways. Allyson Lister Source code available swo:SWO_9000021 A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee. Allyson Lister Source code unavailable swo:SWO_9000022 Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on. Allyson Lister Platform restricted swo:SWO_9000023 Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for. Allyson Lister Platform unrestricted swo:SWO_9000024 A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee. Allyson Lister Number of installations restricted swo:SWO_9000025 A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee. Allyson Lister Number of installations unrestricted swo:SWO_9000026 A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users. Allyson Lister Number of users restricted swo:SWO_9000027 A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource. Allyson Lister Number of users unrestricted swo:SWO_9000028 Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used. Allyson Lister Time for use restricted swo:SWO_9000029 Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for. Time for use unrestricted swo:SWO_9000030 Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used. Allyson Lister Usage unrestricted swo:SWO_9000031 Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license. Allyson Lister Usage restricted swo:SWO_9000032 Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites. Non-commercial use only swo:SWO_9000033 Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only. Allyson Lister Academic use only swo:SWO_9000034 Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license. Allyson Lister derivative code linked same license swo:SWO_9000050 The mode of interaction with a piece of software. software interface swo:SWO_9000070 Microsoft Excel 2010-06-15T0:00:00 swo:SWO_9000071 Microsoft Excel for Windows 2010 swo:SWO_9000072 The Windows Operating System Microsoft Windows 2006-11-08T0:00:00 swo:SWO_9000073 Windows Vista 2001-10-25T0:00:00 swo:SWO_9000074 Windows XP swo:SWO_9000075 Microsoft Office 2001 swo:SWO_9000076 software suite http://get.adobe.com/reader/ swo:SWO_9000077 Andy Brown Adobe Acrobat Reader http://code.google.com/p/annotare/ swo:SWO_9000078 Andy Brown Annotare http://biojava.org swo:SWO_9000079 BioJava http://www.bioperl.org swo:SWO_9000081 Andy Brown BioPerl http://ecobas.org/www-server/rem/mdb/dndc.html http://www.dndc.sr.unh.edu/ swo:SWO_9000083 Andy Brown Soil Chemistry Model DNDC http://sourceforge.net/projects/droid/ swo:SWO_9000089 Digital Record Object Identification DROID www.dropbox.com swo:SWO_9000090 Dropbox http://www.eclipse.org swo:SWO_9000091 Andy Brown The Eclipse IDE Eclipse swo:SWO_9000092 EMBOSS package http://www.endnote.com/ swo:SWO_9000093 Andy Brown Citation management software Endnote http://sf.net/projects/grimoires swo:SWO_9000094 Andy Brown Grimoires swo:ontology Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM data_0582. obsolete_ontology true swo:software_before_Microsoft_2007 http://www.ebi.ac.uk/swo/SWO_1100127 1.7 AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/18 obsolete software before Microsoft 2007 true A stochastic algorithm for population pharmacology modeling http://www.math.u-bordeaux1.fr/MAS10/DOC/PDF-PRES/Lavielle.pdf SAEM A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps. http://en.wikipedia.org/wiki/Dynamic_Bayesian_network, accessed 27 November 2014. dynamic Bayesian network model In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term "ordinary" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable. Ordinary Differential Equation Algorithm http://en.wikipedia.org/wiki/Ordinary_differential_equation, accessed 25 March 2015. Allyson Lister ODE Algorithm Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology http://en.wikipedia.org/wiki/Gillespie_algorithm, accessed 25 March 2015. Allyson Lister Gillespie's Stochastic Simulation Algorithm Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value. http://en.wikipedia.org/wiki/Stochastic_simulation#Monte_Carlo_simulation, accessed 25 March 2015, and http://www.async.ece.utah.edu/iBioSim/docs/iBioSim.html, accessed 25 March 2015. Allyson Lister Monte Carlo Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs. Differential Algebraic Equation Algorithm http://en.wikipedia.org/wiki/Differential_algebraic_equation, accessed 26 March 2015. Allyson Lister DAE Algorithm A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives. Partial Differential Equation Algorithm http://en.wikipedia.org/wiki/Partial_differential_equation, accessed 26 March 2015. Allyson Lister PDE Algorithm A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered. James Malone spreadsheet format A spreadsheet data format designed for Microsoft Excel. James Malone XLS spreadsheet A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity. James Malone XML spreadsheet James Malone Matlab .m file Marked as obsolete by Allyson Lister. 1.5 Equivalence with EDAM http://edamontology.org/format_2332, please use that instead. obsolete_XML true "Resource Description Framework (RDF) format." [http://edamontology.org] format bioinformatics edam formats The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web. http://www.w3.org/TR/REC-rdf-syntax/ James Malone Jon Ison Data in RDF format can be serialised into XML, textual, or binary format. Merged with now-obsolete EDAM class 'RDF' http://edamontology.org/format_2376 by Allyson Lister. RDF A serialisation of RDF into an XML format. James Malone RDF-XML image format DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata http://en.wikipedia.org/wiki/.dwg James Malone DWG DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs. http://en.wikipedia.org/wiki/AutoCAD_DXF James Malone DXF The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). http://www.fileformat.info/format/bmp/egff.htm James Malone BMP Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632. http://en.wikipedia.org/wiki/Computer_Graphics_Metafile James Malone CGM web page specification document exchange format PDF is an open standard for document exchange. Portable Document Format pdf TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry. Tagged Image File Format TIFF JPEG is a lossy file format for storing images JPG JPEG PNG is a bitmapped image format and video codec that employs lossless data compression. Portable Network Graphics PNG The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia] Graphics Interchange Format GIF A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel. raster image format A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering. vector image format Scalable Vector Graphics SVG Adobe Illustrator format AI PostScript is a format used for describing documents. PostScript tex is a format for documents written in the document markup language and document preparation system LaTeX. LaTeX format tex A format specification for data used or produced by outliner software outline document format A proprietary format for documents created and edited using OmniOutliner outliner software, OmniOutline format OPML (Outline Processor Markup Language) is an XML format for outlines Outline Processor Markup Language OPML JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia] JPEG 2000 word processing document format WordStar format A file format for word processing documents for Microsoft Word. Microsoft Word doc programming language format A source code file format which is specified to be used with the Java programming language. James Malone .java file A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine. James Malone .class file An XML-based file format for use with the COPASI software. .cps http://edamontology.org/format_3239 1.7 AL 17.9.2019: The EDAM CopasiML (format_3239) was used elsewhere in SWO and therefore this class was no longer required. obsolete CopasiML true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with the EDAM SBML class format_2585. obsolete_SBML true The Web Ontology Language (OWL) in XML serialization OWL-XML Web Ontology Language version 2 in XML Serialization OWL2-XML Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM term format_2549. obsolete_OBO flat file format true Marked as obsolete by Allyson Lister. 1.5 Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead. obsolete_text file format false true ASCII format plain text file format Marked as obsolete by Allyson Lister. Obsoleted after release 0.4 Equivalent with EDAM format_3162. obsolete_MAGE tab format true Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character. http://en.wikipedia.org/wiki/Tab-separated_values, accessed 6 June 2013. Allyson Lister tab delimited file format Marked as obsolete by Allyson Lister. Obsoleted after the version 0.4 release. Equivalence with EDAM format_3158. obsolete_PSI-MI format true SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012 Allyson Lister SIF GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 GML XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML. http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 XGMML A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input. Allyson Lister Interaction data A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks. Modified from http://en.wikipedia.org/wiki/Knowledge_representation, accessed 10 February 2014 AL 6.9.22: This has been moved from 'role' and used to be called 'knowledge representation role'. The issue in its former placement is to do with the domain and range of role. Bcause this class is intended as a role for a data format, it means that we use it for various children of IAO data format specification (http://purl.obolibrary.org/obo/IAO_0000098). has_role is an RO property with a domain of independent continuant, and data format specification is an ICE (a generically dependent continuant). This means we cannot use has_role for this class. Therefore, we have moved the class out of role and updated the label, and are