en Foundational model of anatomy Information Artefact Ontology NCBI Taxonomy of living organisms Neurological Disease Ontology Ontology for General Medical Science Ontology of Biomedical Investigations Protein Ontology Adam Goldstein Alan Ruttenberg Albert Goldfain Ana Kostovska Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn Ilin Tolovski James A. Overton James Malone Jennifer Fostel Jie Zheng Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Melanie Courtot Michel Dumontier Pance Panov Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki Satya Sahoo Sivaram Arabandi Werner Ceusters William Duncan William Hogan Yongqun (Oliver) He Alan Ruttenberg Albert Goldfain Ana Kostovska Anand Kumar Barry Smith Bill Hogan Cornelius Rosse Daniel Merico Ilin Tolovski Lindsay Cowell Pance Panov Richard Scheuermann Sivaram Arabandi Werner Ceusters 2009-08-07 OWL http://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/ External classes to be imported by the NDDO ontology Ontology for describing data on neurodegenerative diseases in patients Ontology An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any 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. For more information see http://www.obofoundry.org/docs/Citation.html The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to albertgoldfain@gmail.com. Be sure to include a google-account username with your request (this will be the username associated with a gmail address). This ontology is in early development. Expect it to change. This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner 2011-09-20 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term 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 term example 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> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition 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 editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note editor note 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> definition editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note curator note 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 The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type 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 expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg is allocated id range retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg retired from use as of has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime 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 Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type shorthand shortFor sameAs definition definedBy synonym sameAs synonym definition definedBy OntoDT: hasDatatypeRole OntoDT: datatypeRoleOf 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 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 isPartOf isPartOf 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 realizedIn occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl located in at all times https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl has continuant part at all times https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl has occurent part https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl located in at some time https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl part of continuant at some time https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl part of continuant at all times that whole exists The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote obsolete_materially denotes true obsolete_describes true obsolete_represents true relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum is_specified_input_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 Ontology of Biomedical Investigations OBI: objective achieved by bearer of this apple is bearer of this red color this vase is bearer of this fragility 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 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 participates in participatesIn participatesIn 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 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 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 quality 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 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 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 disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary 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 OntoDT: hasIdentifier OntoDT:hasMember OntoDT: hasFieldComponent OntoDT OntoDT: hasAlternativeComponent hasAgent expressedIn extractedFrom hasDatatype hasID hasInformation hasInput hasOutput isOfGender isOutputOf isPreceededBy occuresAt originatesFrom isInPhase measuredFor measuredIn participatesOnSite precedes hasStudyPartner isOfType performedAssessment hasMember assessedOnParticipant has measurement value has x coordinate value has z coordinate value has y coordinate value hasDate hasValue hasDistress hasFrequency hasSeverity hasTotalNPIScore OntoDT OntoDT: datatype role OntoDT OntoDT: string datatype StringDatatype OntoDT OntoDT: primitive datatype OntoDT OntoDT: field component OntoDT OntoDT: alternative component OntoDT: real datatype OntoDT OntoDT: generated datatype OntoDM OntoDT: discrete field component OntoDT OntoDT: defined datatype OntoDT OntoDT: aggregate datatype OntoDT OntoDT: choice datatype OntoDT OntoDT: real field component OntoDT OntoDT: date and time datatype Generic Ontology of Datatypes (OntoDT) OntoDT: datatype OntoDT OntoDT: record of primitives datatype OntoDT OntoDT: discrete datatype OntoDT OntoDT: sequence datatype OntoDT OntoDT: non-aggregate datatype OntoDT: record datatype OntoDT OntoDT: aggregate field component OntoDT OntoDT: field identifier OntoDT OntoDT: primitive field component 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 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:0000005 A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant true BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] 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:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] 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 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 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 (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 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 (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:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) 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:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity 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 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. 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 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] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality 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. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) FMA:242199 Foundational Model of Anatomy (subset) FMA: Cortex of frontal lobe FMA:50801 Foundational Model of Anatomy (subset) FMA: Brain FMA:61824 Foundational Model of Anatomy (subset) FMA: Frontal lobe FMA:62907 Foundational Model of Anatomy (subset) FMA: Substantia nigra pars compacta GAZ:00000448 geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location IAO:0000001 conditional specification a directive information entity that specifies what should happen if the trigger condition is fulfilled PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification 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:0000006 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object 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:0000008 obsolete_artifact true 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 IAO:0000012 obsolete_digital entity A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' person:Chris Stoeckert OBI_0000261 group:OBI obsolete2_digital entity true IAO:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. a report that is published in a journal person:Alan Ruttenberg person:Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000015 information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier IAO:0000017 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number IAO:0000018 obsolete_material_entity true IAO:0000019 binary digital entity MS Word document, ZIP file, DICOM file, JPEG file A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' digital_entity person:Chris Stoeckert OBI_0000244 group:OBI obsolete2_binary digital entity true IAO:0000024 The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_unit of measure true 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. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000058 group:OBI programming language IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is 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 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:0000029 numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral IAO:0000030 information content entity 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 OBI_0000142 information content entity IAO:0000031 integer numeral a numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 IAO:0000032 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum 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 content entity directive information entity IAO:0000034 time trigger revisit? PlanAndPlannedProcess Branch OBI branch derived OBI_0000331 time trigger IAO:0000035 obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." 2009-03-16: work has been done on this term 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. The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter PERSON: Alan Ruttenberg PERSON: Jennifer Fostel PERSON: Melanie Courtot conclusion OBI_0000005 obsolete_study interpretation true 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:0000047 text based digital entity XML file, C++ source code file A text based digital entity is a digital entity that is encoded so that it only contains text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' digital_entity person:Chris Stoeckert OBI_0000132 group:OBI obsolete2_text based digital entity true IAO:0000055 rule example to be added a rule is an executable which guides, defines, restricts actions MSI PRS OBI_0500021 PRS rule IAO:0000057 contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot IAO:0000059 report figure A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister OBI_0000027 group:OBI obsolete2_report figure true 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 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 OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm IAO:0000065 software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter 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:0000079 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term 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. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report IAO:0000091 report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). 2009-03-16: needs some more work (clarify relations). 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. 2009-03-16: work has been done on this term 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. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion Replaced by textual entity and figure There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister PERSON: Melanie Courtot GROUP:OBI OBI_0000001 obsolete_report element true IAO:0000093 binary executable Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel OBI_0000222 group:OBI obsolete2_binary executable true 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:0000097 report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister OBI_0000265 group:OBI obsolete_report table true 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 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. 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg 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 IAO:0000105 digital document A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel OBI_0000195 group:OBI obsolete2_digital document true IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000128 _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. obsolete_identifier true 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 number IAO:0000131 serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number IAO:0000132 lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number IAO:0000140 A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum IAO:0000141 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Need to rework digital entity. Digital quality was suggested by Barry. obsolete_digital quality true IAO:0000144 conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity 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:0000181 Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram IAO:0000182 obsolete_survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm obsolete_survival curve true 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:0000185 A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph IAO:0000186 photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print 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:0000300 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity IAO:0000301 citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. a textual entity intended to identify a particular publication PERSON: Lawrence Hunter citation IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000303 institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification IAO:0000304 caption Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. A textual entity that describes a figure PERSON: Lawrence Hunter caption IAO:0000305 document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title IAO:0000306 table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table IAO:0000307 table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations 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:0000311 publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent IAO:0000314 document part An abstract, introduction, method or results section. an information content entity that is part of a document PERSON: Lawrence Hunter document part IAO:0000315 abstract The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter abstract IAO:0000316 introduction to a publication about an investigation Section labelled 'introduction' of a typical scientific journal article A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter background introduction introduction to a publication about an investigation IAO:0000317 methods section The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter experimental experimental procedures experimental section methods methods section IAO:0000318 results section The section labelled 'results' in a typical scientific journal article A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter results results section IAO:0000319 discussion section of a publication about an investigation A part of a publication about an investigation that is about the study interpretation of the investigation PERSON: Lawrence Hunter discussion discussion section discussion section of a publication about an investigation IAO:0000320 references section The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" A part of a document that has citations as parts PERSON: Lawrence Hunter references section IAO:0000321 author list Lawrence Hunter and Kevin Brettonel Cohen part of a document that enumerates the authors of the document PERSON: Lawrence Hunter author list IAO:0000322 institution list The University of Colorado Denver School of Medicine and the University of Colorado Boulder. part of a document that has parts that are institution identifications associated with the authors of the document PERSON: Lawrence Hunter institution list IAO:0000323 author contributions section LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. A part of a publication that is about the specific contributions of each author PERSON: Lawrence Hunter author contributions contributions by the authors author contributions section IAO:0000324 acknowledgements section The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript Part of a publication that is about the contributions of people or institutions other than the authors. PERSON: Lawrence Hunter acknowledgements acknowledgments acknowledgements section IAO:0000325 footnote The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. PERSON: Lawrence Hunter endnote footnote IAO:0000326 supplementary material to a document part of a document that is segregated from the rest of the document due to its size PERSON: Lawrence Hunter additional information appendix supplemental information supplementary material supporting information supplementary material to a document IAO:0000327 table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents IAO:0000328 table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures IAO:0000329 running title A shorter version of a document title PERSON: Lawrence Hunter running title IAO:0000330 copyright section This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter copyright section 1 IAO:0000400 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 IAO:0000401 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 IAO:0000402 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 IAO:0000403 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum IAO:0000408 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000409 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 IAO:0000414 A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum IAO:0000415 hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity IAO:0000416 A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000422 A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role IAO:0000443 a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article IAO:0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000573 line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph IAO:0000574 A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier IAO:0000575 Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbol PERSON:Alan Ruttenberg associating information with a CRID in the CRID registry associating information with a centrally registered identifier in its registry IAO:0000576 a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. obsolete_establishing a CRID registry true IAO:0000577 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry IAO:0000580 Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier IAO:0000582 time stamped measurement datum IAO:0000584 pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name IAO:0000591 A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software method IAO:0000592 A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module IAO:0000593 A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software library IAO:0000594 A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application IAO:0000595 A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script IAO:0000605 abbreviation textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. A textual entity listing abbreviations and their expansions that are used in a document. PERSON: Bill Baumgartner abbreviation textual entity IAO:0000606 abbreviations section The section labelled 'abbreviations' in a typical scientific journal article. A part of a document where abbreviations and their long-forms used within the document are listed. PERSON: Bill Baumgartner abbreviations abbreviations list abbreviations used list of abbreviations list of abbreviations used abbreviations section IAO:0000607 author information section The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information authors’ information author information section IAO:0000608 author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity IAO:0000609 author summary section The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. PERSON: Bill Baumgartner author summary summary synopsis Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) author summary section IAO:0000610 author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity IAO:0000611 availability section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. PERSON: Bill Baumgartner availability availability section IAO:0000612 availability textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. PERSON: Bill Baumgartner availability textual entity IAO:0000613 case report section The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) A part of a document about the medical history of a specific patient as it relates to the topic of the document. PERSON: Bill Baumgartner case presentation case report case report section IAO:0000614 case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity IAO:0000615 conclusion section The section labelled 'conclusion' in a typical scientific journal