now using 'characteristic of'/'has characteristic' instead. We may wish to refine the placement of this class in future. Knowledge representation AL 6.9.22: I would prefer to use the updated RO label 'has characteristic', but for some reason Protege only allows the use of the label RO deems older, 'bearer of' BioPAX RDF/XML format BioPAX Manchester OWL Syntax format The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013 Allyson Lister CDF ASCII format BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bar.html, accessed 22 May 2013. Allyson Lister BAR CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. Allyson Lister CEL ASCII format Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix. Allyson Lister Affymetrix-compliant data The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type. FCS http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. Allyson Lister Data File Standard for Flow Cytometry FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter. http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. Allyson Lister FCS3.0 NONMEM data format A nucleic acid sequence that indicate the order of nucleotides within some DNA. DNA nucleotide sequence Data about primary biological sequence information, such as DNA neucleotide sequences. biological sequence data Data which contains information about amino acid sequences of proteins. amino acid protein sequence data Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies. Nucleotide-nucleotide BLAST BLASTN sequence feature format Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. http://samtools.sourceforge.net/tabix.shtml tabix file format Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data. http://pmgenomics.ca/hoffmanlab/proj/genomedata/doc/1.3.5/genomedata.html and http://www.hdfgroup.org/why_hdf/, accessed 27 November 2014. Allyson Lister genomedata format The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. http://genome.ucsc.edu/goldenpath/help/bedgraph.html, accessed December 3, 2014. Allyson Lister BedGraph GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network. Graphical Models Toolkit parameter data Allyson Lister http://noble.gs.washington.edu/proj/philius/README, accessed 3 December 2014. Allyson Lister GMTK parameter data MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages. http://www.w3.org/Math/ Allyson Lister James Malone MathML 2.0 FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible. http://www.physiomeproject.org/xml_languages/fieldml James Malone FieldML WKn is a collective name for a spreadsheet format created for Lotus 1-2-3. http://support.sas.com/documentation/cdl/en/acpcref/63184/HTML/default/viewer.htm#a003103772.htm and http://en.wikipedia.org/wiki/Lotus_1-2-3, accessed 3 December 2014. Allyson Lister Please note that this is a collective class for all versions of the WKn format, and the specific version required should be created as necessary and placed as a child of this class. WKn GZipped format .gz Zipped format .zip audio format Resource Interchange File Format RIFF BigWig format .bw Comma-separated value format .csv MASCOT generic format .mgf MySQL format .mysql SQL format .sql A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system. WUI Web UI Allyson Lister web user interface A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser. Desktop GUI Allyson Lister desktop graphical user interface A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations. SOAP Service Modified from http://en.wikipedia.org/wiki/SOAP, accessed 6 June 2013; modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013. Allyson Lister SOAP service A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of "stateless" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces. REST Service Modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013, Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. Allyson Lister REST service A web service in which calls invoked return JSON. JSON web service A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services. Web Service Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. Allyson Lister web service A Graphical user interface is a type of software interface that allows users to interact with electronic devices using images rather than text commands. A GUI represents the information and actions available to a user through graphical icons and visual indicators such as secondary notation, as opposed to text-based interfaces, typed command labels or text navigation. https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013. GUI Allyson Lister graphical user interface A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines). Command line Command line interface Command-line http://en.wikipedia.org/wiki/Command-line_interface, accessed 25 November 2014. command-line interface An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact. API http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014. application programming interface CC Creative Commons Proprietary commercial software license Mozilla Public License Version 1.1 MPL v1.1 Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways. Allyson Lister Distribution clause Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial. Allyson Lister Distribution restricted Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes. Allyson Lister Distribution unrestricted Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways. Allyson Lister Derivatives allowed GNU General Public License GNU GPL http://www.apache.org/licenses/LICENSE-2.0 This is a free software license under the definition of "free" by the GNU Project, and is compatible with version 3 of the GNU GPL. http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. Allyson Lister Apache License Version 2.0 http://www.opensource.org/licenses/afl-3.0.php https://opensource.org/licenses/AFL-3.0 The Academic Free License is a free software license under the definition of "free" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL. AFL http://directory.fsf.org/wiki/License:AFLv3, accessed 12 June 2013; http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 Allyson Lister Andy Brown Academic Free License version 3 http://www.freebsd.org/copyright/freebsd-license.html This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. 2-clause BSD License http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. Allyson Lister Andy Brown FreeBSD Open source software license License without restrictions on derivatives A licensed is a free license according to GNU if the users have the four essential freedoms: The freedom to run the program, for any purpose (freedom 0). The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. The freedom to redistribute copies so you can help your neighbor (freedom 2). The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. “Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013. Allyson Lister Allyson Lister: This class defines those licenses which are free licenses, but which may or may not be compatible with any version of the GNU GPL. GNU Project Free License Type GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. Allyson Lister GNU GPL Compatible License Type Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable. Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. Allyson Lister Copyleft The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. GNU General Public License Version 3 https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016. Allyson Lister GNU GPL v3 The GNU GPL v2 is an earlier version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv2 is, by itself, not compatible with GPLv3. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. GNU General Public License Version 2 https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016. GNU GPL v2 https://creativecommons.org/publicdomain/zero/1.0/ CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL. CC0 1.0 Universal (CC0 1.0) Public Domain Dedication http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. Allyson Lister CC0 1.0 http://creativecommons.org/licenses/by/2.0/ CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 2.0 Generic (CC BY 2.0) Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 and 28 June 2016; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY 2.0 Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used. Allyson Lister Attribution required https://creativecommons.org/licenses/by-sa/2.0/ CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. Creative Commons Attribution-Sharealike 2.0 Generic Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY-SA 2.0 https://latex-project.org/lppl/lppl-1-3c.html LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it. Latex Project Public License v1.3c Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. LPPL v1.3c https://latex-project.org/lppl/lppl-1-2.html LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it. Latex Project Public License v1.2 Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. LPPL v1.2 MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form. http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; http://en.wikipedia.org/wiki/Mozilla_Public_License, accessed 12 June 2013. MPL v2.0 Mozilla Public License Version 2.0 Allyson Lister Artistic License https://opensource.org/licenses/Artistic-2.0 The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0). http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. Allyson Lister Artistic License 2.0 Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource. Allyson Lister Allyson Lister In some ways, purchase cost is similar to the already-extant usage clause hierarchy, which includes restricted and unrestricted usage. However, a usage limitation is not necessarily due to whether or not something costs money: even if the usage is academic only, it could still be either free or non-free. A license could have multiple usage