article. A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartner concluding remarks conclusion conclusions findings summary conclusion section IAO:0000616 conflict of interest section The section labelled 'conflict of interest statement' in a typical scientific journal article. A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. PERSON: Bill Baumgartner competing interests conflict of interest conflict of interest statement declaration of competing interests disclosure of potential conflicts of interest conflict of interest section IAO:0000617 conflict of interest statement SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. PERSON: Bill Baumgartner conflict of interest textual entity IAO:0000618 consent section The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) A part of a document about the consent process that was used to enroll patients in a study. PERSON: Bill Baumgartner consent consent section IAO:0000619 consent textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. A textual entity that documents the consenting process used to enroll patients in a study. PERSON: Bill Baumgartner consent textual entity IAO:0000620 ethical approval section The section labelled 'ethical approval' in a typical scientific journal article. A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. PERSON: Bill Baumgartner ethical approval ethical approval section IAO:0000621 ethical approval textual entity From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. A textual entity that documents the ethical approval of some study design. PERSON: Bill Baumgartner ethical approval textual entity IAO:0000622 figures section The section labelled 'figures' in a typical scientific journal article. A part of a document that contains one or more figures. PERSON: Bill Baumgartner figures figures section IAO:0000623 funding source declaration section The section labelled 'funding' in a typical scientific journal article. A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. PERSON: Bill Baumgartner funding funding information funding sources funding statement funding/support source of funding sources of funding funding source declaration section IAO:0000624 funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity IAO:0000625 future directions section The section labelled 'future directions' in a typical scientific journal article. A part of a document detailing extensions of the described work that may be implemented at some future point in time. PERSON: Bill Baumgartner future challenges future considerations future developments future directions future outlook future perspectives future plans future prospects future research future research directions future studies future work future directions section IAO:0000626 future directions textual entity Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. PERSON: Bill Baumgartner future directions textual entity IAO:0000627 genome announcement section The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) A document part announcing the publication of a novel draft genome sequence. PERSON: Bill Baumgartner genome announcement genome announcement section IAO:0000628 genome announcement textual entity Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). A textual entity that describes the generation and public release of a novel, draft genome sequence. PERSON: Bill Baumgartner genome announcement textual entity IAO:0000629 keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity IAO:0000630 keywords section The section labelled 'keywords' in a typical scientific journal article. A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. PERSON: Bill Baumgartner keywords keywords section IAO:0000631 study limitations section The section labelled 'limitations' in a typical scientific journal article. A part of a document about biases or short comings related to the study design and execution. PERSON: Bill Baumgartner limitations study limitations Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations section IAO:0000632 study limitations textual entity Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. A textual entity addressing a shortcoming or bias of a study design or execution. PERSON: Bill Baumgartner Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations textual entity IAO:0000633 materials section The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) A part of a document about the materials required to reproduce the content of the document. PERSON: Bill Baumgartner materials materials section IAO:0000634 notes section The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner footnotes notes notes section IAO:0000635 patients section The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) A part of a document about the patients that participated in a study. PERSON: Bill Baumgartner patients section IAO:0000636 patients textual entity Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. A textual entity expressing information regarding the patients used in a study. PERSON: Bill Baumgartner patients textual entity IAO:0000637 pre-publication history section The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. PERSON: Bill Baumgartner notice of republication pre-publication history pre-publication history section IAO:0000638 pre-publication history textual entity From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. PERSON: Bill Baumgartner pre-publication history textual entity IAO:0000639 related work section The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) A part of a document about work in other publications that is relevant to the content of the document. PERSON: Bill Baumgartner related literature related work related work section IAO:0000640 related work textual entity Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. PERSON: Bill Baumgartner related work textual entity IAO:0000641 requirements section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. PERSON: Bill Baumgartner requirements requirements section IAO:0000642 requirements textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None A textual entity that expresses the requirements necessary to use a resource, e.g. software. PERSON: Bill Baumgartner requirements textual entity IAO:0000643 statistical analysis textual entity From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. A textual entity documenting statistical analysis tools and techniques employed. PERSON: Bill Baumgartner statistical analysis textual entity IAO:0000644 statistical analysis section The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) A part of the document used to describe the statistical methodologies employed in the work presented in the document. PERSON: Bill Baumgartner statistical analysis statistical analysis section IAO:0000645 tables section The section labelled 'tables' in a typical scientific journal article. A part of a document that contains one or more tables. PERSON: Bill Baumgartner tables tables section IAO:0000650 database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load database extract, transform, and load process NCBITaxon:9606 NCBI ogranismal classification NCBITaxon: Homo sapiens ND:0000001 neurological disease A disease which has material basis in a neurological disorder and, when realized, the resultant pathological processes affect functioning of the nervous system. MJ: Neurological diseases affect the functioning of the nervous system and are caused by structural, biochemical, or electrical abnormalities in the brain, spinal cord, peripheral nerves, plexus or glia. There are varying etiologies and material bases for neurological diseases, resulting in various patholgies, all somewhat loosely associated by "affecting" the nervous system. As the root node in the ontology (disease branch), this may be best regarded as a primitive. Currently, it is an anatomical location-based definition, which is not maintained in subtypes (functional specializations). Alexander P. Cox Mark Jensen nervous system disease http://www.nlm.nih.gov/medlineplus/neurologicdiseases.html http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12681 neurological disease ND:0000004 Alzheimers disease is a neurological disease where episodic memory loss occurs with at least one other cognitive deficit [visual spatial, attention, orientation, executive function, functional] that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of amyloid plaques and neurofibrillary tangles in the medial temporal lobes. Alexander P. Cox typical Alzheimers disease ND:0000006 An acquired organic mental disorder with loss of intellectual abilities of sufficient severity to interfere with social or occupational functioning. The dysfunction is multifaceted and involves memory, behavior, personality, judgment, attention, spatial relations, language, abstract thought, and other executive functions. The intellectual decline is usually progressive, and initially spares the level of consciousness. Dementia is a neurological disease where at least two cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia. a descriptive term for a collection of symptoms that can be caused by a number of disorders that affect the brain. People with dementia have significantly impaired intellectual functioning that interferes with normal activities and relationships. They also lose their ability to solve problems and maintain emotional control, and they may experience personality changes and behavioral problems, such as agitation, delusions, and hallucinations. While memory loss is a common symptom of dementia, memory loss by itself does not mean that a person has dementia. Neither of these defintion are correct. This is a simple "syntactic" class, and as such needs only a straightforward defintion. The explanatory exposition belongs with the description of the syndrome. Eg- A neurological disease which results in [produces] dementia syndrome. -MJ This is a defined class that is included for the purpose of representing all diseases that result in dementia (the syndrome). Alexander P. Cox dementia disease http://www.ninds.nih.gov/disorders/dementias/dementia.htm Should the logical definition for this class be simply: disease and ('results in' some dementia) instead? Alexander P. Cox http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?field=uid&term=D003704 Check Kinga's slides for all 6 domains of cognitive function! *** UPDATE *** There were 8 domains listed in the slides: Memory Language Perceptual skills Attention Constructive abilities Orientation Problem solving Functional abilities *** CHANGE COGNITIVE DEFICITS IN ALL INSTANCES OF DEMENTIA TO WHATEVER LIST IS USED IN THIS DEFINITION *** Update: I think that all affected definitions have been changed, but this should be rechecked. (Alex Cox) disease resulting in dementia ND:0000011 Dementia associated with Huntingtons disease is Huntingtons disease that results in dementia. Huntington disease (HD) is a devastating disorder that destroys nerve cells (neurons) in parts of the brain. It also lowers levels of chemicals called neurotransmitters that carry signals in the brain. Loss of these cells and neurotransmitters causes uncontrolled movements, loss of mental abilities, and changes in personality, emotional state, or behavior. Mental, emotional, or behavioral decline severe enough to interfere with the ability to carry out everyday activities is known as dementia. Alexander P. Cox http://www.emedicinehealth.com/huntington_disease_dementia/article_em.htm *** DOUBLE-CHECK THIS LABEL *** dementia associated with Huntingtons disease ND:0000068 Alpha-synucleinopathy is a neurological disease ................. that results in the degeneration of populations of nerve cells that develop Lewy bodies and Lewy neurites as a result of filamentous inclusions made of the protein alpha-synuclein. *** NEEDS REVIEW *** [PROPOSED] initially affects the medulla oblongata and progresses to more rostral brain areas in a hierarchical sequence ("Braak hypothesis"). Predominant involvement of the amygdala is also described. Alexander P. Cox alpha-synucleinopathies alpha-synucleinopathy α-synucleinopathies α-synucleinopathy http://www.ncbi.nlm.nih.gov/pubmed/18362284 Besides Parkinson's disease, the filamentous inclusions of two additional neurodegenerative diseases, namely, dementia with Lewy bodies and multiple system atrophy, have also been found to be made of alpha-synuclein. Recombinant alpha-synuclein has been shown to assemble into filaments with similar morphologies to those found in the human diseases and with a cross-beta fiber diffraction pattern. The new work has established the alpha-synucleinopathies as a major class of neurodegenerative disease. From: http://www.ncbi.nlm.nih.gov/pubmed/11193145 def [proposed] is hypothetical alpha synucleinopathy ND:0000113 A neurological disease that is characterized by atrophy or death of neurons or related structures progressively affecting the functioning of the nervous system. Hereditary and sporadic conditions which are characterized by progressive nervous system dysfunction. These disorders are often associated with atrophy of the affected central or peripheral nervous system structures. Alexander P. Cox http://neurolex.org/wiki/Category:Neurodegenerative_disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_2086 neurodegenerative disease ND:0000114 A familial disorder inherited as an autosomal dominant trait and characterized by the onset of progressive CHOREA and DEMENTIA in the fourth or fifth decade of life. Common initial manifestations include paranoia; poor impulse control; DEPRESSION; HALLUCINATIONS; and DELUSIONS. Eventually intellectual impairment; loss of fine motor control; ATHETOSIS; and diffuse chorea involving axial and limb musculature develops, leading to a vegetative state within 10-15 years of disease onset. The juvenile variant has a more fulminant course including SEIZURES; ATAXIA; dementia; and chorea. Huntington's disease is an inherited disease that causes the progressive breakdown (degeneration) of nerve cells in the brain. Huntington's disease has a broad impact on a person's functional abilities and usually results in movement, thinking (cognitive) and psychiatric disorders. Huntington's disease, chorea, or disorder (HD), is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and dementia. It typically becomes noticeable in middle age. HD is the most common genetic cause of abnormal involuntary writhing movements called chorea. It is much more common in people of Western European descent than in those of Asian or African ancestry. The disease is caused by an autosomal dominant mutation on either of an individual's two copies of a gene called Huntingtin, which means any child of an affected parent has a 50% risk of inheriting the disease. In the rare situations where both parents have an affected copy, the risk increases to 75%, and when either parent has two affected copies, the risk is 100% (all children will be affected). Physical symptoms of Huntington's disease can begin at any age from infancy to old age, but usually begin between 35 and 44 years of age. About 6% of cases start before the age of 21 years with an akinetic-rigid syndrome; they progress faster and vary slightly. The variant is classified as juvenile, akinetic-rigid or Westphal variant HD. Symptoms of the disease can vary between individuals and among affected members of the same family, but the symptoms progress predictably for most individuals. The earliest symptoms are a general lack of coordination and an unsteady gait. As the disease advances, uncoordinated, jerky body movements become more apparent, along with a decline in mental abilities and behavioral and psychiatric problems. Physical abilities are gradually impeded until coordinated movement becomes very difficult. Mental abilities generally decline into dementia. Alexander P. Cox http://en.wikipedia.org/wiki/Huntington%27s_disease http://neurolex.org/wiki/Category:Huntingtons_disease http://www.mayoclinic.com/health/huntingtons-disease/DS00401 http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12500 Consider adding a class of diseases named 'polyglutamine disease' and make Huntingtons disease a child of polyglutamine disease. Also add the classes 'dentato-rubral and pallido-luysian atrophy' (DRPLA) and 'spino-cerebellar ataxia' (SCA) and make them children of polyglutamine disease. From the paper, "Protein aggregation and neurodegenerative disease" Huntingtons disease ND:0000115 Alexander P. Cox http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12504 akinetic rgid variant of Huntingtons disease ND:0000116 Alexander P. Cox juvenile-onset Huntingtons disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12505 Are late-onset and juvenile-onset two different diseases or should they be eliminated? juvenile onset Huntingtons disease ND:0000117 Alexander P. Cox late-onset Huntingtons disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12506 Are late-onset and juvenile-onset two different diseases or should they be eliminated? late onset Huntingtons disease ND:0000118 A neurodegenerative disease characterized by dementia, mild parkinsonism, and fluctuations in attention and alertness. The neuropsychiatric manifestations tend to precede the onset of bradykinesia, MUSCLE RIGIDITY, and other extrapyramidal signs. DELUSIONS and visual HALLUCINATIONS are relatively frequent in this condition. Histologic examination reveals LEWY BODIES in the CEREBRAL CORTEX and BRAIN STEM. SENILE PLAQUES and other pathologic features characteristic of ALZHEIMER DISEASE may also be present. Lewy body disease is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia as well as visual hallucinations or fluctuations or REM sleep behavior disorder or Parkonsinism occur caused by neurodegeneration as a result of deposition of Lewy bodies in the cerebral cortex and limbic structures. Alexander P. Cox DLB LBD Lewy body dementia cortical Lewy body disease dementia with Lewy bodies diffuse Lewy body disease senile dementia of Lewy type http://neurolex.org/wiki/Category:Lewy_Body_Disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12502 Lewy body disease ND:0000119 Diseases characterized by a selective degeneration of the motor neurons of the spinal cord, brainstem, or motor cortex. Clinical subtypes are distinguished by the major site of degeneration. In AMYOTROPHIC LATERAL SCLEROSIS there is involvement of upper, lower, and brainstem motor neurons. In progressive muscular atrophy and related syndromes (see MUSCULAR ATROPHY, SPINAL) the motor neurons in the spinal cord are primarily affected. With progressive bulbar palsy ( BULBAR PALSY, PROGRESSIVE), the initial degeneration occurs in the brainstem. In primary lateral sclerosis, the cortical neurons are affected in isolation. The motor neuron diseases (or motor neuron diseases) (MND) are a group of neurological disorders that selectively affect motor neurons, the cells that control voluntary muscle activity including speaking, walking, breathing, swallowing and general movement of the body. Forms of motor neuron disease include: amyotrophic lateral sclerosis (ALS) (sometimes called Lou Gehrig's disease) primary lateral sclerosis (PLS) progressive muscular atrophy (PMA) bulbar pseudobulbar palsy - spastic progressive bulbar palsy - spastic and flaccid Alexander P. Cox http://en.wikipedia.org/wiki/Motor_neurone_disease http://neurolex.org/wiki/Category:Motor_Neuron_Disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12565 motor neuron disease ND:0000120 A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts. Amyotrophic lateral sclerosis (ALS), also referred to as Lou Gehrig's disease, is a form of motor neuron disease caused by the degeneration of neurons located in the ventral horn of the spinal cord and the cortical neurons that provide their afferent input. The condition is often called Lou Gehrig's disease in North America, after the famous New York Yankees baseball player who was diagnosed with the disease in 1939. The disorder is characterized by rapidly progressive weakness, muscle atrophy and fasciculations, spasticity, dysarthria, dysphagia, and respiratory compromise. Sensory function generally is spared, as is autonomic, and oculomotor activity. ALS is a progressive, fatal, neurodegenerative disease with most affected patients dying of respiratory compromise and pneumonia after 2 to 3 years; although some perish within a year from the onset of symptoms, and occasional individuals have a more indolent course and survive for many years. Alexander P. Cox ALS Lou Gehrig's disease Lou Gehrigs disease http://en.wikipedia.org/wiki/Amyotrophic_lateral_sclerosis http://neurolex.org/wiki/Category:Amyotrophic_Lateral_Sclerosis See the following link for information on subtypes/variants of ALS:http://www.alshopefoundation.org/understanding-als/types-of-als.php Also see the following for an alternative terms: http://www.alsa.org/about-als/forms-of-als.html -COX 11/21/13 http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12566 amyotrophic lateral sclerosis ND:0000121 A motor neuron disease marked by progressive weakness of the muscles innervated by cranial nerves of the lower brain stem. Clinical manifestations include dysarthria, dysphagia, facial weakness, tongue weakness, and fasciculations of the tongue and facial muscles. The adult form of the disease is marked initially by bulbar weakness which progresses to involve motor neurons throughout the neuroaxis. Eventually this condition may become indistinguishable from AMYOTROPHIC LATERAL SCLEROSIS. Fazio-Londe syndrome is an inherited form of this illness which occurs in children and young adults. Progressive bulbar palsy (also known simply as PBP) is a medical condition. It belongs to a group of disorders known as motor neuron diseases (Lapiedra 2002). PBP is a disease that attacks the nerves supplying the bulbar muscles. These disorders are characterized by the degeneration of motor neurons in the cerebral cortex, spinal cord, brain stem, and pyramidal tracts. This specifically involves the glossopharyngeal nerve (IX), vagus nerve (X), and hypoglossal nerve (XII) (Hughes 1998). This disorder should not be confused with pseudobulbar palsy or progressive spinal muscular atrophy (Hughes 1998). The term Infantile progressive bulbar palsy is used to describe progressive bulbar palsy in children. Some neurologists consider this disorder to be a subset of amyotrophic lateral sclerosis (ALS), but others disagree with that classification. Alexander P. Cox http://en.wikipedia.org/wiki/Progressive_bulbar_palsy http://neurolex.org/wiki/Category:Progressive_Bulbar_Palsy http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12567 progressive bulbar palsy ND:0000122 A group of recessively inherited diseases that feature progressive muscular atrophy and hypotonia. They are classified as type I (Werdnig-Hoffman disease), type II (intermediate form), and type III (Kugelberg-Welander disease). Type I is fatal in infancy, type II has a late infantile onset and is associated with survival into the second or third decade. Type III has its onset in childhood, and is slowly progressive. Spinal Muscular Atrophy (SMA) is a neuromuscular disease characterized by degeneration of motor neurons, resulting in progressive muscular atrophy (wasting away) and weakness. The clinical spectrum of SMA ranges from early infant death to normal adult life with only mild weakness. These patients often require comprehensive medical care involving multiple disciplines, including pediatric pulmonology, pediatric neurology, pediatric orthopedic surgery, Lower Extremity & Spinal Orthosis, pediatric critical care, and physical medicine and rehabilitation; and physical therapy, occupational therapy, respiratory therapy, and clinical nutrition. Genetic counseling is also helpful for the parents and family members. Sensation and the ability to feel are not affected. Intellectual activity is normal and it is often observed that patients with SMA are unusually bright and sociable. The term "juvenile spinal muscular atrophy" refers to Kugelberg-Welander syndrome. Alexander P. Cox http://en.wikipedia.org/wiki/Spinal_muscular_atrophy http://neurolex.org/wiki/Category:Spinal_Muscular_Atrophy_(SMA) http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12568 spinal muscular atrophy ND:0000129 Multiple system atrophy (MSA) is a degenerative neurological disorder. MSA is associated with the degeneration of nerve cells in specific areas of the brain. This cell degeneration causes problems with movement, balance and other autonomic functions of the body such as bladder control or blood pressure regulation. The cause of MSA is unknown. *** LIST THE SPECIFIC AREAS OF THE BRAIN AFFECTED *** Alexander P. Cox MSA http://en.wikipedia.org/wiki/Multiple_system_atrophy This class already appears in NIF-Dysfunction!!! It is a duplicate of ND_0000022. http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12573 multiple system atrophy ND:0000130 A group of inherited and sporadic disorders which share progressive ataxia in combination with atrophy of the CEREBELLUM; PONS; and inferior olivary nuclei. Additional clinical features may include MUSCLE RIGIDITY; NYSTAGMUS, PATHOLOGIC; RETINAL DEGENERATION; MUSCLE SPASTICITY; DEMENTIA; URINARY INCONTINENCE; and OPHTHALMOPLEGIA. The familial form has an earlier onset (second decade) and may feature spinal cord atrophy. The sporadic form tends to present in the fifth or sixth decade, and is considered a clinical subtype of MULTIPLE SYSTEM ATROPHY. Alexander P. Cox http://neurolex.org/wiki/Category:Olivopontocerebellar_Atrophy http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12574 olivopontocerebellar atrophy ND:0000132 A sporadic neurodegenerative disease with onset in middle-age characterized clinically by Parkinsonian features (e.g., MUSCLE RIGIDITY; HYPOKINESIA; stooped posture) and HYPOTENSION. This condition is considered a clinical variant of MULTIPLE SYSTEM ATROPHY. Pathologic features include a prominent loss of neurons in the zona compacta of the SUBSTANTIA NIGRA and PUTAMEN. Alexander P. Cox http://neurolex.org/wiki/Category:Striatonigral_Degeneration http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12577 striatonigral degeneration ND:0000133 Paraneoplastic syndromes of the nervous system are a group of rare disorders that develop in some people with cancer. Paraneoplastic syndromes of the nervous system occur when cancer-fighting agents of the immune system attack nerve or muscle cells. Cancers commonly associated with these disorders include lung, breast and ovarian cancer. Depending on the location of the cell damage, these syndromes can cause problems with muscle movement or coordination, sensory perception, memory or thinking skills, or sleep. In cases where extensive cell damage has occurred, paraneoplastic syndromes of the nervous system can't be reversed. However, treatment of the underlying cancer and other interventions may prevent further damage, improve symptoms and result in better quality of life. From NIF-Dysfunction: Note that all of teh progeny of this class are in fact neurodegenerative diseases. In holding with the "realist" orientation and the effort to represent the CORE subsumptive hierarchy as a related set of functional or function-structure classes - as opposed to using causal relations to specify nervous system disease - Nervous System Paraneoplastic Syndromes have been made a sub-class of neurodegerative disease as opposed to metastatic nervous system neoplastic disease. Causal relations - such as specify a specific neoplastic condition as the cause for the resulting degeration of nervous system structure and function - will be provided via ObjectProperties. Certain disorders which are in fact Nervous System Paraneoplastic Syndromes - e.g., Lambert-Eaton Myasthenic Syndrome, Transverse Myelitis, Opsoclonus-Myoclonus Syndrome - are left as children of the functional disease categories based on the affected function (BB: 2007-10-06). Alexander P. Cox http://www.mayoclinic.com/health/paraneoplastic-syndromes/DS00840 http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12643 Make sister class of neurodegenerative disease. nervous system paraneoplastic syndrome ND:0000134 Limbic encephalitis is a form of encephalitis. In a small number of cases, the pathogens responsible for encephalitis attack primarily the limbic system (a collection of structures at the base of the brain responsible for emotions and many other basic functions), often causing memory deficits similar to those observed in Alzheimer's disease or Creutzfeldt-Jakob disease (although limbic encephalitis does not cause the same cognitive deficits as these diseases. However, for 20% of people with the diagnosis of limbic encephalitis an MRI will not show any neurological abnormalities. 60% of the time, limbic encephalitis is paraneoplastic in origin. Paraneoplastic limbic encephalitis (PLE) is a particularly severe form of limbic encephalitis caused by neoplasms most commonly associated with small cell lung carcinoma. Whereas the majority of encephalitides are viral in nature, PLE is often associated with cancer. In fact, it is thought that up to 1 in 100 people with cancer have paraneoplastic limbic encephalitis which is commonly misdiagnosed as neurological diseases such as Alzheimer's. Alexander P. Cox http://en.wikipedia.org/wiki/Limbic_encephalitis http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12644 Should this class be labeled 'limbic encephalitis' or 'paraneoplastic limbic encephalitis'? The latter term is more consistent with the labels of its sister classes. limbic encephalitis ND:0000135 Cerebellar degeneration associated with a remote neoplasm. Clinical manifestations include progressive limb and GAIT ATAXIA; DYSARTHRIA; and NYSTAGMUS, PATHOLOGIC. The histologic type of the associated neoplasm is usually carcinoma or lymphoma. Pathologically the cerebellar cortex and subcortical nuclei demonstrate diffuse degenerative changes. Anti-Purkinje cell antibodies (anti-Yo) are found in the serum of approximately 50% of affected individuals. Paraneoplastic cerebellar degeneration is a paraneoplastic phenomenon associated with lung, ovarian, breast, and other cancers. It is believed to be due to an autoimmune reaction targeted against components of the central nervous system (specifically Purkinje cells and large brain stem nuclei). It is thought to be caused by an anti-neuronal antibody known as anti-Yo but in lung paraneoplastic cerebellar degeneration, it is thought to be caused by antibody called "anti-Hu". One of the better characterized paraneoplastic neurologic syndrome is cerebellar ataxia caused by Purkinji cell drop-out in the cerebellum; it is manifested by dysarthria, limb and gait ataxia, and nystagmus. Radiologic imaging reveals cerebellar atrophy. Many antibodies have been associated with this syndrome including anti-Yo, anti-Tr and antibodies to glutamate receptor. A large number of patients with neoplasm-associated cerebellar ataxia who display anti-Yo anti-bodies in the serum typically have a breast or ovarian cancer. Alexander P. Cox http://en.wikipedia.org/wiki/Paraneoplastic_cerebellar_degeneration http://neurolex.org/wiki/Category:Paraneoplastic_Cerebellar_Degeneration http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12645 paraneoplastic cerebellar degeneration ND:0000136 A diffuse or multifocal peripheral neuropathy related to the remote effects of a neoplasm, most often carcinoma or lymphoma. Pathologically, there are inflammatory changes in peripheral nerves. The most common clinical presentation is a symmetric distal mixed sensorimotor polyneuropathy. (Adams et al., Principles of Neurology, 6th ed, p1334) Alexander P. Cox http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12646 It is worth noting that all of the definitions of 'paraneoplastic polyneuropathy' that I was able to find were exact replicas of the definition found in (Adams et al., Principles of Neurology, 6th ed, p1334). paraneoplastic polyneuropathy ND:0000137 Neuronal Ceroid Lipofuscinoses (NCL) is the general name for a family of at least eight genetically separate neurodegenerative disorders that result from excessive accumulation of lipopigments (lipofuscin) in the body's tissues. These lipopigments are made up of fats and proteins. Their name comes from the word stem lipo-, which is a variation on "lipid" or "fat", and from the term pigment, used because the substances take on a greenish-yellow color when viewed under an ultraviolet light microscope. These lipofuscin materials build up in neuronal cells and many organs, including the liver, spleen, myocardium, and kidneys. Alexander P. Cox http://en.wikipedia.org/wiki/Neuronal_ceroid_lipofuscinosis http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12831 There have been at least 9 types of neuronal ceroid lipofuscinosis identified based on the associated gene. These subtypes should be added to the ontology as well. See http://en.wikipedia.org/wiki/Neuronal_ceroid_lipofuscinosis for a list of these subtypes. neuronal ceroid lipofuscinosis ND:0000138 Neuronal intranuclear hyaline inclusion disease (NIHID) is a rare childhood neurodegenerative disease, usually with unremarkable imaging. Epidemiology Typically NIHID presents in childhood (3 - 12 years of age) 2-3 although adult onset has also been described 3. Hereditary cases have been described, and an autosomal recessive pattern of inheritance is suspected 1-2. Clinical presentation The clinical presentation of patients with NIHID can be varied and includes 1-3: pyramidal tract signs extrapyramidal sings including parkinsonism abnormal ocular movements and oculogyric crises generalised cognitive degeneration and behavioural changes peripheral neuropathy severe muscle atrophy and weakness sensory impairment in the distal limbs dysphagia autonomic neuropathy episodic intestinal pseudoobstruction urinary and faecal incontinence cardiomyopathy : reported but uncommon epilepsy : reported but uncommon The diagnosis can be made using peripheral nerve biopsy (e.g. sural nerve)1 or myenteric plexus biopsy (e.g rectal biopsy)2-3. Pathology NIHID is characterised by accumulation of eosinophilic intranuclear inclusions which can be found widely within both the central and peripheral nervous system including sympathetic and myenteric ganglion neurons, dorsal root ganglion neurons, and spinal motor neurons 1-3. It is believed to be due to abnormal proteolysis, although the exact mechanism has as yet not been established 2-3. The intranuclear inclusions fluoresce under ultraviolet light and are composed of uniform, fine straight filaments haphazardly arranged 3. Radiographic features Usually imaging is non-contributory 3 and its primary role is to exclude other entities which may mimic the condition clinically (see below). Severe cerebellar cortical atrophy has been reported, particularly involving the vermis 3. Treatment and prognosis Neuronal intranuclear hyaline inclusion disease (NIHID) is slowly progressive and has no proven therapy. Death usually occurs before the age of 30 years 3. Differential diagnosis Clinically the differential diagnosis includes 3: juvenile parkinsonism spinocerebellar degneration GM2 gangliosidosis infantile neuroaxonal dystrophy Alexander P. Cox http://radiopaedia.org/articles/neuronal-intranuclear-hyaline-inclusion-disease http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#nlx_dys_100201 Very little information about neuronal intranuclear hyaline inclusion disease is readily available online. neuronal intranuclear hyaline inclusion disease ND:0000139 Parkinsons disease is a neurological disease where abnormal movement [tremor, rigidity, bradykinesia, postural instability] occurs resulting in a movement disorder caused by neurodegeneration as a result of death of dopaminergic cells in the substantia nigra. ---------- Parkinsons disease is a degenerative disorder of the central nervous system. It results from the death of dopamine-generating cells in the substantia nigra, a region of the midbrain; the cause of cell-death is unknown. Early in the course of the disease, the most obvious symptoms are movement-related, including shaking, rigidity, slowness of movement and difficulty with walking and gait. Later, cognitive and behavioural problems may arise, with dementia commonly occurring in the advanced stages of the disease. Other symptoms include sensory, sleep and emotional problems. PD is more common in the elderly with most cases occurring after the age of 50. The main motor symptoms are collectively called parkinsonism, or a "parkinsonian syndrome". Parkinson's disease is often defined as a parkinsonian syndrome that is idiopathic (having no known cause), although some atypical cases have a genetic origin. Many risk and protective factors have been investigated: the clearest evidence is for an increased risk of PD in people exposed to certain pesticides and a reduced risk in tobacco smokers. The pathology of the disease is characterized by the accumulation of a protein called alpha-synuclein into inclusions called Lewy bodies in neurons, and from insufficient formation and activity of dopamine produced in certain neurons within parts of the midbrain. Diagnosis of typical cases is mainly based on symptoms, with tests such as neuroimaging being used for confirmation. Modern treatments are effective at managing the early motor symptoms of the disease, mainly through the use of levodopa and dopamine agonists. As the disease progresses and dopamine neurons continue to be lost, a point eventually arrives at which these drugs become ineffective at treating the symptoms and at the same time produce a complication called dyskinesia, marked by involuntary writhing movements. Diet and some forms of rehabilitation have shown some effectiveness at alleviating symptoms. Surgery and deep brain stimulation have been used to reduce motor symptoms as a last resort in severe cases where drugs are ineffective. Research directions include a search of new animal models of the disease and investigations of the potential usefulness of gene therapy, stem cell transplants and neuroprotective agents. Medications to treat non-movement-related symptoms of PD, such as sleep disturbances and emotional problems, also exist. The disease is named after the English doctor James Parkinson, who published the first detailed description in An Essay on the Shaking Palsy in 1817. belongs to a group of conditions called motor system disorders, which are the result of the loss of dopamine-producing brain cells. The four primary symptoms of PD are tremor, or trembling in hands, arms, legs, jaw, and face; rigidity, or stiffness of the limbs and trunk; bradykinesia, or slowness of movement; and postural instability, or impaired balance and coordination. (A disease characterized as a progressive motor disability manifested by tremors, shaking, muscular rigidity, and lack of postural reflexes. (PSY) * A progressive, degenerative neurologic disease characterized by a TREMOR that is maximal at rest, retropulsion (i.e. a tendency to fall backwards), rigidity, stooped posture, slowness of voluntary movements, and a masklike facial expression. Pathologic features include loss of melanin containing neurons in the substantia nigra and other pigmented nuclei of the brainstem. LEWY BODIES are present in the substantia nigra and locus coeruleus but may also be found in a related condition (LEWY BODY DISEASE, DIFFUSE) characterized by dementia in combination with varying degrees of parkinsonism. (Adams et al., Principles of Neurology, 6th ed, p1059, pp1067-75) (MSH) * progressive, degenerative disorder of the nervous system characterized by tremors, rigidity, bradykinesia, postural instability, and gait abnormalities; caused by a loss of neurons and a decrease of dopamine in the basal ganglia. (CSP) ) Alexander P. Cox PD Parkinson disease Parkinson's Parkinson's disease Parkinsons idiopathic parkinsonism paralysis agitans primary parkinsonism http://en.wikipedia.org/wiki/Parkinson%27s_disease http://www.ninds.nih.gov/disorders/parkinsons_disease/parkinsons_disease.htm http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_2098 Parkinson's disease is the second most common neurodegenerative disease, after Alzheimer's disease. Neuropathologically, it is characterized by the degeneration of populations of nerve cells that develop filamentous inclusions in the form of Lewy bodies and Lewy neurites. Recent work has shown that the filamentous inclusions of Parkinson's disease are made of the protein alpha-synuclein and that rare, familial forms of Parkinson's disease are caused by missense mutations in the alpha-synuclein gene. From: http://www.ncbi.nlm.nih.gov/pubmed/11193145 Should we include 'idiopathic Parkinsons disease' (IPD) as a sub class or super class of Parkinsons disease? The main pathological characteristic of PD is cell death in the substantia nigra and more specifically the ventral part of the pars compacta, affecting up to 70% of the cells by the time the patient dies. The mechanisms by which the brain cells are lost are varied. One mechanism consists of an abnormal accumulation of the protein alpha-synuclein bound to ubiquitin in the damaged cells. This protein accumulation forms inclusions called Lewy bodies. According to the Braak staging Lewy bodies first appear in the olfactory bulb, medulla oblongata and pontine tegmentum, individuals at this stage being asymptomatic. As the disease evolves, Lewy bodies later attain the substantia nigra, areas of the midbrain and basal forebrain, and finally reach areas of the neocortex. From: http://en.wikipedia.org/wiki/Braak_staging Parkinsons disease ND:0000140 a clinical syndrome associated with shrinking of the frontal and temporal anterior lobes of the brain. Originally known as Pick’s disease, the name and classification of FTD has been a topic of discussion for over a century. The current designation of the syndrome groups together Pick’s disease, primary progressive aphasia, and semantic dementia as FTD. Some doctors propose adding corticobasal degeneration and progressive supranuclear palsy to FTD and calling the group Pick Complex. These designations will continue to be debated. As it is defined today, the symptoms of FTD