clauses, e.g. academic only when free, and unrestricted if a fee is paid. Purchase cost was created which, together with a usage clause, defines both limitations and cost. Purchase cost Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free. Allyson Lister Allyson Lister This class refers only to the cost of the resource, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). Free Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost. Allyson Lister Allyson Lister This class refers only to the cost of the resource, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). Not Free A license which allows any form of usage of the artifact. free to use license true http://creativecommons.org/licenses/by/4.0/ The CC BY 4.0 license is a Creative Commons license. This is a non-copyleft free license that is good for art and entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. People are free to: Share — copy and redistribute the material in any medium or format; Adapt — remix, transform, and build upon the material for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. But they must conform to the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. Creative Commons Attribution 4.0 International (CC BY 4.0) http://creativecommons.org/licenses/by/4.0/ accessed June 22, 2016; https://www.gnu.org/licenses/license-list.html, accessed on June 28, 2016. Allyson Lister Allyson Lister: The only restriction on derivatives is that of the attribution requirement. CC BY 4.0 Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used. Allyson Lister Allyson Lister Attribution not required https://creativecommons.org/licenses/by/2.0/uk/ CC BY 2.0 UK is a UK-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 2.0 UK: England & Wales (CC BY 2.0 UK) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 2.0 UK This is the latest version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv3. It is therefore recommend for special circumstances only. Please note that LGPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. GNU Lesser General Public License (LGPL) version 3 https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016. GNU LGPL v3 GNU AGPL This is a free software, copyleft license. Its terms effectively consist of the terms of GPLv3, with an additional paragraph in section 13 to allow users who interact with the licensed software over a network to receive the source for that program. It is recommended that developers consider using the GNU AGPL for any software which will commonly be run over a network. GNU Affero General Public License (AGPL) version 3 https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016. Allyson Lister GNU AGPL v3 This is the previous version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv2 and GPLv3. We generally recommend the latest version of the LGPL, for special circumstances only. GNU Lesser General Public License (LGPL) version 2.1 https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. GNU LGPL v2.1 http://creativecommons.org/licenses/by/2.1/jp/deed.en CC BY 2.1 JP is a Japan-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 2.1 Japan (CC BY 2.1 JP) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 2.1 JP https://creativecommons.org/licenses/by/2.5/ CC BY 2.5 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 2.5 Generic (CC BY 2.5) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 2.5 https://creativecommons.org/licenses/by/3.0/au/ CC BY 3.0 AU is an Australia-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 3.0 Australia (CC BY 3.0 AU) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 3.0 AU https://creativecommons.org/licenses/by/3.0/ CC BY 3.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 3.0 Unported (CC BY 3.0) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 3.0 https://creativecommons.org/licenses/by/3.0/us/ CC BY 3.0 US is a US-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. Creative Commons Attribution 3.0 United States (CC BY 3.0 US) Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. Allyson Lister CC BY 3.0 US https://creativecommons.org/licenses/by-nd/3.0/ CC BY-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation. Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016. Allyson Lister CC BY-ND 3.0 https://creativecommons.org/licenses/by-nd/4.0/ CC BY-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation. Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016. Allyson Lister CC BY-ND 4.0 https://creativecommons.org/licenses/by-nc/3.0/ CC BY-NC 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC 3.0 https://creativecommons.org/licenses/by-nc/4.0/ CC BY-NC 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC 4.0 https://creativecommons.org/licenses/by-nc-nd/3.0/ CC BY-NC-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-ND 3.0 https://creativecommons.org/licenses/by-nc-nd/2.5/ CC BY-NC-ND 2.5 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-ND 2.5 http://creativecommons.org/licenses/by-nc-nd/2.5/ch/deed.en CC BY-NC-ND 2.5 CH is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Switzerland (CC BY-NC-ND 2.5 CH) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-ND 2.5 CH https://creativecommons.org/licenses/by-nc-nd/4.0/ CC BY-NC-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND 4.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-ND 4.0 https://creativecommons.org/licenses/by-nc-sa/2.5/ CC BY-NC-SA 2.5 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Generic (CC BY-NC-SA 2.5) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-SA 2.5 https://creativecommons.org/licenses/by-nc-sa/3.0/ CC BY-NC-SA 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-SA 3.0 https://creativecommons.org/licenses/by-nc-sa/3.0/us/ CC BY-NC-SA 3.0 US is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States (CC BY-NC-SA 3.0 US) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-SA 3.0 US https://creativecommons.org/licenses/by-nc-sa/2.5/in/ CC BY-NC-SA 2.5 IN is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial-ShareAlike 2.5 India (CC BY-NC-SA 2.5 IN) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-SA 2.5 IN https://creativecommons.org/licenses/by-nc-sa/4.0/ CC BY-NC-SA 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. Allyson Lister CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-sa/2.1/jp/deed.en CC BY-SA 2.1 JP is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. Creative Commons Attribution-Sharealike 2.1 Japan Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY-SA 2.1 JP http://creativecommons.org/licenses/by-sa/3.0/ CC BY-SA 3.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. Creative Commons Attribution-Sharealike 3.0 Unported Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY-SA 3.0 http://creativecommons.org/licenses/by-sa/3.0/us/ CC BY-SA 3.0 US is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. Creative Commons Attribution-Sharealike 3.0 United States Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY-SA 3.0 US http://creativecommons.org/licenses/by-sa/4.0/ CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. Creative Commons Attribution-Sharealike 4.0 International Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. Allyson Lister CC BY-SA 4.0 Open Data Commons http://www.opendatacommons.org/licenses/odbl/1.0/ The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Open Database License (ODbL) v1.0 http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016. Allyson Lister ODbL v1.0 http://opendatacommons.org/licenses/dbcl/1.0/ The DbCL v1.0 allows a user of the database contents to share, create and adapt the contents. You must attribute any public use of the contents, or works produced from them. For redistribution or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original. If you publicly use any adapted version, or works produced from an adapted version, you must also offer it under the DbCL. If you redistribute the contents, or an adapted version of them, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Users of the DbCL must comply with the ODbL v1.0. ODC Database Contents License (DbCL) v1.0 http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016; http://opendatacommons.org/licenses/dbcl/1.0/, accessed 5 July 2016. Allyson Lister DbCL v1.0 http://elm.eu.org/media/Elm_academic_license.pdf The EMBLEM ELM Academic LIcense was developed as the license for the ELM (Eukaryotic Linear Motif) resource. Non-commerical use is allowed under this license, an additional commercial license is also available. This license makes the Licensed Software available free of charge for the licensee, which is a non-profit educational, academic and/or research institution. The software can only be used for academic research projects. This explicitly excludes projects which charge a fee, or projects that are done in collaboration with a third party that is funding the research in whole or in part in exchange for commercial rights on the results and/or possible delay in publication of any relevant results to the academic community. The user and any research assistants, co-workers or other workers who may use the Software agree to not grant licenses on any software that includes the Licensed Software, alone or integrated into other software, to third parties. Modification of the Licensed Software code is prohibited without the prior written consent of EMBLEM. ELM Software License Agreement http://elm.eu.org/media/Elm_academic_license.pdf, accessed 6 July 2017; http://elm.eu.org/infos/about.html accessed 6 July 2016. Allyson Lister EMBLEM ELM Academic License http://flowrepository.org/terms_of_service The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing. http://flowrepository.org/terms_of_service, accessed 6 July 2016. Allyson Lister FlowRepository Open Access Terms of Use http://opendatacommons.org/licenses/by/1.0/ The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Open