fall into two clinical patterns that involve either (1) changes in behavior, or (2) problems with language. Pick's disease, is a rare neurodegenerative disease that causes progressive destruction of nerve cells in the brain. Symptoms include loss of speech (aphasia), and dementia. While some of the symptoms can initially be alleviated, the disease progresses and patients often die within two to ten years. A defining characteristic of the disease is build up of tau proteins in neurons, accumulating into silver-staining, spherical aggregations known as "Pick bodies". While the term Pick's disease was once used to represent a class of clinical syndromes with symptoms attributable to frontal and temporal lobe dysfunction, it is now used among professionals to mean a specific pathology that is just one of the causes of frontotemporal lobar degeneration. Some people still use the term Pick's disease to mean the more general clinical syndrome of frontotemporal lobar degeneration, but this has previously led to confusion among both professionals and patients and so its use should be restricted to the specific pathological subtype described below. It is also known as Pick disease and PiD (not to be confused with Pelvic Inflammatory Disease (PID) or Parkinson's Disease (PD)). Alexander P. Cox http://en.wikipedia.org/wiki/Pick%27s_disease http://www.ninds.nih.gov/disorders/picks/picks.htm http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#nlx_dys_090801 NIF-Dysfunction does not provide a definition for Picks disease. *** TO DO *** Picks disease should be made a subclass of frontotemporal dementia. Picks disease ND:0000151 Neurodegenerative disorders involving deposition of abnormal tau protein isoforms ( TAU PROTEINS) in neurons and glial cells in the brain. Pathological aggregations of tau proteins are associated with mutation of the tau gene on chromosome 17 in patients with ALZHEIMER DISEASE; DEMENTIA; PARKINSONIAN DISORDERS; progressive supranuclear palsy ( SUPRANUCLEAR PALSY, PROGRESSIVE); and corticobasal degeneration (MeSH). Tauopathies are a class of neurodegenerative diseases resulting from the pathological aggregation of tau protein in the human brain. The best known of these illnesses is Alzheimer's disease (AD), where tau protein is deposited within neurons in the form of neurofibrillary tangles (NFTs). They were first described by the eponymous Alois Alzheimer in one of his patients suffering from the disorder. Tangles are formed by hyperphosphorylation of a microtubule-associated protein known as tau, causing it to aggregate in an insoluble form. (These aggregations of hyperphosphorylated tau protein are also referred to as PHF, or "paired helical filaments"). The precise mechanism of tangle formation is not completely understood, and it is still controversial whether tangles are a primary causative factor in the disease or play a more peripheral role. AD is also classified as an amyloidosis because of the presence of senile plaques. The degree of NFT involvement in AD is defined by Braak stages. Braak stages I and II are used when NFT involvement is confined mainly to the transentorhinal region of the brain, stages III and IV when there's also involvement of limbic regions such as the hippocampus, and V and VI when there's extensive neocortical involvement. This should not be confused with the degree of senile plaque involvement, which progresses differently. Other conditions in which neurofibrillary tangles are commonly observed include: Progressive supranuclear palsy although with straight filament rather than PHF tau Dementia pugilistica (chronic traumatic encephalopathy) Frontotemporal dementia and parkinsonism linked to chromosome 17 however without detectable β-amyloid plaques. Lytico-Bodig disease (Parkinson-dementia complex of Guam) Tangle-predominant dementia, with NFTs similar to AD, but without plaques. Tends to appear in the very old. Ganglioglioma and gangliocytoma Meningioangiomatosis Subacute sclerosing panencephalitis As well as lead encephalopathy, tuberous sclerosis, Hallervorden-Spatz disease, and lipofuscinosis In Pick's disease and corticobasal degeneration tau proteins are deposited in the form of inclusion bodies within swollen or "ballooned" neurons. Argyrophilic grain disease (AGD), another type of dementia, is marked by the presence of abundant argyrophilic grains and coiled bodies on microscopic examination of brain tissue. Some consider it to be a type of Alzheimer disease. It may co-exist with other tauopathies such as progressive supranuclear palsy and corticobasal degeneration. Some other tauopathies include: Frontotemporal dementia Frontotemporal lobar degeneration The non-Alzheimer's tauopathies are sometimes grouped together as "Pick's complex". Alexander P. Cox http://en.wikipedia.org/wiki/Tauopathy http://neurolex.org/wiki/Category:Tauopathy http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12696 There have been many more subtypes of tauopathy than the two that are included in NIF-Dysfunction. These additional tauopathies should probably be added to ND. tauopathy ND:0000152 An amyloidopathy where cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of amyloid plaques and neurofibrillary tangles in the medial temporal lobes. Alexander P. Cox AD Alzheimer disease Alzheimer's Alzheimer's disease Alzheimers old-timers' disease primary degenerative dementia of the Alzheimers type senile dementia of the Alzheimers type http://www.ninds.nih.gov/disorders/alzheimersdisease/alzheimersdisease.htm http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_2092 an age-related, non-reversible brain disorder that develops over a period of years. Initially, people experience memory loss and confusion, which may be mistaken for the kinds of memory changes that are sometimes associated with normal aging. However, the symptoms of AD gradually lead to behavior and personality changes, a decline in cognitive abilities such as decision-making and language skills, and problems recognizing family and friends. AD ultimately leads to a severe loss of mental function. Alzheimers disease ND:0000153 Semantic dementia (SD) is a progressive neurodegenerative disorder characterized by loss of semantic memory in both the verbal and non-verbal domains. The most common presenting symptoms are in the verbal domain however (with loss of word meaning) and it is therefore often characterized (incorrectly) as a primary language disorder (a so-called progressive fluent aphasia). SD patients sometimes show symptoms of surface dyslexia, a relatively selective impairment in reading low-frequency words with exceptional or atypical spelling-to-sound correspondences. SD is one of the three canonical clinical syndromes associated with frontotemporal lobar degeneration. SD is a clinically-defined syndrome, but is associated with predominantly temporal lobe atrophy (left greater than right) and hence is sometimes called temporal variant FTLD (tvFTLD). The majority of patients with SD will have ubiquitin-positive, TDP-43 positive, tau-negative inclusions, although other pathologies have been described more infrequently, namely tau-positive Pick's disease and Alzheimer's pathology. aphasia characterized by the loss of recognition of the meaning of words and phrases. Alexander P. Cox SD http://en.wikipedia.org/wiki/Semantic_dementia http://www.merriam-webster.com/medical/semantic%20aphasia *** TO DO *** Revise definition. Confirm that this is a disease and not just a syndrome. semantic aphasia ND:0000157 Primary progressive aphasia (PPA) is a type of dementia characterized most prominently by an insidious and progressive disorder of language and speech abilities. Alexander P. Cox PPA http://en.wikipedia.org/wiki/Primary_progressive_aphasia *** TO DO *** Revise definition. Also see: http://www.brain.northwestern.edu/ppa/ Confirm that this is a disease and not just a syndrome. Synonym(s): Pick's Disease, Primary Progressive Aphasia, Semantic Dementia, Dementia - Semantic consider merging terms source for it:http://www.ninds.nih.gov/disorders/picks/picks.htm primary progressive aphasia ND:0000159 Neurodegenerative dementia is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration. I believe this class is unecessary, it overlaps with 'disease resulting in dementia'. -MJ Alexander P. Cox neurodegenerative dementia TO DO neurodegenerative disease resulting in dementia ND:0000160 ALS with Dementia Frontotemporal dementia with motor neuron disease is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, exceutive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of tau in the frontal and temporal cortices and where abnormal movement [tremor, rigidity, bradykinesia, postural instability] also occurs resulting in a movement disorder caused by neurodegeneration as a result of ________. *** DOUBLE-CHECK THE MOVEMENT DISORDER, ITS CAUSE, AND ITS SYMPTOMS *** Alexander P. Cox FTD-MND Nakano, Imaharu. "frontotemporal dementia with motor neuron disease ." Neuropathology 1.1 (2000): 68-75. Print. Should be inferred to be a subtype of motor neuron disease. frontotemporal dementia with motor neuron disease ND:0000161 Atypical Alzheimers disease is a type of Alzheimers disease where episodic memory loss is not present but other cognitive deficits [visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of amyloid plaques and neurofibrillary tangles in the medial temporal lobes. Alexander P. Cox atypical Alzheimers disease ND:0000166 Genetic frontotemporal dementia is frontotemporal dementia that is caused by one or more genetic defects. Alexander P. Cox genetic FTD genetic frontotemporal dementia ND:0000167 Frontotemporal dementia is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of tau in the frontal and temporal cortices. Alexander P. Cox FTD frontotemporal dementia ND:0000168 Parkinsons dementia is a neurological disease where abnormal movement [tremor, rigidity, bradykinesia, postural instability] occurs resulting in a movement disorder caused by neurodegeneration as a result of death of dopaminergic cells in the substantia nigra, which is followed by cognitive deficits [memory, visual spatial, attention, orientation, exceutive function, functional] that represent a decline from previous levels of functioning resulting in dementia years after the diagnosis of Parkinsons disease caused by neurodegeneration as a result of deposition of Lewy bodies in the cerebral cortex and limic structures. Alexander P. Cox PD-D PDD Parkinson disease dementia Parkinson's dementia Parkinson's disease dementia Parkinsons dementia Parkinsons disease dementia Parkinson dementia ND:0000169 A rare neurological disease in which several regions of the brain deteriorate. The cortex is severely affected, especially the fronto-parietal regions, located near the center-top of the head. Other, deeper brain regions are also affected, including parts of the basal ganglia, hence the name "corticobasal" degeneration. The combined loss of brain tissue in all these areas causes the symptoms and findings seen in people with CBD. Corticobasal degeneration is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, exceutive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia associated with other asymmetrical cortical signs [apraxia, cortical sensory, dysphasia, speech apraxia] and where abnormal movement [akinetic rigid syndrome, hyperkinetic movement disorder, alien limb] occurs resulting in a movement disorder caused by neurodegeneration in the anterior frontal lobe, basal ganglia, and premotor area of the cerebral cortex associated with astroglial inclusions due to a tauopathy. Alexander P. Cox CBD CBGD corticobasal ganglionic degeneration http://neurolex.org/wiki/Category:Corticobasal_Degeneration *** TO DO *** Should corticobasal degeneration be made a subtype of tauopathy??? corticobasal degeneration ND:0000170 Frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17) is an autosomal dominant neurodegenerative disorder, which has three cardinal features: behavioral and personality changes, cognitive impairment, and motor symptoms. It is caused by mutations in the MAPT gene, which encodes a microtubule-associated protein tau. Over 100 families with 38 different mutations in the MAPT gene have been identified worldwide. The phenotype of FTDP-17 varies not only between families carrying different mutations but also between and within families carrying the same mutations. The pathogenetic mechanisms underlying the disorder are thought to be related to the altered proportion of tau isoforms or to the ability of tau to bind microtubules and to promote microtubule assembly. Alexander P. Cox FTDP-17 frontotemporal dementia and Parkinsonism linked to chromosome 17 http://en.wikipedia.org/wiki/Frontotemporal_dementia_and_parkinsonism_linked_to_chromosome_17 caused by MAPT mutations frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0000171 FTDU-17 caused by caused by progranulin mutations is frontotemporal dementia that is caused by progranulin mutations on chromosome 17. Alexander P. Cox FTDU-17 caused by caused by progranulin mutations ND:0000172 A degenerative disease of the central nervous system characterized by balance difficulties; OCULAR MOTILITY DISORDERS (supranuclear ophthalmoplegia); DYSARTHRIA; swallowing difficulties; and axial DYSTONIA. Onset is usually in the fifth decade and disease progression occurs over several years. Pathologic findings include neurofibrillary degeneration and neuronal loss in the dorsal MESENCEPHALON; SUBTHALAMIC NUCLEUS; RED NUCLEUS; pallidum; dentate nucleus; and vestibular nuclei. Progressive supranuclear palsy is a degenerative tauopathic disease involving the gradual deterioration and death of specific areas of the brain. The affected brain cells are both neurons and glial cells. The neurons display neurofibrillary tangles, which are clumps of tau protein, a normal part of a brain cell's internal structural skeleton. These tangles are often different from those seen in Alzheimer's disease, but may be structurally similar when they occur in the cerebral cortex. Their chemical composition is usually different, however, and is similar to that of tangles seen in corticobasal degeneration. Lewy bodies are seen in some cases, but it is not clear whether this is a variant or an independent co-existing process. The principal areas of the brain affected are: the basal ganglia, particularly the subthalamic nucleus, substantia nigra and globus pallidus; the brainstem, particularly the portion of the midbrain where "supranuclear" eye movement resides; the cerebral cortex, particularly that of the frontal lobes; the dentate nucleus of the cerebellum; and the spinal cord, particularly the area where some control of the bladder and bowel resides. The initial symptoms in two-thirds of cases are loss of balance, lunging forward when mobilizing, fast walking, bumping into objects or people, and falls. Other common early symptoms are changes in personality, general slowing of movement, and visual symptoms. Later symptoms and signs are dementia (typically including loss of inhibition and ability to organize information), slurring of speech, difficulty swallowing, and difficulty moving the eyes, particularly in the vertical direction. The latter accounts for some of the falls experienced by these patients as they are unable to look up or down. Some of the other signs are poor eyelid function, contracture of the facial muscles, a backward tilt of the head with stiffening of the neck muscles, sleep disruption, urinary incontinence and constipation. Alexander P. Cox PSP Steele-Richardson-Olszewski syndrome http://en.wikipedia.org/wiki/Progressive_supranuclear_palsy http://neurolex.org/wiki/Category:Progressive_Supranuclear_Palsy http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#birnlex_12697 PSP cases are often split into two subgroups, PSP-Richardson, the classic type, and PSP-Parkinsonism, where a short-term response to levodopa can be obtained. progressive supranuclear palsy ND:0000174 Dementia associated with Parkinsonism is a neurological disease where cognitive deficits [memory, visual spatial, attention, orientation, executive function, functional] occur that represent a decline from previous levels of functioning resulting in dementia along with motor deficits resulting in Parkinsonism caused by neurodegeneration in the brain and/or spinal cord. Alexander P. Cox dementia associated with Parkinsonism disease resulting in dementia associated with Parkinsonism ND:0000175 Normal pressure hydrocephalus occurs when there is an increase in intracranial pressure (ICP) due to an abnormal accumulation of cerebrospinal fluid (CSF) in the ventricles of the brain, which can cause ventriculomegaly. The ICP gradually falls but still maintains a slightly elevated level and the CSF pressure reaches a high normal level of 150 to 200 mmH2O. Measurements of CSF, therefore, are not usually elevated. Because of this equilibration, patients do not exhibit the classic signs that accompany increased intracranial pressure such as headache, nausea, vomiting, or altered consciousness. (Though some studies have shown pressure elevations to occur only intermittently). However, the enlarged ventricles put increased pressure on the adjacent cortical tissue and cause myriad effects in the patient. Although the exact mechanism is unknown, normal-pressure hydrocephalus is thought to be a form of communicating hydrocephalus with impaired CSF reabsorption at the arachnoid granulations. There are 2 types of normal pressure hydrocephalus: idiopathic and secondary. The term idiopathic means that it has no known cause. The secondary type of NPH can be due to a subarachnoid haemorrhage, head trauma, tumour, CNS infection, or a complication of cranial surgery. NPH may exhibit a classic triad of clinical findings (known as the Adams triad or Hakim's triad) of urinary incontinence, gait disturbance, and dementia (commonly referred to as "wet, wobbly and wacky" or "weird walking water"). Alexander P. Cox NPH symptomatic hydrocephalus http://en.wikipedia.org/wiki/Normal_pressure_hydrocephalus normal pressure hydrocephalus ND:0000176 Genetic Alzheimers disease is a neurological disease where episodic memory loss occurs with at least one other cognitive deficit [visual spatial, attention, orientation, executive function, functional] that represent a decline from previous levels of functioning resulting in dementia caused by neurodegeneration as a result of deposition of amyloid plaques and neurofibrillary tangles in the medial temporal lobes due to a genetic defect. *** ALTERNATE DEFINITION *** Genetic Alzheimers disease is Alzheimers disease in which the deposition of amyloid plaques and neurofibrillary tangles in the medial temporal lobes is due to a[n identified???] genetic defect. Alexander P. Cox genetic Alzheimers disease ND:0000184 Neoplastic neurological disease is a neurological disease caused by neoplasticism. Alexander P. Cox neoplastic neurological disease ND:0000185 Paraneoplastic neurological disease is a neurological disease caused by paraneoplasticism. Alexander P. Cox paraneoplastic neurological disease ND:0000186 Amyloidopathy is a neurological disease that results in the degeneration of populations of nerve cells due to the formation of extracellular amyloid plaques. *** NEEDS REVIEW *** Alexander P. Cox Is this term unique to neurological diseases? According to the following wikipedia entry, amyloidosis can occur in other organs such as the heart. Does this pose a problem for our classification schema? http://en.wikipedia.org/wiki/Amyloidosis "In medicine, amyloidosis refers to a variety of conditions wherein amyloid proteins are abnormally deposited in organs or tissues and cause harm. A protein is described as being amyloid if, due to an alteration in its secondary structure, it takes on a particular aggregated insoluble form, similar to the beta-pleated sheet. Symptoms vary widely depending upon where in the body amyloid deposits accumulate. Amyloidosis may be inherited or acquired." UPDATE [01/14/2014]: Discussions about this issue have led to the proposal that 'amyloidopathy' be retained as a neurological disease specific term while 'amyloidosis' (which amyloidopathy is a subclass of) should be used as a general term for diseases that involve abnormal deposition of amyloid in any region of the body. A compelling reason for this decision is that the term 'amyloid' is historically applied loosely in the medical literature. For example, at least 24 proteins have been identified as constituents in amyloids and, in most cases, amyloid is not the primary protein constituent. amyloidopathy ND:0000187 Early personality change is the most common feature which can include less concern for others, an unkempt appearance, disinhibition, inappropriate emotional responses and restlessness which later can be accompanied by aggression. Apathy can also occur as the disease progresses. Hyperorality is also common, encompassing mouthing of non-food objects, over-eating of sweet foods and chain smoking. A progressive aphasia develops during the course of the disease, although normally not with features of PNFA or SD. It is characterised by reduced spontaneous speech with relative preservation of reading and repetition, most consistent with a dynamic aphasia. An overt motor syndrome develops late in the disease course which can include parkinsonian features, dystonia, pyramidal signs and myoclonus, ultimately leaving the patients bedridden. None of the patients have had any clinical signs of either upper or lower motor neuron impairment, and no neurophysiological EMG studies have been done so far in the Danish FTD-3 patients. A new branch of the FTD-3 family was recently identified and clinical descriptions of a further two cases were similar to those previously reported [21]. The average age of onset for FTD-3 is 58 years of age and the mean duration is 10 years. Ongoing neuropsychological studies indicate that some of the patients can have impaired memory function in the earlier phases of the disease, but this is not a prominent feature and most often not a subjective complaint by the patients. FTD caused by CHMP2B mutations is frontotemporal dementia that is caused by CHMP2B mutations. Alexander P. Cox http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182073/?tool=pubmed FTD caused by CHMP2B mutations ND:0000188 A heterogeneous group of sporadic or familial disorders characterized by AMYLOID deposits in the walls of small and medium sized blood vessels of CEREBRAL CORTEX and MENINGES. Clinical features include multiple, small lobar CEREBRAL HEMORRHAGE; cerebral ischemia ( BRAIN ISCHEMIA); and CEREBRAL INFARCTION. Cerebral amyloid angiopathy is unrelated to generalizedAMYLOIDOSIS. Amyloidogenic peptides in this condition are nearly always the same ones found in ALZHEIMER DISEASE. Cerebral amyloid angiopathy (CAA), also known as congophilic angiopathy, is a form of angiopathy in which amyloid deposits form in the walls of the blood vessels of the central nervous system. The amyloid material is only found in the brain and as such the disease is not related to other forms of amyloidosis. Alexander P. Cox CAA amyloid angiopathy congophilic angiopathy Kumar: Robbins and Cotran: Pathologic Basis of Disease, 7th ed., 2005 http://en.wikipedia.org/wiki/Cerebral_amyloid_angiopathy cerebral amyloid angiopathy ND:0001000 *** REVISE *** A diagnosis of cognitive impairments beyond those expected based on the age and education of the individual, but which are not significant enough to interfere with their daily activities. Alexander P. Cox Adapted from: http://en.wikipedia.org/wiki/Mild_cognitive_impairment diagnosis of mild cognitive impairment ND:0001001 A diagnosis that a patient has dementia. Alexander P. Cox diagnosis of dementia ND:0001004 A diagnosis of dementia in a patient that is hypothesized to be the result of a neurodegenerative process (disorder???, disease???). Alexander P. Cox creation date: 2011-09-01 diagnosis of neurodegenerative dementia ND:0001015 A diagnosis that a patient possibly has frontotemporal dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible frontotemporal dementia ND:0001016 A diagnosis that a patient probably has frontotemporal dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable frontotemporal dementia ND:0001017 A diagnosis that a patient definitely has frontotemporal dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite frontotemporal dementia ND:0001018 A diagnosis that a patient possibly has dementia with Lewy bodies. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible dementia with Lewy bodies ND:0001019 A diagnosis that a patient probably has dementia with Lewy bodies. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable dementia with Lewy bodies ND:0001020 A diagnosis that a patient definitely has dementia with Lewy bodies. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite dementia with Lewy bodies ND:0001021 A diagnosis that a patient possibly has Parkinson dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible Parkinson dementia ND:0001023 A diagnosis that a patient possibly has frontotemporal dementia with Parkinsonism linked to chromosome 17. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001026 A diagnosis that a patient probably has Parkinson dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable Parkinson dementia ND:0001028 A diagnosis that a patient probably has frontotemporal dementia with Parkinsonism linked to chromosome 17. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001031 A diagnosis that a patient definitely has Parkinson dementia. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite Parkinson dementia ND:0001033 A diagnosis that a patient definitely has frontotemporal dementia with Parkinsonism linked to chromosome 17. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001036 A diagnosis that a patient possibly has Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible Alzheimers disease ND:0001037 A diagnosis that a patient possibly has atypical Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible atypical Alzheimers disease ND:0001038 A diagnosis that a patient probably has Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable Alzheimers disease ND:0001039 A diagnosis that a patient possibly has frontal variant of Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of possible frontal variant of Alzheimers disease ND:0001043 A diagnosis that a patient probably has atypical Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable atypical Alzheimers disease ND:0001044 A diagnosis that a patient probably has frontal variant of Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of probable frontal variant of Alzheimers disease ND:0001048 A diagnosis that a patient definitely has Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite Alzheimers disease ND:0001049 A diagnosis that a patient definitely has atypical Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite atypical Alzheimers disease ND:0001050 A diagnosis that a patient definitely has frontal variant of Alzheimers disease. Alexander P. Cox creation date: 2011-09-01 diagnosis of definite frontal variant of Alzheimers disease ND:0001054 A diagnosis which indicates a neurological disease is hypothosized to inhere in an organsim. Alexander P. Cox Mark Jensen diagnosis of nervous system disease TO DO diagnosis of neurological disease ND:0001061 A diagnosis which indicates that a disease is hypothosized to inhere in an organsim. Alexander P. Cox TO DO diagnosis of disease ND:0001062 A diagnosis which indicates that a syndrome is hypothosized to inhere in an organsim. Alexander P. Cox Is the presence of a syndrome hypothosized? Since a syndrome is a pattern of signs and symptoms, which are by definition observed or reported, is there a need to hypothesize their occurrence? Perhaps the pattern can be hypothesized, but this too will typically (if not always) be observed or reported. Perhaps the definition should be changed to: "A diagnosis which indicates that a syndrome is exhibited by an organsim."? diagnosis of syndrome ND:0001063 A diagnosis which indicates that a disorder is either observed to inhere or hypothosized to inhere in an organsim. Alexander P. Cox diagnosis of disorder ND:0001100 A directive information entity that specifies how to establish a diagnosis according to one or more clinical findings, the concretization of which is realized in a diagnostic process. Mark Jensen A directive information entity the concretization of which is realized in a diagnostic process and which has a set of diagnostic criteria that consist of clinical findings that have been agreed upon by the medical community to provide sufficient, necessary, or sufficient and necessary warrant for a clinician to reach a particular diagnosis concerning a patient whose clinical picture satisfies the relevant diagnostic criteria. A diagnostic guideline has as parts the objective of accurately diagnosing patients according to its diagnostic criteria and the directive for the clinician to make the associated diagnosis when the diagnostic criteria have been determined to be satisfied. Alexander P. Cox Alexander P. Cox This class belongs in the domain of OGMS, will be a subtype of IAO_0000033:'directive information entity'. Refer to: http://code.google.com/p/ogms/wiki/DiagnosisGuideline http://code.google.com/p/ogms/issues/detail?id=75 https://groups.google.com/forum/?fromgroups=#!topic/ogms-discuss/9oVK5dLdZQs diagnostic guideline ND:0001101 *** REVISE *** Cognitive impairments beyond those expected based on the age and education of the individual, but which are not significant enough to interfere with their daily activities. The diagnosis of MCI requires considerable clinical judgement as well as a comprehensive clinical assessment including clinical observation, neuroimaging, blood tests and neuropsychological testing in order to rule out an alternate diagnosis. MCI is diagnosed when there is: 1. Evidence of memory impairment 2. Preservation of general cognitive and functional abilities 3. Absence of diagnosed dementia Memory complaint, preferably corroborated by an informant Objective memory impairment (below 1.5 standard deviations) Normal general cognitive functioning Intact activities of daily living Not demented Alexander P. Cox Adapted from: http://en.wikipedia.org/wiki/Mild_cognitive_impairment http://www.mejfm.com/journal/Oct2004/Dementia.htm diagnostic guideline for mild cognitive impairment ND:0001102 *** REVISE *** A diagnosis of dementia in a patient based on findings from blood tests, neuroimaging, and cognitive testing that indicate the presence of cognitive deficits [visual spatial, attention, orientation, exceutive function, functional] severe enough to interfere with the patient's daily life in a previously unimpaired person. Alexander P. Cox diagnostic guideline for dementia ND:0001105 Alexander P. Cox diagnostic guideline for neurodegenerative dementia ND:0001113 *** REVISE *** Diagnosis of NPH is usually first led by a lumbar puncture, followed by the evaluation of clinical response to removal of CSF. This can be followed by a CT, MRI, and continuous external lumbar CSF drainage during 3 or 4 days. Lumbar puncture is usually the first step in diagnosis and the CSF opening pressure is measured carefully. In most cases, CSF pressure is usually above 155 mmH2O. Clinical improvement after removal of CSF (30 mL or more) has a high predictive value for subsequent success with shunting. This is called the "lumbar tap test" or Miller Fisher test. On the contrary, a "negative" test has a very low predictive accuracy, as many patients may improve after a shunt in spite of lack of improvement after CSF removal. Infusion test is a test with higher sensitivity and specificity than a lumbar puncture. The outflow conductance (Cout) of the cerebrospinal fluid (CSF) system is a parameter considered to be predictive in selection for hydrocephalus surgery. Cout can be determined through an infusion test. In some centers, External lumbar drainage has been shown to have the highest sensitivity and specificity with regards to predicting a successful outcome following surgery. CT scan may show enlarged ventricles without convolutional atrophy. MRI may show some degree of transependymal migration of CSF surrounding the ventricles on T2/FLAIR sequence. Imaging however cannot differentiate between pathologies with similar clinical picture like Alzheimer's dementia, vascular dementia or Parkinson's disease. Alexander P. Cox http://en.wikipedia.org/wiki/Normal_pressure_hydrocephalus#Diagnosis diagnostic guideline for possible normal pressure hydrocephalus ND:0001114 Alexander P. Cox diagnostic guideline for probable normal pressure hydrocephalus ND:0001115 Alexander P. Cox diagnostic guideline for definite normal pressure hydrocephalus ND:0001116 *** REVISE *** Insidious onset, slow progression Impaired behavior: -loss of personal awareness, Disinhibition, mental rigidity, Hyperorality, Stereotypy, Perseveration, utilization behavior, Distractibility, poor social judgment Altered affect: -Depression, Anxiety, Delusions, Somatic preoccupations, Apathy, Amimia Speech disorder: -Reduced, stereotypic, echolalic, perseveration, mutism Physical signs: -Primitive reflexes, Incontinence, Parkinsonism Alexander P. Cox diagnostic guideline for possible frontotemporal dementia ND:0001117 Alexander P. Cox diagnostic guideline for probable frontotemporal dementia ND:0001118 Alexander P. Cox diagnostic guideline for definite frontotemporal dementia ND:0001119 Dementia plus one of the following: fluctuation, visual hallucination, parkinsonism, REM sleep behavioral disorder. Alexander P. Cox diagnostic guideline for possible dementia with Lewy bodies ND:0001120 Dementia plus two or more of the following: fluctuation, visual hallucination, parkinsonism, REM sleep behavioral disorder. Alexander P. Cox diagnostic guideline for probable dementia with Lewy bodies ND:0001121 Alexander P. Cox diagnostic guideline for definite dementia with Lewy bodies ND:0001122 Features of dementia associated with Parkinson’s disease: I. Core features 1. Diagnosis of Parkinson’s disease according to Queen Square Brain Bank criteria 2. A dementia syndrome with insidious onset and slow progression, developing within the context of established Parkinson’s disease and diagnosed by history, clinical, and mental examination, defined as: • Impairment in more than one cognitive domain • Representing a decline from premorbid level • Deficits severe enough to impair daily life (social, occupational, or personal care), independent of the impairment ascribable to motor or autonomic symptoms II. Associated clinical features 1. Cognitive features: • Attention: Impaired. Impairment in spontaneous and focused attention, poor performance in attentional tasks; performance may fluctuate during the day and from day to day • Executive functions: Impaired. Impairment in tasks requiring initiation, planning, concept formation, rule finding, set shifting or set maintenance; impaired mental speed (bradyphrenia) • Visuo-spatial functions: Impaired. Impairment in tasks requiring visual-spatial orientation, perception, or construction • Memory: Impaired. Impairment in free recall of recent events or in tasks requiring learning new material, memory usually improves with cueing, recognition is usually better than free recall • Language: Core functions largely preserved. Word finding difficulties and impaired comprehension of complex sentences may be present 2. Behavioral features: • Apathy: decreased spontaneity; loss of motivation, interest, and effortful behavior • Changes in personality and mood including depressive features and anxiety • Hallucinations: mostly visual, usually complex, formed visions of people, animals or objects • Delusions: usually paranoid, such as infidelity, or phantom boarder (unwelcome guests living in the home) delusions • Excessive daytime sleepiness III. Features which do not exclude PD-D, but make the diagnosis uncertain: • Co-existence of any other abnormality which may by itself cause cognitive impairment, but judged not to be the cause of dementia, e.g. presence of relevant vascular disease in imaging • Time interval between the development of motor and cognitive symptoms not known IV. Features suggesting other conditions or diseases as cause of mental impairment, which, when present make it impossible to reliably diagnose PD-D: • Cognitive and behavioral symptoms appearing solely in the context of other conditions such as: Acute confusion due to: a. Systemic diseases or abnormalities b. Drug intoxication Major Depression according to DSM IV • Features compatible with “Probable Vascular dementia” criteria according to NINDS-AIREN (dementia in the context of cerebrovascular disease as indicated by focal signs in neurological exam such as hemiparesis, sensory deficits, and evidence of relevant cerebrovascular disease by brain imaging AND a relationship between the two as indicated by the presence of one or more of the following: onset of dementia within 3 months after a recognized stroke, abrupt deterioration in cognitive functions, and fluctuating, stepwise progression of cognitive deficits) Criteria for the diagnosis of possible PD-D: A. Core features: Both must be present B. Associated clinical features: • Atypical profile of cognitive impairment in one or more domains, such as prominent or receptive-type (fluent) aphasia, or pure storage-failure type amnesia (memory does not improve with cueing or in recognition tasks) with preserved attention • Behavioral symptoms may or may not be present OR C. One or more of the group III features present D. None of the group IV features present From the article "Clinical Diagnostic Criteria for Dementia Associated with Parkinson’s Disease". Alexander P. Cox From the article "Clinical Diagnostic Criteria for Dementia Associated with Parkinson’s Disease". Movement Disorders Vol. 22, No. 12, 2007, pp. 1689-1707 © 2007 Movement Disorder Society diagnostic guideline for possible Parkinson dementia ND:0001123 Insidious onset and progression of assymetric cortical and basal ganglionic features. Akinetic, rigid syndrome; hyperkinetic movement disorder; alien limb. Cortical dysfunction: dementia, apraxia, cortical sensory, dysphasia, speech apraxia Alexander P. Cox diagnostic guideline for possible corticobasal degeneration ND:0001124 Alexander P. Cox diagnostic guideline for possible frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001125 Alexander P. Cox diagnostic guideline for possible multiple system atrophy ND:0001126 Alexander P. Cox diagnostic guideline for possible progressive supranuclear palsy ND:0001127 Features of dementia associated with Parkinson’s disease: I. Core features 1. Diagnosis of Parkinson’s disease according to Queen Square Brain Bank criteria 2. A dementia syndrome with insidious onset and slow progression, developing within the context of established Parkinson’s disease and diagnosed by history, clinical, and mental examination, defined as: • Impairment in more than one cognitive domain • Representing a decline from premorbid level • Deficits severe enough to impair daily life (social, occupational, or personal care), independent of the impairment ascribable to motor or autonomic symptoms II. Associated clinical features 1. Cognitive features: • Attention: Impaired. Impairment in spontaneous and focused attention, poor performance in attentional tasks; performance may fluctuate during the day and from day to day • Executive functions: Impaired. Impairment in tasks requiring initiation, planning, concept formation, rule finding, set shifting or set maintenance; impaired mental speed (bradyphrenia) • Visuo-spatial functions: Impaired. Impairment in tasks requiring visual-spatial orientation, perception, or construction • Memory: Impaired. Impairment in free recall of recent events or in tasks requiring learning new material, memory usually improves with cueing, recognition is usually better than free recall • Language: Core functions largely preserved. Word finding difficulties and impaired comprehension of complex sentences may be present 2. Behavioral features: • Apathy: decreased spontaneity; loss of motivation, interest, and effortful behavior • Changes in personality and mood including depressive features and anxiety • Hallucinations: mostly visual, usually complex, formed visions of people, animals or objects • Delusions: usually paranoid, such as infidelity, or phantom boarder (unwelcome guests living in the home) delusions • Excessive daytime sleepiness III. Features which do not exclude PD-D, but make the diagnosis uncertain: • Co-existence of any other abnormality which may by itself cause cognitive impairment, but judged not to be the cause of dementia, e.g. presence of relevant vascular disease in imaging • Time interval between the development of motor and cognitive symptoms not known IV. Features suggesting other conditions or diseases as cause of mental impairment, which, when present make it impossible to reliably diagnose PD-D: • Cognitive and behavioral symptoms appearing solely in the context of other conditions such as: Acute confusion due to: a. Systemic diseases or abnormalities b. Drug intoxication Major Depression according to DSM IV • Features compatible with “Probable Vascular dementia” criteria according to NINDS-AIREN (dementia in the context of cerebrovascular disease as indicated by focal signs in neurological exam such as hemiparesis, sensory deficits, and evidence of relevant cerebrovascular disease by brain imaging AND a relationship between the two as indicated by the presence of one or more of the following: onset of dementia within 3 months after a recognized stroke, abrupt deterioration in cognitive functions, and fluctuating, stepwise progression of cognitive deficits) Criteria for the diagnosis of probable PD-D: A. Core features: Both must be present B. Associated clinical features: • Typical profile of cognitive deficits including impairment in at least two of the four core cognitive domains (impaired attention which may fluctuate, impaired executive functions, impairment in visuo-spatial functions, and impaired free recall memory which usually improves