Data Commons Attribution License (ODC-By) v1.0 http://opendatacommons.org/licenses/by/summary/, accessed 6 July 2016. Allyson Lister ODC-By v1.0 https://creativecommons.org/publicdomain/zero/1.0/ The ODC Public Domain Dedication and Licence is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This licence is intended for use on databases or their contents (“data”), either together or individually. The goal is to eliminate restrictions held by the original creator of the data and database on the use of it by others. Rightsholders will not be able to “dual license” their work by releasing the same work under different licences. This is because they have allowed anyone to use the work in whatever way they choose. Rightsholders therefore can’t re-license it under copyright or database rights on different terms because they have nothing left to license. ODC Public Domain Dedication and Licence http://opendatacommons.org/licenses/pddl/1.0/, accessed 7 July 2016. Allyson Lister PDDL v1.0 This is the original BSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery. obsolete_3-clause BSD License http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. Marked as obsolete by Allyson Lister Allyson Lister Andy Brown 1.6 (expected version number, after 1.5) This class is a duplicate of http://www.ebi.ac.uk/swo/license/SWO_9000085. obsolete_Modified BSD License true A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization. Allyson Lister Allyson Lister Vendor-specific License https://www.drugabuse.gov/researchers/research-resources/genetics-research-resources/distribution-genetic-data-biomaterials-nida-center-gene The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. Researchers may gain access to clinical data, genetic analysis data, and DNA by obtaining formal approval from the NIDA Genetic Data Access Request Committee. Allyson Lister Allyson Lister NIDA NIH Data Access Policy https://www.addgene.org/terms-of-use/ The Addgene Terms of Use specifies under what legal requirements Addgene data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of Addgene to exploit the data for commercial purposes. All copyright, trademark and other proprietary notices must be retained on the data. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). https://www.addgene.org/terms-of-use/, accessed 7 July 2016 Allyson Lister Addgene Terms of Use http://www.cas.org/legal/infopolicy The CAS Information Use Policy specifies under what legal requirements CAS Information may be accessed. Attribution to ACS must be included whenever creating derivatives or redistributing data covered under this license.Each User is permitted to download and retain a maximum of 5,000 Records and a maximum of 5,000 Molfiles at any given time for personal use or to share within a Project team for the life of the Project. There are also limits on how long records may be stored with the licensee, and how records may be linked. http://www.cas.org/legal/infopolicy accessed 7 July 2016. Allyson Lister CAS Information Use Policy http://cellfinder.de/contact/disclaimer/ The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. The operators of these pages aim to observe the copyright of others or will refer to their own or license-free works. http://cellfinder.de/contact/disclaimer/, accessed 7 July 2016. Allyson Lister CellFinder Copyright http://www.lincsproject.org/data/data-release-policy/ The LINCS Data Policy is a license which allows redistribution and derivative works as long as the original data is attributed correctly. All investigators are encouraged, to publish results based on LINCS data. These results may include, but would not be limited to, integrating LINCS data with data from other sources. LINCS data are released with the sole restriction that they must be correctly cited so that others can establish provenance and access the original data; the correct citation will be released with each data set and will comprise either a PMID/PMCID reference or a unique LINCS identifier. http://www.lincsproject.org/data/data-release-policy/, accessed 7 July 2016. Allyson Lister LINCS Data Policy http://www.genenetwork.org/conditionsofUse.html The GeneNetwork Conditions of Use describes the data licensing for the resource covered. Commercial and non-commercial use is allowed, though attribution is requested via either acknowledgement or co-authorship. Further restrictions on the bulk download of as-yet unpublished data is also described. (While mentioned in the document, software licensing is not the focus of this conditions of use and therefore is not modelled here.) http://www.genenetwork.org/conditionsofUse.html, accessed 7 July 2016. Allyson Lister GeneNetwork Conditions of Use http://gmd.mpimp-golm.mpg.de/termsconditions.aspx The GMD Academic License is a vendor-specific license which allows the access and use of the licensed data for non-commercial purposes, as long as the appropriate attribution is used and copyright notices retained. A separate license agreement is required for commercial users and as such, they are not covered by this license. Without written consent by the GMD, no part of the GMD - in its original or in any way processed or reformatted form - may be re-distributed in any way. Golm Metabolome Database Academic License http://gmd.mpimp-golm.mpg.de/termsconditions.aspx, accessed 7 July 2016. GMD Academic License http://www.geneprof.org/GeneProf/terms_and_conditions.jsp The GeneProf Academic License is a vendor-specific license which allows the access and use of the licensed resource for non-commercial purposes. http://www.geneprof.org/GeneProf/terms_and_conditions.jsp, accessed 7 July 2016. GeneProf Academic License http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp The European Medicines Agency Copyright states that the Agency is the owner of copyright and other intellectual property rights for documents and other content published on their website. Information and documents made available on the Agency's webpages are public and may be reproduced and/or distributed, totally or in part, irrespective of the means and/or the formats used, for non-commercial and commercial purposes, provided that the Agency is always acknowledged as the source of the material. Such acknowledgement must be included in each copy of the material. Citations may be made from such material without prior permission, provided the source is always acknowledged. The above-mentioned permissions do not apply to content supplied by third parties. Therefore, for documents where the copyright vests in a third party, permission for reproduction must be obtained from this copyright holder. http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp, accessed 12 July 2016. Allyson Lister European Medicines Agency Copyright http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE miRTaBase Data License is a simple vendor license which allows academic users to make use of the data for free. http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE, accessed 12 July 2016 Allyson Lister miRTaBase Data License http://www.gbif.org/terms/licences/data-sharing GBIF Data Sharing Agreement is a simple vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. http://www.gbif.org/terms/licences/data-sharing, accessed 12 July 2016 Allyson Lister GBIF Data Sharing Agreement http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf IUPAC/InChI-Trust InChI Licence No. 1.0 is a vendor license which allows all users to make use of the resource, including the source code, for free, as long as its source is properly attributed. It is broadly compatible with the GNU GPL v3 and v2 in that it states in the license that you can change the license from this one to the GNU GPL if you wish. IUPAC/InChI-Trust Licence for the International Chemical Identifier (InChI) Software version 1.04 http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf, accessed 12 July 2016 Allyson Lister IUPAC/InChI-Trust InChI Licence No. 1.0 http://www.labome.com/about/copyright.html The Labome copyright makes the contents of their resource freely available for browsing. Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material. You may not, except with our express written permission, distribute or commercially exploit the content. http://www.labome.com/about/copyright.html, accessed 12 July 2016. Allyson Lister Labome Copyright http://ctdbase.org/about/legal.jsp The CTD Legal Notice and Terms of Data Use specifies under what legal requirements the CTD data may be accessed. Data is available for use for non-commercial purposes as long as the data is properly attributed, but users must get express written consent of CTD to exploit the data for commercial purposes. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Additionally,You must notify CTD and describe your use of their data. For quality control purposes, you must provide CTD with periodic access to your publication of their data. Comparative Toxicogenomics Database Legal Notice and Terms of Use http://ctdbase.org/about/legal.jsp, accessed 12 July 2016 Allyson Lister CTD Legal Notice and Terms of Data Use https://loinc.org/terms-of-use/ LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used. https://loinc.org/terms-of-use/, accessed 12 July 2016 Allyson Lister LOINC RELMA Terms of Use http://miaca.sourceforge.net/copyrightNotice.txt MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English. http://miaca.sourceforge.net/copyrightNotice.txt, accessed 12 July 2016 Allyson Lister MIACA Full Copyright https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. "The above license does not apply to the branding or the "look and feel" of the websites located at the orcid.org URL even if elements thereof are contained in the Software."; 2. "Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under "Policies"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md, accessed 12 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. ORCID MIT-Style License (MIT) https://gds.nih.gov/03policy2.html The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data access mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs). https://gds.nih.gov/PDF/NIH_GDS_Policy.pdf Allyson Lister NIH Genomic Data Sharing Policy https://www.facebase.org/methods/policies/ The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data). https://www.facebase.org/methods/policies/, accessed 12 July 2016 Allyson Lister Facebase Data Access Policy http://orcid.org/content/orcid-terms-use The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses. http://orcid.org/content/orcid-terms-use, accessed 12 July 2016 Allyson Lister ORCID Terms of Use http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi The PPDB Academic Licens specifies under what legal requirements PPDB data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of PPDB to exploit the data for commercial purposes. The resource will be used for teaching or not-for-profit research purposes only. The resource will not be further distributed to others. The recipient agrees to acknowledge the source of the material in any publication reporting its use. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Plant Promoter Database Academic License http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi, accessed 12 July 2016 Allyson Lister PPDB Academic License https://neuinfo.org/page/terms The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear. https://neuinfo.org/page/terms, accessed 12 July 2016. Allyson Lister SciCrunch Terms and Conditions http://prodom.prabi.fr/prodom/current/html/downcom.php The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license. http://prodom.prabi.fr/prodom/current/html/downcom.php, accessed 12 July 2016. ProDom Commercial License http://www.sbgn.org/About The SBGN Open License with Attribution is a very simple statement of openness for the SBGN standard and related resources available on its website. No one—not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else—owns SBGN; it is a free and open community effort that extends beyond any single group, and they view themselves only as organizers and fellow developers. Systems Biology Graphical Notation Open License with Attribution http://www.sbgn.org/About, accessed 12July 2016. Allyson Lister SBGN Open License with Attribution https://www.nlm.nih.gov/copyright.html The NLM Open License with Attribution is a vendor-specific license which is similar to public domain, but which requests attribution. Government information at NLM Web sites is in the public domain. Public domain information may be freely distributed and copied, but it is requested that in any subsequent use the National Library of Medicine (NLM) be given appropriate acknowledgement. When using NLM Web sites, you may encounter documents, illustrations, photographs, or other information resources contributed or licensed by private individuals, companies, or organizations that may be protected by U.S. and foreign copyright laws. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the written permission of the copyright owners. Specific NLM Web sites containing protected information provide additional notification of conditions associated with its use. National Library of Medicine Open License with Attribution https://www.nlm.nih.gov/copyright.html, accessed 12 July 2016. Allyson Lister NLM Open License with Attribution http://regenbase.org/terms-of-use.html The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party. http://regenbase.org/terms-of-use.html, accessed 12 July 2016 Allyson Lister RegenBase Terms of Use http://sabiork.h-its.org/layouts/content/termscondition.gsp The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here. http://sabiork.h-its.org/layouts/content/termscondition.gsp, accessed 13 July 2016 Allyson Lister SABIO-RK Non-Commercial Purpose License http://www.ebi.ac.uk/about/terms-of-use The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page. http://www.ebi.ac.uk/about/terms-of-use, accessed 13 July 2016. Allyson Lister Terms of Use for EMBL-EBI Services http://unitsofmeasure.org/trac/wiki/TermsOfUse The UCUM Terms of Use is a vendor-specific license which allows the resource it references to be used for commercial or non-commercial purposes without restriction of any kind, provided that appropriate attribution is given. However, the resource itself may not be modified in any way. Users may make and distribute an unlimited number of copies of the Licensed Materials. Each copy thereof must include the Copyright Notice and License. The Unified Code for Units of Measure Terms of Use http://unitsofmeasure.org/trac/wiki/TermsOfUse, accessed 13 July 2016 Allyson Lister UCUM Terms of Use https://uts.nlm.nih.gov/license.html The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application. https://uts.nlm.nih.gov/license.html, accessed 13 July 2016. Allyson Lister UMLS Metathesaurus License http://www.mhasweb.org/Data.aspx The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users. http://www.mhasweb.org/Data.aspx, accessed 13 July 2016. Allyson Lister MHAS Data Policy hhttps://alfred.med.yale.edu/alfred/fullcopyrightpage.asp The ALFRED Copyright is a vendor-specific license which states that the resource is freely available to the scientific community for statistical analysis, the only condition being that attribution is required. The ALlele FREquency Database Copyright https://alfred.med.yale.edu/alfred/fullcopyrightpage.asp, accessed 13 July 2016. Allyson Lister ALFRED Copyright Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites. Allyson Lister Allyson Lister Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use. Commercial use only Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee. Allyson Lister Allyson Lister Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category. Fee-Based Commercial License http://www.brenda-enzymes.org/copy.php The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA. http://www.brenda-enzymes.org/copy.php, accessed 13 July 2016. Allyson Lister BRENDA License http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014 The TCGA Data Use Certification is a vendor-specific license which specifies the certification which must be officially agreed to before data may be accessed. There are a number of requirements in this license including attribution, non-transferability, annual progress updates, and a number of security measures. The Cancer Genome Atlas Data Use Certification http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014, accessed 13 July 2016 Allyson Lister TCGA Data Use Certification Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost. Allyson Lister Allyson Lister Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category. Non-Commercial No-Fee License http://www.drugbank.ca/about DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). http://www.drugbank.ca/about, accessed 13 July 2016 Allyson Lister DrugBank Academic License http://genome.cse.ucsc.edu/license/ The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license. http://genome.cse.ucsc.edu/license/gblicense.pdf, accessed 13 July 2016. UCSC Genome Browser Commercial Software License Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource. Allyson Lister Allyson Lister Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use. Permission required for commercial use Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource. Allyson Lister Allyson Lister Permission required for derivative work http://www.xenbase.org/other/static/aboutXenbase.jsp Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase. The contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). http://www.xenbase.org/other/static/aboutXenbase.jsp, accessed 13 July 2016 Allyson Lister Xenbase Academic Conditions of Use http://www.riken.jp/en/terms/ The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission. http://www.riken.jp/en/terms/, accessed 14 July 2016 Allyson Lister RIKEN Copyright https://www.gnu.org/licenses/dsl.html The Design Science License is a license intended to be a general "copyleft" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first "generalized copyleft" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment "over" and no longer recommended its use. https://www.gnu.org/licenses/dsl.html, accessed 13 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 13 July 2016; https://en.wikipedia.org/wiki/Design_science_license, accessed 13 July 2016. Allyson Lister Design Science License http://www.concordia.ca/web/terms.html The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material. http://www.concordia.ca/web/terms.html, accessed 14 July 2016 Allyson Lister University of Concordia Terms of Use All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public "copyleft" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public "copyleft" license. For questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page. Bio-Formats - under the terms of the GNU public "copyleft" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements. The core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; "This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment". See further information about using OME-XML in your work. This website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below. http://www.openmicroscopy.org/site/about/licensing-attribution/licensing, accessed on 23 June 2016. Allyson Lister OME Software Conditons of Use https://aspera-immport.niaid.nih.gov:9443/displayAgreement The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution. https://aspera-immport.niaid.nih.gov:9443/displayAgreement, accessed 14 July 2016 Allyson Lister ImmPort Conditions of Use Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices). Andy Brown Andy Brown Distribution with notices https://opensource.org/licenses/MIT