with cueing) • The presence of at least one behavioral symptom (apathy, depressed or anxious mood, hallucinations, delusions, excessive daytime sleepiness) supports the diagnosis of Probable PD-D, lack of behavioral symptoms, however, does not exclude the diagnosis C. None of the group III features present D. None of the group IV features present From the article "Clinical Diagnostic Criteria for Dementia Associated with Parkinson’s Disease". Alexander P. Cox From the article "Clinical Diagnostic Criteria for Dementia Associated with Parkinson’s Disease". Movement Disorders Vol. 22, No. 12, 2007, pp. 1689-1707 © 2007 Movement Disorder Society diagnostic guideline for probable Parkinson dementia ND:0001128 Alexander P. Cox diagnostic guideline for probable corticobasal degeneration ND:0001129 Alexander P. Cox diagnostic guideline for probable frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001130 Alexander P. Cox diagnostic guideline for probable multiple system atrophy ND:0001131 Alexander P. Cox diagnostic guideline for probable progressive supranuclear palsy ND:0001132 Alexander P. Cox diagnostic guideline for definite Parkinson dementia ND:0001133 Alexander P. Cox diagnostic guideline for definite corticobasal degeneration ND:0001134 *** REVISE *** Definite diagnosis of FTDP-17 requires a combination of characteristic clinical and pathological features and molecular genetic analysis. Alexander P. Cox http://en.wikipedia.org/wiki/Frontotemporal_dementia_and_parkinsonism_linked_to_chromosome_17 diagnostic guideline for definite frontotemporal dementia with Parkinsonism linked to chromosome 17 ND:0001135 *** REVISE *** A definite diagnosis of multiple system atrophy can only be made post-mortem based on pathology in which abundant glial cytoplasmic inclusions are found in the central nervous system. Alexander P. Cox http://en.wikipedia.org/wiki/Multiple_system_atrophy#Diagnosis diagnostic guideline for definite multiple system atrophy ND:0001136 Alexander P. Cox diagnostic guideline for definite progressive supranuclear palsy ND:0001137 *** REVISE *** There is a dementia syndrome with an atypical onset, presentation or progression; and without a known etiology; but no co-morbid diseases capable of producing dementia are believed to be in the origin of it. Similar to the NINCDS-ADRDA Alzheimer's Criteria are the DSM-IV-TR criteria published by the American Psychiatric Association. At the same time the advances in functional neuroimaging techniques such as PET or SPECT that have already proven their utility to differentiate Alzheimer's disease from other possible causes, have led to proposals of revision of the NINCDS-ADRDA criteria that take into account these techniques. A. The development of multiple cognitive deficits manifested by both (1) memory impairment (impaired ability to learn new information or to recall previously learned information) (2) one (or more) of the following cognitive disturbances: (a) aphasia (language disturbance) (b) apraxia (impaired ability to carry out motor activities despite intact motor function) (c) agnosia (failure to recognize or identify objects despite intact sensory function) (d) disturbance in executive functioning (i.e., planning, organizing, sequencing, abstracting) B. The cognitive deficits in Criteria A1 and A2 each cause significant impairment in social or occupational functioning and represent a significant decline from a previous level of functioning. C. The course is characterized by gradual onset and continuing cognitive decline. D. The cognitive deficits in Criteria A1 and A2 are not due to any of the following: (1) other central nervous system conditions that cause progressive deficits in memory and cognition (e.g., cerebrovascular disease, Parkinson's disease, Huntington's disease, subdural hematoma, normal-pressure hydrocephalus, brain tumor) (2) systemic conditions that are known to cause dementia (e.g., hypothyroidism, vitamin B or folic acid deficiency, niacin deficiency, hypercalcemia, neurosyphilis, HIV infection) (3) substance-induced conditions E. The deficits do not occur exclusively during the course of a delirium. F. The disturbance is not better accounted for by another Axis I disorder (e.g., Major Depressive Episode, Schizophrenia). DSM IV I. Probable AD: Core Diagnostic Features A. Dementia established by clinical examination (including MMSE, BRDRS, and neuropsychological testing) B. Deficit in at least two areas of cognition i. Memory (required) ii. Other area besides memory C. Deficits characterized by gradual onset and progression, onset after age 40 D. Other systemic disorders or brain disease do not account for the progressive deficits in memory and cognition in and of themselves II. Possible AD: Core Diagnostic Features A. Dementia syndrome in the absence of other neurologic, psychiatric, or systemic disorder, OR B. Presence of a second systemic or brain disorder sufficient to produce dementia, which is not considered to be the primary cause of the dementia III. Features that make a diagnosis of Probable or Possible AD unlikely or uncertain A. Sudden apoplectic onset B. Focal neurologic findings such as hemiparesis, sensory loss, visual field deficits, and incoordination early in the course of the illness C. Seizures or gait disturbances at the onset or very early in the course of the illness Alexander P. Cox NINCDS-ADRDA Criteria for the Diagnosis of Alzheimer's Disease http://behavenet.com/dementia-alzheimers-type http://en.wikipedia.org/wiki/NINCDS-ADRDA_Alzheimer%27s_Criteria diagnostic guideline for possible Alzheimers disease ND:0001138 Alexander P. Cox diagnostic guideline for possible atypical Alzheimers disease ND:0001139 A. Presence of an early and significant episodic memory impairment that includes the following features: 1. Gradual and progressive change in memory function reported by patients or informants over more than 6 months 2. Objective evidence of significantly impaired episodic memory on testing: this generally consists of recall deficit that does not improve significantly or does not normalize with cueing or recognition testing and after effective encoding of information has been previously controlled 3. The episodic memory impairment can be isolated or associated with other cognitive changes at the onset of AD or as AD advances Plus one or more of the following supportive features B, C, D, and E: B. Presence of medial temporal lobe atrophy • Volume loss of hippocampi, entorhinal cortex, amygdala evidenced on MRI with qualitative ratings using visual scoring (referenced to well characterised population with age norms) or quantitative volumetry of regions of interest (referenced to well characterised population with age norms) C. Abnormal cerebrospinal fluid biomarker • Low amyloid β1–42 concentrations, increased total tau concentrations, or increased phospho-tau concentrations, or combinations of the three • Other well validated markers to be discovered in the future D. Specific pattern on functional neuroimaging with PET • Reduced glucose metabolism in bilateral temporal parietal regions • Other well validated ligands, including those that foreseeably will emerge such as Pittsburg compound B or FDDNP E. Proven AD autosomal dominant mutation within the immediate family And LACKS the following: History • Sudden onset • Early occurrence of the following symptoms: gait disturbances, seizures, behavioural changes Clinical features • Focal neurological features including hemiparesis, sensory loss, visual field deficits • Early extrapyramidal signs • Other medical disorders severe enough to account for memory and related symptoms • Non-AD dementia • Major depression • Cerebrovascular disease • Toxic and metabolic abnormalities, all of which may require specific investigations • MRI FLAIR or T2 signal abnormalities in the medial temporal lobe that are consistent with infectious or vascular insults I. Probable AD: Core Diagnostic Features A. Dementia established by clinical examination (including MMSE, BRDRS, and neuropsychological testing) B. Deficit in at least two areas of cognition i. Memory (required) ii. Other area besides memory C. Deficits characterized by gradual onset and progression, onset after age 40 D. Other systemic disorders or brain disease do not account for the progressive deficits in memory and cognition in and of themselves II. Features that make a diagnosis of Probable or Possible AD unlikely or uncertain A. Sudden apoplectic onset B. Focal neurologic findings such as hemiparesis, sensory loss, visual field deficits, and incoordination early in the course of the illness C. Seizures or gait disturbances at the onset or very early in the course of the illness Alexander P. Cox NINCDS-ADRDA Criteria for the Diagnosis of Alzheimer's Disease diagnostic guideline for probable Alzheimers disease ND:0001140 Possible bvFTD Three of the following behavioral/cognitive symptoms must be present to meet criteria. These symptoms should occur repeatedly, not just as a single instance. Early behavioral disinhibition (one of the following must be present) Socially inappropriate behavior: touching or kissing strangers, inappropriate sexual acts, public urination, criminal behavior, etc. Loss of manners or decorum: examples include crude or sexually explicit remarks, jokes or opinions which may be offensive to others; lack of response to social cues (e.g., will continue talking despite other’s attempts to end a conversation); physical behaviors such as flatulence, touching private body parts, belching or spitting; poor hygiene or grooming (malodorous, stained, torn or inappropriate clothing), loss of respect for interpersonal space Impulsive, rash or careless actions: impulsive behaviors which may or may not be performed in a social context (e.g., new- onset gambling, taking things, stealing (usually food or visually stimulating objects), buying or selling property without regard for consequences) Early apathy or inertia (one of the following must be present) Apathy: loss of interest, drive or motivation (e.g., passivity, lack of spontaneity, does not engage in previously rewarding activities) Inertia: decreased initiation of behavior (e.g., needs prompting to initiate or continue routine activities, less likely to initiate or sustain conversations) Early loss of sympathy or empathy (one of the following must be present) Diminished response to other people’s needs and feelings: positive rating of this feature should be based on specific examples that reflect a lack of understanding or indifference to other people’s feelings – e.g., hurtful comments, disregard for other’s pain or distress, making inappropriate jokes Diminished social interest, interrelatedness or personal warmth: general decrease in social engagement (coldness, lack of eye contact, etc.) Early perseverative, stereotyped or compulsive/ritualistic behavior (one of the following must be present) Simple repetitive movements: tapping, clapping, rubbing, scratching, picking at skin or clothing, pursing lips, lip smacking, etc. Complex, compulsive or ritualistic behaviors: counting and cleaning rituals, collecting, checking, repetitive trips to the bathroom, ordering objects, walking fixed routes, etc. Stereotypy of speech: repeating words or phrases that have no communicative value Hyperorality and dietary changes (one of the following must be present) Altered food preferences: carbohydrate craving (particularly sweets) or food fads Binge eating, increased consumption of alcohol or cigarettes: patient continues to eat despite satiety (weight gain ____ lb); compulsive smoking, chewing tobacco or gum; or alcohol ingestion Oral exploration or consumption of inedible objects Neuropsychological profile: executive/generation deficits with relative sparing of memory and visuospatial functions (all of the following must be present) Deficits in executive tasks: Trails-B, generation tasks (letter fluency/design fluency) or presence of errors (e.g., perseverations or rule violations) Relative sparing of episodic memory Relative sparing of visuospatial skills e.g., ability to copy simple line drawings Exclusion Criteria for bvFTD Criteria 1 and 2 must both be answered negatively for any bvFTD diagnosis. Criterion 3 can be positive for possible bvFTD but must be negative for probable bvFTD. Pattern of deficits is better accounted for by other non-degenerative nervous system or medical disorders (excludes all bvFTD diagnoses) e.g., delirium, cerebrovascular disease, cerebellar disorder, systemic disorders (e.g., hypothyroidism) or substance-induced conditions Behavioral disturbance is better accounted for by a psychiatric diagnosis (excludes all bvFTD diagnoses) e.g., depression, bipolar disorder, schizophrenia, pre-existing personality disorder Biomarkers strongly indicative of Alzheimer’s disease or other neurodegenerative process (excludes diagnosis of probable bvFTD) e.g., genetic mutations, extensive PIB binding, CSF markers Alexander P. Cox http://memory.ucsf.edu/ftd/medical/diagnosis/criteria/single Only biopsy can determine difference between FTD and frontal variant alzhiemers diagnostic guideline for possible frontal variant of Alzheimers disease ND:0001141 Alexander P. Cox diagnostic guideline for possible logopenic aphasia ND:0001142 Alexander P. Cox diagnostic guideline for possible posterior cortical atrophy ND:0001143 Alexander P. Cox diagnostic guideline for possible primary progressive non-fluent aphasia ND:0001144 Alexander P. Cox diagnostic guideline for probable atypical Alzheimers disease ND:0001145 Alexander P. Cox diagnostic guideline for probable frontal variant of Alzheimers disease ND:0001146 Alexander P. Cox diagnostic guideline for probable logopenic aphasia ND:0001147 Alexander P. Cox diagnostic guideline for probable posterior cortical atrophy ND:0001148 Alexander P. Cox diagnostic guideline for probable primary progressive non-fluent aphasia ND:0001149 *** REVISE *** The patient meets the criteria for probable Alzheimer's disease and has either: 1. Both clinical and histopathological (brain biopsy or autopsy) evidence of the disease, as required by the NIA-Reagan criteria for the post-mortem diagnosis of alzheimers disease or 2. Both clinical and genetic evidence (mutation on chromosome 1, 14, or 21) of alzheimers disease I. Probable AD: Core Diagnostic Features A. Dementia established by clinical examination (including MMSE, BRDRS, and neuropsychological testing) B. Deficit in at least two areas of cognition i. Memory (required) ii. Other area besides memory C. Deficits characterized by gradual onset and progression, onset after age 40 D. Other systemic disorders or brain disease do not account for the progressive deficits in memory and cognition in and of themselves II. Possible AD: Core Diagnostic Features A. Dementia syndrome in the absence of other neurologic, psychiatric, or systemic disorder, OR B. Presence of a second systemic or brain disorder sufficient to produce dementia, which is not considered to be the primary cause of the dementia III. Features that make a diagnosis of Probable or Possible AD unlikely or uncertain A. Sudden apoplectic onset B. Focal neurologic findings such as hemiparesis, sensory loss, visual field deficits, and incoordination early in the course of the illness C. Seizures or gait disturbances at the onset or very early in the course of the illness IV. Criteria for diagnosis of Definite Alzheimer's disease: A. Clinical criteria for probable Alzheimer's disease B. Histopathologic evidence obtained from a biopsy or autopsy As AD progresses, patients frequently suffer from neuropsychiatric complications such as agitation, apathy, delusions, hallucinations or depression. In many cases, these constitute a greater burden for caregivers than the cognitive deficits and may require treatment with psychoactive medications. Alexander P. Cox Adapted from: http://en.wikipedia.org/wiki/NINCDS-ADRDA_Alzheimer%27s_Criteria NINCDS-ADRDA Criteria for the Diagnosis of Alzheimer's Disease diagnostic guideline for definite Alzheimers disease ND:0001150 Alexander P. Cox diagnostic guideline for definite atypical Alzheimers disease ND:0001151 Alexander P. Cox diagnostic guideline for definite frontal variant of Alzheimers disease ND:0001152 Alexander P. Cox diagnostic guideline for definite logopenic aphasia ND:0001153 Alexander P. Cox diagnostic guideline for definite posterior cortical atrophy ND:0001154 At least one of the core features (1 and 2) must be present, and at least two of the following other features (3-5) must be present. Agrammatism in language production Effortful, halting speech with inconsistent distortions, deletions, substitutions, insertions, or transpositions of speech sounds, particularly in polysyllabic words (often considered to reflect "apraxia of speech") Impaired comprehension of syntactically complex sentences Spared single word comprehension Spared object knowledge Imaging-Supported NFAV-PPA Diagnosis Both of the following criteria must be present. Clinical diagnosis of NFAV-PPA Imaging must show one or more of the following results: Predominant left posterior fronto-insular atrophy on MRI Predominant left posterior fronto-insular hypoperfusion or hypometabolism on SPECT or PET Alexander P. Cox http://memory.ucsf.edu/ftd/medical/diagnosis/criteria/single diagnostic guideline for definite primary progressive non-fluent aphasia ND:0003000 Dementia is the co-occurence of cognitive deficits in at least two domains [memory, visual spatial, attention, orientation, executive function, functional] resulting in a decline of previous functioning. It typically results from the realization of a dementia disease. *** TEMPLATE FOR SYNDROME DEFINITIONS??? *** I think this is incorrect. First it should be defined wrt its parent. I don't think the parent of "dementia syndrome" will turn out to be "MCI syndrome". Admittedly that will depend on the specifics to the aggreed upon definitions. Currently they are both in need or refinement. Second, the definition is too Alzheimer-centric, and I believe would rule out other instances of dementia. Dementia does not typically result from a "dementia disease". Even if true, whatever “typical” means, that assertion is informative, not explanatory — i.e., it belongs in an elucidation not the definition. Mark Jensen Alexander P. Cox Mark Jensen dementia ND:0003001 Parkinsonism is the co-occurence of any combination of the classical features of Parkinson's disease [tremor, rigidity, akinesia/bradykinesia, postural instability]. It typically results from the realization of either Parkinsons disease, progressive supranuclear palsy, or multiple system atrophy. Alexander P. Cox Parkinsonian syndrome idiopathic parkinsonism Parkinsonism ND:0003002 Typical Alzheimers syndrome is the insidious onset of dementia syndrome that is characterized by episodic memory loss. It typically results from the realization of Alzheimers disease. Alexander P. Cox typical Alzheimers syndrome ND:0003003 Parkinson plus syndrome is the co-occurence of any combination of the classical features of Parkinsons disease [tremor, rigidity, akinesia/bradykinesia, postural instability] with additional features [supranuclear palsy, paralysis of downward gaze, autonomic dysfunction, additional cortical signs, etc] that distinguishes it from simple idiopathic Parkinsons disease. It typically results from the realization of either multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration, or Lewy body dementia. Alexander P. Cox atypical parkinsonian disorder of multiple system degeneration Parkinson plus syndrome ND:0003004 Mild cognitive impairment is the occurence of one or more cognitive deficits [visual spatial, attention, orientation, executive function, functional] that are beyond those expected based on the age and education of the individual, but which are not significant enough to interfere with their daily activities. It is typically the result of _________ . Remove last sentence of defintion. "Typically" doesn't ontologize well. Nor do fill-in-the-blanks ;-) Mark Jensen Suggest removing 'mild' from label. Dementia is not a type of mild cognitive impairment. A syndrome of cognitive impairment makes more sense and tracks far better with reality. A diagnosis of MCI can be non-pathological, ie- normal ageing related cognitive decline. Mark Jensen Alexander P. Cox Mark Jensen MCI mild cognitive impairment ND:0003005 Atypical Alzheimers syndrome is the insidious onset of dementia syndrome that is typically characterized by the absence of episodic memory loss. It typically results from the realization of either frontal variant of Alzheimers disease, logopenic aphasia, posterior cortical atrophy, or primary progressive nonfluent aphasia. Alexander P. Cox atypical Alzheimers syndrome ND:0003007 ALS without family history Alexander P. Cox sporadic ALS See: http://www.alshopefoundation.org/understanding-als/types-of-als.php sporadic amyotrophic lateral sclerosis ND:0003008 Familial ALS cases comprise 5 to 10 percent of all cases of ALS. Familial ALS (FALS) is inherited as an autosomal dominant trait. Almost 20 % of people with FALS have damage (called a mutation) in the gene that codes for the protein Cu/Zn superoxide dismutase (SOD 1) located on chromosome 21. There are no differences between familial and sporadic ALS on neurological exam except for occasional sensory loss in people with FALS. Other genes that, when damaged, can lead to ALS, have been identified on chromosomes 2, 9, 15, 18 and the X chromosome. Alexander P. Cox familial ALS See: http://www.alshopefoundation.org/understanding-als/types-of-als.php familial amyotrophic lateral sclerosis ND:0003009 Western Pacific ALS occurs primarily on the island of Guam, the Kii Peninsula of Japan, and New Guinea. The people on Guam have the same clinical characteristics seen in sporadic ALS and also can have a dementia and Parkinsons like illness. The illness on Guam is the first to be tied to a toxin, the cycad nut. This nut contains a compound that is toxic to nerve cells called BMAA and is similar to glutamate. The nut is eaten by the fruit bat which was a delicacy among the Chamorro population of Guam. This allowed a very high concentration of the toxin to be eaten and it has been postulated but not proven, that this caused the disease. The fruit bat was eaten to extinction and now fruit bats for consumption are imported, the disease has all but disappeared! Alexander P. Cox Guamanian western pacific ALS See: http://www.alshopefoundation.org/understanding-als/types-of-als.php western pacific amyotrophic lateral sclerosis ND:0003010 Rare cases of adolescent motor neuron disease that are clinically indistinguishable from ALS have been reported. Onset is between ages twelve and sixteen. Although ALS can occur at young ages, these cases are probably different from sporadic ALS. Alexander P. Cox juvenile ALS See: http://www.alshopefoundation.org/understanding-als/types-of-als.php juvenile amyotrophic lateral sclerosis ND:0003011 This is a rare disorder seem in young men. In this variant there is localized atrophy of one arm associated with increased reflexes implicating the presence of upper and lower motor neuron damage. However, the disorder is a problem at the junction between the cervical spine and the skull where there is pressure on the cervical spinal cord. In order to detect it, MRI of the neck needs to be performed in different positions including neck flexion and extension. Alexander P. Cox See: http://www.alshopefoundation.org/understanding-als/types-of-als.php hiramaya disease ND:0003012 Alexander P. Cox JP PARK2 PDJ Parkinson disease 2 autosomal recessive juvenile Parkinsonism early onset Parkinson disease juvenile Parkinsonism autosomal recessive juvenile Parkinson disease ND:0005013 Tau proteins are proteins that stabilize microtubules. They are abundant in neurons of the central nervous system and are less common elsewhere, but are also expressed at very low levels in CNS astrocytes and oligodendrocytes. When tau proteins are defective, and no longer stabilize microtubules properly, they can result in dementias such as Alzheimer's disease. The tau proteins are the product of alternative splicing from a single gene that in humans is designated MAPT (microtubule-associated protein tau). Tau protein is a highly soluble microtubule-associated protein (MAP). In humans, these proteins are mostly found in neurons compared to non-neuronal cells. One of tau's main functions is to modulate the stability of axonal microtubules. Six tau isoforms exist in human brain tissue, and they are distinguished by their number of binding domains. Three isoforms have three binding domains and the other three have four binding domains. Hyperphosphorylation of the tau protein (tau inclusions, pTau) can result in the self-assembly of tangles of paired helical filaments and straight filaments, which are involved in the pathogenesis of Alzheimer's disease and other tauopathies. All of the six tau isoforms are present in an often hyperphosphorylated state in paired helical filaments from Alzheimer's disease brain. In other neurodegenerative diseases, the deposition of aggregates enriched in certain tau isoforms has been reported. When misfolded, this otherwise very soluble protein can form extremely insoluble aggregates that contribute to a number of neurodegenerative diseases. Recent research suggests that tau may be released extracellularly by an exosome based mechanism in Alzheimer's disease. Some aspects of how the disease functions also suggests that it has some similarities to prion proteins. Alexander P. Cox tau http://en.wikipedia.org/wiki/Tau_protein tau protein ND:0005015 Amyloid beta (Aβ or Abeta) is a peptide of 36–43 amino acids that is processed from the Amyloid precursor protein. While best known as a component of amyloid plaques in association with Alzheimer's disease, evidence has been found that Aβ is a highly multifunctional peptide with significant non-pathological activity. Aβ is the main component of deposits found in the brains of patients with Alzheimer's disease. Several potential activities have been discovered for Aβ that are not associated with disease, including activation of kinase enzymes, protection against oxidative stress, regulation of cholesterol transport, functioning as a transcription factor, and anti-microbial activity (potentially associated with Aβ's pro-inflammatory activity). Aβ is the main component of amyloid plaques (deposits found in the brains of patients with Alzheimer's disease). Similar plaques appear in some variants of Lewy body dementia and in inclusion body myositis (a muscle disease), while Aβ can also form the aggregates that coat cerebral blood vessels in cerebral amyloid angiopathy. The plaques are composed of a tangle of regularly ordered fibrillar aggregates called amyloid fibers, a protein fold shared by other peptides such as the prions associated with protein misfolding diseases. Recent research suggests that soluble oligomeric forms of the peptide may be causative agents in the development of Alzheimer's disease. A number of genetic, cell biology, biochemical and animal studies support the concept that Aβ plays a central role in the development of Alzheimer’s disease pathology. Brain Aβ is elevated in patients with sporadic Alzheimer’s disease. Aβ is the main constituent of brain parenchymal and vascular amyloid, it contributes to cerebrovascular lesions and is neurotoxic. It is unresolved how Aβ accumulates in the central nervous system and subsequently initiates the disease of cells. Significant efforts have been focused on the mechanisms responsible for Aβ production, including the proteolytic enzymes alpha- and ß-secretases which generate Aβ from its precursor protein, APP (amyloid precursor protein). Aβ circulates in plasma, cerebrospinal fluid (CSF) and brain interstitial fluid (ISF) mainly as soluble Aβ40 Senile plaques contain both Aβ40 and Aβ42, while vascular amyloid is predominantly the shorter Aβ40. Several sequences of Aβ were found in both lesions. Generation of Aβ in the CNS may take place in the neuronal axonal membranes after APP-mediated axonal transport of ß-secretase and presenilin-1. Aβ is formed after sequential cleavage of the amyloid precursor protein (APP), a transmembrane glycoprotein of undetermined function. APP can be processed by α-, β- and γ-secretases; Aβ protein is generated by successive action of the β and γ secretases. The γ secretase, which produces the C-terminal end of the Aβ peptide, cleaves within the transmembrane region of APP and can generate a number of isoforms of 36-43 amino acid residues in length. The most common isoforms are Aβ40 and Aβ42; the shorter form is typically produced by cleavage that occurs in the endoplasmic reticulum, while the longer form is produced by cleavage in the trans-Golgi network. The Aβ40 form is the more common of the two, but Aβ42 is the more fibrillogenic and is thus associated with disease states. Alexander P. Cox Abeta Aβ amyloid beta amyloid-beta beta amyloid beta-amyloid http://en.wikipedia.org/wiki/Beta_amyloid http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=PR:000004168 *** possibly CHANGE LABEL TO 'amyloid beta (A4) precursor protein' *** amyloid beta protein ND:0005016 An amyloid beta protein fragment is a protein fragment that has been proteolytically derived from an amyloid beta protein. Amyloid beta protein fragments often aggregate and become parts of protein aggregates, such as amyloid beta plaques, which are thought to frequently form the material basis of many neurological diseases. Alexander P. Cox amyloid beta fragment amyloid beta protein fragment ND:0005017 An amyloid beta protein part is a peptide or polypeptide that is a fiat object part of a larger amyloid beta protein. When an amyloid beta protein part is proteolytically derived from an amyloid beta protein, it becomes an amyloid beta protein fragment. Alexander P. Cox amyloid beta part amyloid beta protein part ND:0005018 A protein fragment is a protein part that has been proteolytically derived from a protein and is now a detached independent continuant. Alexander P. Cox protein fragment ND:0005019 A tau protein fragment is a protein fragment that has been proteolytically derived from a tau protein. Tau protein fragments often aggregate and become parts of protein aggregates, such as neurofibrillary tangles, Lewy bodies, and Lewy neurites, which are thought to frequently form the material basis of many neurological diseases. Alexander P. Cox tau protein fragment ND:0005020 A tau protein part is a peptide or polypeptide that is a fiat object part of a larger tau protein. When a tau protein part is proteolytically derived from a tau protein, it becomes a tau protein fragment. Alexander P. Cox tau protein part ND:0005021 Alexander P. Cox alpha-synuclein protein alpha synuclein protein ND:0005022 Alexander P. Cox alpha-synuclein protein part alpha synuclein protein part ND:0005023 Alexander P. Cox alpha-synuclein protein fragment alpha synuclein protein fragment ND:0005024 Alexander P. Cox ubiquitin protein ND:0005025 Alexander P. Cox ubiquitin protein part ND:0005026 Alexander P. Cox ubiquitin protein fragment ND:0005027 Alexander P. Cox neurofilament protein ND:0005028 Alexander P. Cox neurofilament protein part ND:0005029 Alexander P. Cox neurofilament protein fragment ND:0005030 Alexander P. Cox alpha B crystallin protein ND:0005031 Alexander P. Cox alpha B crystallin protein part ND:0005032 Alexander P. Cox alpha B crystallin protein fragment ND:0005033 Alexander P. Cox I don't think this class and its subclasses add anything to the ontology. I think that everything that I originally wanted 'protein part' to do can be accommodated by using 'protein fragment', but this will require further review. The original intention in creating this class was to identify fiat parts of longer amino acid chains in order to identify protein fragments as having originated in a larger amino acid chain which was later subjected to a "snipping" process that separated the fiat protein part and generated an independent continuant that is equivalent to the appropriate protein fragment. Alexander P. Cox protein part ND:0005500 An amyloid plaque is an extracellular protein aggregate that develops in the brain and is composed primarily of amyloid beta A4 protein. Alexander P. Cox amyloid plaque beta-amyloid plaque senile plaque amyloid beta plaque ND:0005501 A disorder which is the material basis of a neurologcal disease. Mark Jensen TO DO neurological disorder ND:00055012 A protein is a biochemical compound consisting of one or more polypeptides typically folded into a globular or fibrous form, that facilitates a biological function. Alexander P. Cox http://en.wikipedia.org/wiki/Protein We may or may not want to add more terms related to proteins such as: A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. From: http://en.wikipedia.org/wiki/Protein protein ND:0005502 Neurofibrillary tangle is an intracellular aggregation of tau proteins that develop in neurons in the brain. The development of neurofibrillary tangles typically results in the disruption of the transportation of nutrients and other important substances within the neuron, which typically results in the destruction and death of the cell. Alexander P. Cox NFT PHF paired helical filaments tangle tau tangle Alexander P. Cox Neurofibrillary Tangles (NFTs) are aggregates of hyperphosphorylated tau protein that are most commonly known as a primary marker of Alzheimer's Disease. Their presence is also found in numerous other diseases known as Tauopathies. Little is known about their exact relationship to the different pathologies. Neurofibrillary tangles are formed by hyperphosphorylation of a microtubule-associated protein known as tau, causing it to aggregate, or group, in an insoluble form. (These aggregations of hyperphosphorylated tau protein are also referred to as PHF, or "paired helical filaments"). The precise mechanism of tangle formation is not completely understood, and it is still controversial whether tangles are a primary causative factor in disease or play a more peripheral role. From: http://en.wikipedia.org/wiki/Neurofibrillary_tangles neurofibrillary tangle ND:0005504 An amyloid aggregate is a typically extracellular aggregation of amyloid fibrils. TO DO: Revise Alexander P. Cox amyloid Pathogenesis of amyloidosis: When a native cell creates a protein, it could either make the actual protein or protein fragments. These fragments could come and join together to form the actual protein. Such a protein can sometimes regress into the protein fragments. This process of "flip flopping" happens frequently in certain proteins, especially the ones that cause this disease. The fragments or actual proteins are at risk of mis-folding as they are synthesized, to make a bad protein. This causes proteolysis, which is the directed degradation of proteins by cellular enzymes called proteases or by intramolecular digestion; proteases come and digest the mis-folded fragments and proteins. The problem occurs when the proteins do not dissolve in proteolysis. This happens because the mis-folded proteins sometimes become robust enough that they are not dissolved by normal proteolysis. When the fragments do not dissolve, they get spit out of proteolysis and they aggregate to form oligomers. The reason they aggregate is that the parts of the protein that do not dissolve in proteolysis are the β-pleated sheets, which are extremely hydrophobic. They are usually sequestered in the middle of the protein, while parts of the protein that are more soluble are found near the outside. When they are exposed to water, these hydrophobic pieces tend to aggregate with other hydrophobic pieces. This ball of fragments gets stabilized by GAG's (glycosaminoglycans) and SAP (serum amyloid P), a component found in amyloid aggregations that is thought to stabilize them and prevent proteolytic cleavage). The stabilized balls of protein fragments are called oligomers. The oligomers can aggregate together and further stabilize to make amyloid fibrils. Both the oligomers and amyloid fibrils can cause cell toxicity and organ dysfunction. From: http://en.wikipedia.org/wiki/Amyloidosis Also see: http://en.wikipedia.org/wiki/Amyloid amyloid aggregate ND:0005505 Lewy body is an abnormal aggregate of protein that develops inside nerve cells in Parkinson's disease (PD), Lewy Body Dementia and some other disorders. They are identified under the microscope when histology is performed on the brain. Lewy bodies appear as spherical masses that displace other cell components. There are two morphological types: classical (brain stem) Lewy bodies and cortical Lewy bodies. A Lewy body is composed of the protein alpha-synuclein associated with other proteins such as ubiquitin, neurofilament protein, and alpha B crystallin. Tau proteins may also be present, and Lewy bodies may occasionally be surrounded by neurofibrillary tangles. It is believed that Lewy bodies represent an aggresome response in the cell. Alexander P. Cox WEB:http://en.wikipedia.org/wiki/Lewy_body@2012-08-15 Lewy body ND:0005508 Similar to Lewy bodies, Lewy neurites are proteinaceous formations found in neurons of the disease brain, comprising abnormal α-synuclein filaments and granular material. They are a feature of α-synucleinopathies such as Dementia with Lewy bodies, Parkinson's disease and multiple system atrophy (MSA), and are found in the CA2-3 region of the hippocampus in Alzheimer's disease. Alexander P. Cox http://en.wikipedia.org/wiki/Lewy_body Lewy neurite ND:0005509 Alexander P. Cox filamentous inclusion made of the protein alpha-synuclein This should probably be a subclass of 'amyloid aggregate' -APC alpha synuclein aggregate ND:0005511 A protein aggregate is a grouping of misfolded proteins that is often rigid and insoluble. I don't think it is correct to have this typed as a disorder. Are ALL protein aggregates the material basis of some disease? -MJ This is a place holder until PR takes over this term. This term label assumes that all protein aggregates are pathological in nature. A review of the literature supports this interpretation; however, it is still an open question wether there are some nonpathological protein aggregates. If this is the case, then this lable should be changed to 'pathological protein aggregate' and another class should be created labled 'protein aggregate' that is not a subclass of 'disorder'. Alexander P. Cox http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-P/protein_aggregate.html protein aggregate ND:0006000 Neurodegeneration is a pathological bodily process that produces the loss of structure or function of neurons and can also produce the death of neurons. Alexander P. Cox Source? neurodegeneration ND:0006003 Protein aggregation is the process through which misfolded protein fragments group together to form a protein aggregate. Alexander P. Cox Are 'pathological aggresomal response' and 'protein aggregation' the same process? If not, what differentiates them? Is 'protein aggregation' a subclass of 'pathological aggresomal response' as I have currently asserted? If so, what other types of 'pathological aggresomal response' are there? If not, why not? Is it correct to give this a logical definition that includes: 'has specified output' some aggresome ??? In other words, does every aggresomal response generate an aggresome? See also: 'aggresomal response' Alexander P. Cox Consider adding subclasses of 'protein aggregate' to represent the following properties that they can have: Aggregates of proteins may arise from several mechanisms and may be classified in numerous ways, including soluble/insoluble, covalent/noncovalent, reversible/irreversible, and native/denatured. Source: http://www.aapsj.org/view.asp?art=aapsj080366 protein aggregation ND:0006004 Tau protein aggregation is the pathological bodily process through which a neurofibrillary tangle is formed from tau protein fragments. Alexander P. Cox tau aggregation tau protein aggregation ND:0006005 Amyloid beta protein aggregation is the pathological bodily process through which an amyloid beta plaque is formed from amyloid beta protein fragments. Alexander P. Cox amyloid beta aggregation amyloid beta protein aggregation ND:0006007 A progressive disease course that realizes typical Alzheimers disease. Alexander P. Cox *** TO DO *** Revise definition and add disease courses for each of the subclasses of Alzheimers disease. typical Alzheimers disease course ND:0006008 A progressive disease course that realizes atypical Alzheimers disease. Alexander P. Cox *** TO DO *** Revise definition and add disease courses for each of the subclasses of Alzheimers disease. atypical Alzheimers disease course ND:0006020 A progressive disease course that realizes frontotemporal dementia disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox frontotemporal dementia disease course ND:0006021 A progressive disease course that realizes Parkinsons disease and involves degeneration of pigmented neurons in the substantia nigra pars compacta. Alexander P. Cox Parkinsons disease course ND:0006023 A progressive disease course that realizes tauopathy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox tauopathy disease course ND:0006024 A progressive disease course that realizes coticobasal degeneration disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox corticobasal degeneration disease course ND:0006025 A chronic disease course that realizes normal pressure hydrocephalus disease and involves elevated cerebral spinal fluid pressure in the brain and spinal cord. ***Expand on this! Alexander P. Cox normal pressure hydrocephalus disease course ND:0006026 A progressive disease course that realizes frontotemporal dementia with motor neuron disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox frontotemporal dementia with motor neuron disease course ND:0006027 A progressive disease course that realizes Picks disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox Picks disease course ND:0006028 A progressive disease course that realizes primary progressive aphasia disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox primary progressive aphasia disease course ND:0006029 A progressive disease course that realizes semantic aphasia disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox semantic aphasia disease course ND:0006030 A progressive disease course that realizes progressive supranuclear palsy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox progressive supranuclear palsy disease course ND:0006031 A progressive disease course that realizes amyloidopathy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox amyloidopathy disease course ND:0006032 A progressive disease course that realizes motor neuron disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox motor neuron disease course ND:0006033 A progressive disease course that realizes amyotrophic lateral sclerosis disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox amyotrophic lateral sclerosis disease course ND:0006034 A progressive disease course that realizes progressive bulbar palsy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox progressive bulbar palsy disease course ND:0006035 A progressive disease course that realizes spinal muscular atrophy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox spinal muscular atrophy disease course ND:0006036 A progressive disease course that realizes cerebral amyloid angiopathy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox cerebral amyloid angiopathy disease course ND:0006037 A progressive disease course that realizes alpha synucleinopathy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox alpha synucleinopathy disease course ND:0006038 A progressive disease course that realizes Lewy body disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox Lewy body disease course ND:0006039 A progressive disease course that realizes Parkinsons dementia disease, results in dementia, and involves degeneration of pigmented neurons in the substantia nigra pars compacta. Alexander P. Cox Parkinson dementia disease course ND:0006040 A progressive disease course that realizes multiple system atrophy disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox multiple system atrophy disease course ND:0006041 A progressive disease course that realizes Huntingtons disease and involves degeneration of neurons in the brain. ***Expand on this! Alexander P. Cox Huntingtons disease course ND:0006042 A progressive disease course that realizes a neurological disease that involves degeneration of neurons in the brain. Alexander P. Cox Mark J: This defintion needs fixing. Makes no sense to say "involves". What is that? And why the complicated axiom and equivalency here? Why not simply: "A disease course that realizes a neurodegenerative disease"? neurodegenerative disease course ND:0006043 Alpha synuclein protein aggregation is the pathological bodily process through which a filamentous inclusion is formed from alpha synuclein protein fragments. Alexander P. Cox alpha synuclein aggregation alpha synuclein protein aggregation NPT:0011015 assay design OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity 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.) 