This is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. It is sometimes ambiguously referred to as the MIT License. For substantial programs it is better to use the Apache 2.0 license since it blocks patent treachery. Expat License https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. MIT License The GNU Lesser General Public License (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate LGPL software into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own software-parts. The license requires that only the LGPL software-parts be modifiable by end-users via source code availability. GNU Lesser General Public License http://en.wikipedia.org/wiki/GNU_Lesser_General_Public_License, accessed 27 March 2015. Allyson Lister GNU LGPL https://opensource.org/licenses/Artistic-1.0 The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are &quot;too clever for their own good&quot;, and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl. http://www.gnu.org/licenses/license-list.html, accessed 13 June 2013. Allyson Lister Andy Brown Artistic License 1.0 https://www.eclipse.org/legal/epl-v10.html The Eclipse Public License is similar to the Common Public License. This is a free software license. Unfortunately, its weak copyleft and choice of law clause make it incompatible with the GNU GPL. The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program. Eclipse Public License Version 1.0 https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. EPL v1 https://opensource.org/licenses/BSD-3-Clause The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery. 3 clause BSD License http://www.gnu.org/licenses/license-list.html, accessed June 12, 2013. Allyson Lister Andy Jones Modified BSD Latex Project Public License LPPL OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer. Open Public License Version 1.0 http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. OPL v1.0 Mozilla Public License MPL Development status is an information content entity which indicates the maturity of a software entity within the context of the software life cycle. Allyson Lister Andy Brown Development status Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly. Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. Allyson Lister alpha Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. Allyson Lister beta A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge. http://en.wikipedia.org/wiki/Software_release_life_cycle#Release_candidate, accessed 22 October 2014. Release candidate Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase Production Allyson Lister, Jon Ison, and Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. Allyson Lister Live Sofware is no longer being supplied by the developers/publishers Obsolete An updated version of the software is available. Andy Brown Superseded The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released. James Malone First release The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release. James Malone Latest release Software has developers actively maintaining it (fixing bugs) Andy Brown Maintained matrix manipulation spreadsheet editing document outlining image compression ontology engineering word processing http://www.ebi.ac.uk/swo/organization/SWO_9000056 1.7 AL 24.9.2019: Duplicate of http://www.ebi.ac.uk/swo/organization/SWO_9000056 obsolete software development true simulation and analysis of biochemical networks Manage Laboratory information such is commonly performed by LIMS software. laboratory information management the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware. manage computer operations Text editing is the objective of editing plain text files. text editing Renders a file in such a way that its contents can be understood by users. file rendering annotation editing biological data processing http://edamontology.org/operation_2426 1.7 AL 18.9.2019: Redundant with EDAM 'Modelling and simulation'. obsolete modelling true molecular sequence analysis Andy Brown citation management Allyson Lister sequence alignment Allyson Lister multiple sequence alignment Allyson Lister pairwise sequence alignment An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. James Malone averaging A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone center calculation A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone class discovery A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. PERSON: Elisabetta Manduchi PERSON: James Malone class prediction A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself. PERSON: James Malone PERSON: Melanie Courtot correction A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. PERSON: Elisabetta Manduchi James Malone background correction An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. PERSON: James Malone James Malone error correction cross validation curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. PERSON: Elisabetta Manduchi Elisabetta Manduchi James Malone curve fitting A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone James Malone data normalization A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. PERSON: James Malone James Malone decision tree induction mean calculation A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. James Malone PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation differential expression analysis A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. feature extraction The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product. Andy Brown software publishing process The process of developing software, typically involving the design, implementation and testing of software. Andy Brown AL 24.9.19: Merged the now-obsolete http://www.ebi.ac.uk/swo/objective/SWO_4000007 into this class as they were describing the same concept. See also https://github.com/allysonlister/swo/issues/2 software development oboInOwl:ObsoleteClass Obsolete Class A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output. OntoDM ensemble specification A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification. data mining algorithm Clustering algorithm is a data mining algorithm that solves a clustering task and as a result produces a clustering. clustering algorithm A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T. OntoDM pattern specification Estimating the (Joint) Probability Distribution. A set of data (of type T) is often assumed to be a sample taken from a population according to a probability distribution. A probability distribution/density function assigns a non-negative probability/density to each object of type T. Probably the most general data mining task (Hand et al. 2001) is the task of estimating the (joint) probability distribution D over type T from a set of data items or a sample drawn from that distribution. As mentioned above, in the most typical case we would have T = Tuple(T1, . . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about the joint probability distribution to emphasize the difference to the marginal distributions of each of the variables of type T1, . . ., Tk: the joint distribution captures the interactions among the variables. Representing multi-variate distributions is a non-trivial task. Two approaches are commonly used in data mining. In the density-based clustering paradigm, mixtures of multi-variate Gaussian distributions are typically considered (Hand et al. 2001). Probabilistic graphical models, most notably Bayesian networks, represent graphically the (in)dependencies between the variables: Learning their structure and parameters is an important approach to the problem of estimating the joint probability distribution. probability distribution estimation task the task of pattern discovery is to find all local patterns from a given pattern language that satisfy the required conditions. A prototypical instantiation of this task is the task of finding frequent itemsets (sets of items, such as {bread, butter}), which are often found together in a transaction (e.g., a market basket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to satisfy in this case is to appear in (hold true for) a sufficiently high proportion (called support and denoted by s) of the transactions in the input dataset. With the increasing interest in mining complex data, mining frequent patterns is also considered for structured data. We can thus talk about mining frequent subsequences or mining frequent subgraphs in sequence or graph data. We can consider as frequency the multiple occurrences of a pattern in a single data structure (e.g., sequence or graph) or the single occurrences of a pattern in multiple data structures. pattern discovery task A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization. data mining task Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data. OntoDM clustering specification Predictive modeling algorithm is a data mining algorithm that solves a predictive modeling task and as a result produces a predictive model. predictive modeling algorithm Pattern discovery algorithm is a data mining algorithm that solves a pattern discovery task and as a result produces a set of patterns. pattern discovery algorithm OntoDM A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types. Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To. predictive model specification Learning a (Probabilistic) Predictive Model. In this task, we are given a dataset that consists of examples of the form (d, c), where each d is of type Td and each c is of type Tc. We will refer to d as the description and c as the class or target. To learn a predictive model means to find a mapping from the description to the target, m :: Td → Tc, that fits the data closely. This means that the observed target values and the target values predicted by the model, i.e., c and ˆc = m(d), have to match closely. predictive modeling task probability distribution estimation algorithm Clustering. Clustering in general is concerned with grouping objects into classes of similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object descriptions), the task of clustering is to partition these examples into subsets, called clusters. clustering task A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one. A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm. OntoDM probability distribution specification Examples of such generalization types are: decision trees, desicion rules, neural networks, frequent itemsets, clusters etc. A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output. OntoDM single generalization specification Ensemble algorithms are algorithms that generate an ensemble when executed on a dataset. The ensemble algorithms include a specification of single generalization algorithms which are executed in oreder to produce the single generalizations that compose the ensemble. Examples of ensemble algorithms include bagging, boosting, stacking, random forests, random subspaces,bagging of random subspaces etc. For example, bagging of decision trees algorithm includes the specification of a bagging algorithm and having a decision tree algorithm for generating the base models composing the ensemble. ensemble algorithm single generalization algorithms are data mining algorithms that given a dataset on input produce a generalization at the output. single generalization algorithm owl:Thing example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML Transformation-ML file describing parameter transformations used in a GvHD experiment. Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML ACS d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS XML RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ XML RDF A FOAF file, a SKOS file, an OWL file. RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ RDF zip MagicDraw MDZIP archive, Java JAR file. zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip tar Example.tar file. tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar FCS d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS Compensation-ML compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML Gating-ML foogate.xml, Gating-ML file describing gates used in a GvHD experiment. Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML OWL OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences NanoString Technologies An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies Thermo Fisher Scientific An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G1: Well differentiated G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G2: Moderately differentiated G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G3: Poorly differentiated G4: Undifferentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G4: Undifferentiated G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI NCI BBRB G1 (Fuhrman) G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI NCI BBRB G2 (Fuhrman) G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI NCI BBRB G3 (Fuhrman) G4 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI NCI BBRB G4 (Fuhrman) Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI NCI BBRB Low grade ovarian tumor High grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI NCI BBRB High grade ovarian tumor G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI NCI BBRB G1 (WHO) G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI NCI BBRB G2 (WHO) G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI NCI BBRB G3 (WHO) G4 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI NCI BBRB G4 (WHO) pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT0 (colon) pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pTis (colon) pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT1 (colon) pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT2 (colon) pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT3 (colon) pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4a (colon) pT4b (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4b (colon) pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT0 (lung) pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pTis (lung) pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1 (lung) pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1a (lung) pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1b (lung) pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2 (lung) pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2a (lung) pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2b (lung) pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT3 (lung) pT4 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT4 (lung) pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT0 (kidney) pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1 (kidney) pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1a (kidney) pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1b (kidney) pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2 (kidney) pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2a (kidney) pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2b (kidney) pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3 (kidney) pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3a (kidney) pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3b (kidney) pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3c (kidney) pT4 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT4 (kidney) pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT0 (ovary) pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1 (ovary) pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1a (ovary) pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1b (ovary) pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1c (ovary) pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2 (ovary) pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2a (ovary) pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2b (ovary) pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2c (ovary) pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3 (ovary) pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3a (ovary) pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3b (ovary) pT3c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3c (ovary) pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN0 (colon) pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1 (colon) pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1a (colon) pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1b (colon) pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1c (colon) pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2 (colon) pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2a (colon) pN2b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2b (colon) pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN0 (lung) pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN1 (lung) pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN2 (lung) pN3 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN3 (lung) pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN0 (kidney) pN1 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN1 (kidney) pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN0 (ovary) pN1 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN1 (ovary) cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM0 (colon) cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM1 (colon) cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1a (colon) cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1b (colon) pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1 (colon) pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1a (colon) pM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1b (colon) cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM0 (lung) cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1 (lung) cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1a (lung) cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1b (lung) pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1 (lung) pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1a (lung) pM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1b (lung) cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM0 (kidney) cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM1 (kidney) pM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB pM1 (kidney) cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM0 (ovary) cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM1 (ovary) pM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB pM1 (ovary) Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 NCI BBRB Occult Carcinoma (AJCC 7th) Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage 0 (AJCC 7th) Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage I (AJCC 7th) Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIA (AJCC 7th) Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIB (AJCC 7th) Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIC (AJCC 7th) Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIA (AJCC 7th) Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIB (AJCC 7th) Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIC (AJCC 7th) Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVA (AJCC 7th) Stage IVB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVB (AJCC 7th) Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA (FIGO) Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA1 (FIGO) Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA2 (FIGO) Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB (FIGO) Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB1 (FIGO) Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB2 (FIGO) Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA (FIGO) Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA1 (FIGO) Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA2 (FIGO) Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIB (FIGO) Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIA (FIGO) Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIB (FIGO) Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVA (FIGO) Stage IVB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVB (FIGO) Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1 (FIGO) Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1A (FIGO) Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1B (FIGO) Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1C (FIGO) Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2 (FIGO) Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2A (FIGO) Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2B (FIGO) Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2C (FIGO) Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3 (FIGO) Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3A (FIGO) Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3B (FIGO) Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3C (FIGO) Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 4 (FIGO) Stage Unknown (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage Unknown (FIGO) 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 3: symptomatic in bed more than 50% of the day but not bed ridden 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 2: symptomatic but in bed less than 50% of the day 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 4: bed ridden 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 0: asymptomatic 1: symptomatic but fully ambulatory An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 1: symptomatic but fully ambulatory 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 100: asymptomatic 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 80-90: symptomatic but fully ambulatory 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 60-70: symptomatic but in bed less than 50% of the day 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden Oxford Nanopore Technologies An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies Oxford Nanopore Technologies BioGents An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hr hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter https://github.com/allysonlister/swo/issues/59 AL 5.4.23: We believe this was erroneously created some time ago and therefore are obsoleting it with no recommended alternative individual. OBSOLETE OBI_0000245_1 true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Affymetrix true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Agilent Technologies true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Applied Biosystems true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Applied Precision Life Science true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Bahler Lab true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Bio-Rad Laboratories true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Bio Discovery true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Bioconductor true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Biometric Research Branch true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete COSE true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Clontech Laboratories true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Dana-Farber Cancer Institute and Harvard School of Public Health true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete EMBL true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Fujifilm true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete GE Healthcare Life Sciences true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Genedata true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Genicon Sciences true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Grid grinder true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Havard School of Public Health true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Illumina true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Incyte Genomics true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Institute for Genomics and Bioinformatics Graz University of Technology true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete J. Craig Venter Institute true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete MWG Biotech true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Matforsk true Marked as obsolete by Allyson Lister. 0.3 MathWorks (SWO_0000291 and SWO_9000002), SWO_9000002 was retained, whileSWO_0000291 became an instance of obsolete class. Please use SWO_9000002 instead. obsolete_MathWorks true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Molecular Devices true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Molecular Neuroscience Core true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Molecular Dynamics true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Motorola Life Sciences true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete NIH true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete PerkinElmer true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Raytest true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Research Genetics true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Rosetta Biosoftware true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete SAS Institute Inc. true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Speed Berkeley Research Group true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete obsolete_Stanford University true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete TIBCO Software Inc true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Technological Advances for Genomics and Clinics true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete UC Irvine true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete University Of California true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Walter and Eliza Hall Institute true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Cambridge Bluegnome true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete Strand Life Sciences true Agilent Technologies Applied Biosystems Applied Precision Life Science Genedata Genicon Sciences Grid grinder Havard School of Public Health Illumina Incyte Genomics Institute for Genomics and Bioinformatics Graz University of Technology J. Craig Venter Institute MWG Biotech Matforsk Molecular Devices Motorola Life Sciences NIH PerkinElmer Raytest Research Genetics Rosetta Biosoftware SAS Institute Inc. Speed Berkeley Research Group Marked as obsolete by Allyson Lister. 0.3 Stanford University (SWO_0000431 and SWO_9000003). SWO_9000003 was retained, while SWO_0000431 became an instance of obsolete class. Please use SWO_9000003 instead. obsolete_Stanford University TIBCO Software Inc Technological Advances for Genomics and Clinics, France UC Irvine University Of California, Berkeley Walter and Eliza Hall Institute Cambridge Bluegnome Strand Life Sciences Affymetrix Bahler Lab Bio-Rad Laboratories, Inc. Bio Discovery Bioconductor Biometric Research Branch COSE, France Clontech Laboratories, Inc Dana-Farber Cancer Institute and Harvard School of Public Health European Molecular Biology Laboratory EMBL Fujifilm GE Healthcare Life Sciences Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta Molecular Dynamics FCS Data Standard Version 3.0 Microsoft MathWorks Stanford University Omni PLT Scheme Inc MicroPro International JetBrains Free Software Foundation Adobe Systems Andy Brown An undefined, or ill-defined, group of people. May be used, for example, to denote software development as being done by 'the community', with contributions by many individuals, but no over-arching organisation. The Community University of New Hampshire The National Archives Eclipse Foundation Dropbox Thompson Reuters OMII-UK Apple Inc. The University of Manchester European Bioinformatics Institute EPCC The National Archives, Tessella Spotify Ltd. Mozilla Foundation Altova The GIMP Development Team Canonical Ltd Apache Software Foundation European Patent Office National Cancer Institute Drive5 Conway Institute UCD Dublin Centre for Genomic Regulation (CRG) of Barcelona IBM Allyson Lister AL 8.10.2019: References https://github.com/allysonlister/swo/issues/19 Uppsala Molekylmekaniska HB UC Santa Cruz Computational Biology Group beta alpha Microsoft 98 version Microsoft 2002 version Microsoft 2003 version Microsoft 95 version Microsoft 2007 version Microsoft 2010 version version 3 version 4 Matlab R14 Matlab R12 R2011a Microsoft XP Excel 14 Windows 5.1 3.5.1 Adobe Acrobat 10.1 1 3.0.1 1.6.9 6.02 Helios Service Release 2 6.3.0 2.0.0 Allyson Lister BLAST+ version 2.2.26 Allyson Lister ClustalW version 2.1 Allyson Lister ClustalX version 2.1 Allyson Lister Clustal Omega version 1.1 Allyson Lister MUSCLE version 3.8.31 CRG TCoffee version 9.02.r1228 Python version 2.6 Python version 2.7 4.2.2 7.2.0 Segway version 1.2 Windows 6.0 2023-03-05 .sam Sequence Alignment/Map format Wiggle format .maf has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of has characteristic this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has_role Allyson Lister Andy Brown Duncan Hull Helen Parkinson James Malone Jon Ison Nandini Badarinarayan Robert Stevens The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. https://creativecommons.org/licenses/by/4.0/ Software Ontology The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licensing, provenance and associated data. It contains SWO-specific classes and axioms as well as imports from: 1. BFO 2. IAO 3. OBI 4. EDAM 2023-03-05 The inverse property. 'part of', contains the full official RO definition. has part has_part true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X