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:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification investigation OBI:0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role OBI:0000116 worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel worker OBI worker role OBI:0000202 investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. investigation agent role OBI:0000207 health care provider role a worker role of providing medical care either within or outside the study timeline Person:Jennifer Fostel health care provider health care provider 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 organization is a continuant entity which can play 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000272 protocol PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice. a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) protocol OBI:0000338 interpreting data Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis. the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters interpreting data OBI:0000339 planning the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. a process of creating or modifying a plan. 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters PPPB branch planning OBI:0000471 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out a study design a planned process that realizes the concretization of a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution OBI:0500000 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design study specification OGMS:0000014 A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding OGMS:0000015 A series of statements representing health-relevant qualities of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:59Z clinical history OGMS:0000016 A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:20:20Z clinical picture OGMS:0000017 A representation of an image that supports an inference to an assertion about some quality of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:10Z image finding OGMS:0000018 A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding OGMS:0000019 A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:22:44Z preclinical finding OGMS:0000020 A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. note: defined class http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:02:10Z symptom OGMS:0000022 A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:12:33Z manifestation of a disease OGMS:0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:13:49Z phenotype OGMS:0000024 A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance. note: defined class Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:14:36Z sign OGMS:0000025 A manifestation of a disease that is detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:15:43Z clinical manifestation of a disease OGMS:0000026 A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:16:50Z preclinical manifestation of a disease OGMS:0000027 A clinically abnormal phenotype. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:18:05Z clinical phenotype OGMS:0000028 A clinically abnormal phenotype that is characteristic of a single disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:18:39Z disease phenotype OGMS:0000029 A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:19:17Z vital sign OGMS:0000030 A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:20:25Z predisposition to disease of type X OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z disease OGMS:0000032 Albert Goldfain creation date: 2009-06-23T11:22:01Z homeostasis OGMS:0000033 A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:23:07Z genetic predisposition to disease of type X OGMS:0000034 A disease whose physical basis is an acquired genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:05Z acquired genetic disease OGMS:0000035 A disease whose physical basis is a constitutional genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:59Z constitutional genetic disease OGMS:0000037 Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:26:44Z abnormal homeostasis OGMS:0000038 Homeostasis of a type that is not clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:27:28Z normal homeostasis OGMS:0000039 A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:24Z configuration OGMS:0000040 A configuration which deviates in some way from a canonical configuration for a particular organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:58Z pathological physical configuration OGMS:0000045 A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder OGMS:0000046 A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:40:27Z epigenetic disorder OGMS:0000047 A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:41:14Z genetic disorder OGMS:0000050 A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:09Z acquired genetic disorder OGMS:0000051 A genetic disorder inherited during conception that is part of all cells in the organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:44Z constitutional genetic disorder OGMS:0000055 A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:16Z clinical history taking OGMS:0000056 A measurement assay that has as input a patient-derived specimen and as output a data itme that is about a quality of the specimen. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:49Z laboratory test OGMS:0000057 A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:50:18Z Physical Assessment Physical Examination A systemic evaluation of the body and its functions using visual inspection, palpation, percussion and auscultation. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. (NCIT) NCIT physical examination physical state examination OGMS:0000059 A process in an organism that leads to a subsequent disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:53:07Z etiological process OGMS:0000060 Albert Goldfain creation date: 2009-06-23T11:53:49Z bodily process OGMS:0000061 A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process OGMS:0000063 The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course OGMS:0000064 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:56:26Z chronic disease course OGMS:0000065 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:09Z progressive disease course OGMS:0000066 A disease course that terminates in a return to normal homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:44Z transient disease course OGMS:0000067 Albert Goldfain creation date: 2009-06-23T11:58:22Z _undefined primitive term OGMS:0000069 Albert Goldfain creation date: 2009-06-23T11:59:24Z clinically abnormal OGMS:0000070 Albert Goldfain creation date: 2009-06-23T12:00:09Z physical basis OGMS:0000071 Albert Goldfain creation date: 2009-06-23T12:00:39Z realization OGMS:0000073 The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis OGMS:0000074 A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-26T10:31:34Z normal value OGMS:0000077 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:59Z pathological formation OGMS:0000078 An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:05Z pathological anatomical structure OGMS:0000079 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:15:17Z portion of pathological body substance OGMS:0000080 A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:07Z pathological transformation OGMS:0000081 A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:24Z pathological derivation OGMS:0000082 TODO: Define. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:47Z pathological invasion OGMS:0000083 TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 creation date: 2009-11-24T04:51:11Z physical examination finding OGMS:0000084 An aggregate of organisms of the same type. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=33 creation date: 2009-11-24T04:51:11Z organism population OGMS:0000085 A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage. Albert Goldfain http://www.referent-tracking.com/RTU/sendfile/?file=painTokyo1_27_2011.pdf creation date: 2009-11-24T04:51:11Z pain OGMS:0000086 A pattern of signs and symptoms that typically co-occur. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=32 creation date: 2009-11-24T04:51:11Z syndrome OGMS:0000087 An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z extended organism OGMS:0000088 A communication from a patient about something they perceive as being abnormal about their body or life. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=12 creation date: 2010-01-25T04:51:11Z patient symptom report OGMS:0000089 A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=28 creation date: 2010-03-31T04:51:11Z congenital malformation OGMS:0000090 A planned process whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z treatment OGMS:0000091 A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z convalescence OGMS:0000092 A process which has as parts all the processes in which a given organism is participant. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=38 creation date: 2010-03-31T04:51:11Z EDIT: 10 NOV 2015 life course OGMS:0000093 A hypothesis about some future part of a disease course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T12:42:23Z prognosis OGMS:0000094 a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset. Albert Goldfain http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 creation date: 2010-07-19T11:57:44Z acute disease course OGMS:0000095 A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 creation date: 2010-07-19T11:57:44Z Updated: 10 NOV 2015 inflammatory process OGMS:0000096 A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18 health care process OGMS:0000097 A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z health care encounter OGMS:0000098 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z hospitalization OGMS:0000099 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z outpatient encounter OGMS:0000100 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z inpatient encounter OGMS:0000101 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z ED encounter OGMS:0000102 A disorder that involves some structural damage that is immediately caused by a catastrophic external force. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015 injury OGMS:0000103 A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder. Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e creation date: 2011-09-20T09:57:44Z disease prophylaxis OGMS:0000104 A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e creation date: 2011-09-20T09:57:44Z diagnostic process OGMS:0000105 a disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease. A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=73 10 NOV 2015 relapse OGMS:0000106 a disease stage which is characterized by the lack of a manifestation of a disease. A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=73 10 NOV 2015 remission OGMS:0000107 A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient. 2017-04-18 Sagar Jain ancillary health care process OGMS:0000108 A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. creation: 16MAY2017 Sagar Jain health care process assay OGMS:0000109 A health care process which results in physical changes in a specified input material creation: 16MAY2017 Sagar Jain health care process biomaterial transformation OGMS:0000110 A health care process that produces output from input data creation: 16MAY2017 Sagar Jain health care process data transformation PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. length PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass PR:000004168 Protein Ontology PO:amyloid-beta A4 protein 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 elevated_cerebral_spinal_fluid:pressure Change entity URI I had to move this term here in order to keep the reasoner (FaCT++) from telling me that 'normal pressure hydrocephalus' is equivalent to NOTHING. This was due to the use of 'has material basis at all times', which has a domain/range restriction that limits it to material entities. Alexander P. Cox elevated cerebral spinal fluid pressure histopathological (brain biopsy or autopsy) evidence of Alzheimers disease genetic evidence (mutation on chromosome 1, 14, or 21) of Alzheimers disease The objective of a diagnostic guideline is for a clinician to determine whether or not the patient should be diagnosed with the relevant disease, disorder, or syndrome. Alexander P. Cox diagnostic guideline objective specification dementia in the absence of other neurologic, psychiatric, or systemic disorders dementia in the presence of a second systemic or brain disorder sufficient to produce dementia, which is not considered to be its primary cause presence of an early and significant episodic memory impairment presence of medial temporal lobe atrophy abnormal cerebrospinal fluid biomarker reduced glucose metabolism in bilateral temporal parietal regions measured by functional neuroimaging with PET proven AD autosomal dominant mutation within the immediate family sudden onset of episodic memory impairment This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105 disease stage oboInOwl:DbXref oboInOwl:Definition oboInOwl:ObsoleteClass Obsolete Class oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType DM-dataset data example OntoDT OntoDT: void datatype OntoDT OntoDT: boolean datatype OntoDT OntoDT: integer datatype OntoDT: extended datatype OntoDT OntoDT: non-numeric primitive datatype OntoDT OntoDT: numeric primitive datatype OntoDT OntoDT: numeric ordered primitive datatype OntoDT OntoDT: non-numeric unordered primitive datatype OntoDT OntoDT: non-numeric ordered primitive datatype OntoDT OntoDT: descriptive data without missing values component OntoDT OntoDT: descriptive record of primitives without missing values field component OntoDT: positive integer OntoDT OntoDT: unlabeled data with missing values OntoDT OntoDT: primitive alternative component OntoDT OntoDT: choice (primitive,void) datatype OntoDT OntoDT: void alternative component OntoDT OntoDT: descriptive record of primitives with missing values field component OntoDT OntoDT: choice(primitive,void) field component OntoDT OntoDT: unlabeled data OntoDT OntoDT: descriptive data with missing values field component OntoDT OntoDT: unlabeled data without missing values OntoDT OntoDT: record of choice(primitive,void) OntoDT OntoDT: choice field component OntoDT OntoDT: feature-based unlabeled data with missing values OntoDT: feature-based unlabeled data without missing values 1 OntoDT OntoDT: record with one component NDDO:Geriatric_Depression_Scale_Assessment_design Geriatric Depression Scale Assessment design NDDO:NDDO_00000003 biomarker assessment NDDO:NDDO_00000004 clinical assessment NDDO:NDDO_00000005 imaging assessment NDDO:NDDO_00000006 biospecimen collection NDDO:NDDO_00000007 blood sampling NDDO:NDDO_00000008 lumbar puncture sampling NDDO:NDDO_00000011 vital signs assessment NDDO:NDDO_00000012 screening labs assessment NDDO:NDDO_00000013 neurological assessment NDDO:NDDO_00000015 clinical assessment of study partner NDDO:NDDO_00000016 clinical assessment of study subject NDDO:NDDO_00000017 clinical assessment of study subject and partner NDDO:NDDO_00000020 telephone check assessment NDDO:NDDO_00000021 visit NDDO:NDDO_00000022 diagnostic data NDDO:NDDO_00000023 MRI image NDDO:NDDO_00000024 clinical data NDDO:NDDO_00000025 biomarker data NDDO:NDDO_00000027 PET image NDDO:NDDO_00000028 personal and social history data NDDO:NDDO_00000029 protocol data NDDO:NDDO_00000030 image data score NDDO:NDDO_00000035 biospecimen collection data NDDO:NDDO_00000036 Telephone visit NDDO:NDDO_00000037 Physical visit NDDO:NDDO_00000052 clinical assessment questionnaire NDDO:NDDO_00000056 Geriatric Depression Scale Assessment Questionnaire NDDO:NDDO_00000058 Symbol Digit Modalities Test (SDMT) NDDO:NDDO_00000059 MoCA score Montreal Cognitive Assessment (MoCA) NDDO:NDDO_00000060 Semantic Fluency Assessment NDDO:NDDO_00000061 Geriatric Depression Scale Assessment NDDO:NDDO_00000062 cognitive assessment NDDO:NDDO_00000063 http://purl.bioontology.org/ontology/SNOMEDCT/113091000 Magnetic resonance study MR - Magnetic resonance MRI MRI - Magnetic resonance imaging Magnetic resonance imaging (procedure) NMR - Nuclear magnetic resonance Magnetic Resonance Imaging (MRI) NDDO:NDDO_00000064 http://purl.bioontology.org/ontology/SNOMEDCT/82918005 PET scan PET - Positron emission tomography Positron emission tomography (procedure) Positron Emission Tomography (PET) NDDO:NDDO_00000065 demographic assessment NDDO:NDDO_00000066 education assessment NDDO:NDDO_00000067 personal history assessment NDDO:NDDO_00000068 adverse events assessment NDDO:NDDO_00000069 adverse events data NDDO:NDDO_00000070 neurological examination data NDDO:NDDO_00000071 cognitive assessment data NDDO:NDDO_00000073 blood sample data NDDO:NDDO_00000074 lumbar puncture data NDDO:NDDO_00000075 DNA data NDDO:NDDO_00000076 study subject NDDO:NDDO_00000077 study participant NDDO:NDDO_00000078 MRI image data score NDDO:NDDO_00000079 PET image data score NDDO:NDDO_00000080 medical device NDDO:NDDO_00000081 medical image device NDDO:NDDO_00000082 MRI scanner NDDO:NDDO_00000083 PET scanner NDDO:NDDO_00000085 image provider role 0 4 0 4 NDDO:NDDO_00000086 Semantic Fluency Assessment Score NDDO:NDDO_00000087 Montreal Cognitive Assessment (MoCA) Score 0 93 0 93 NDDO:NDDO_00000088 Symbol Digit Modalities Test Score NDDO:NDDO_00000089 Geriatric Depression (GDS-15) Score NDDO:NDDO_00000090 http://purl.bioontology.org/ontology/SNOMEDCT/273481004 Geriatric depression scale (assessment scale) GDS - Geriatric depression scale Geriatric Depression Scale (GDS-15) SNOMED CT 0.0 15.0 0.0 15.0 NDDO:NDDO_00000091 Geriatric Depression Scale (GDS-15) Datatype NDDO:NDDO_00000092 http://purl.bioontology.org/ontology/SNOMEDCT/443597000 Model of creative ability assessment scale Montreal Cognitive Assessment scale (MoCA scale) SNOMED CT NDDO:NDDO_00000093 Montreal Cognitive Assessment Datatype (MoCA Datatype) NDDO:NDDO_00000094 The scale for digit symbol substitution assessment has positive integer values that range from 0 to 93. Symbol Digit Modalities Test Scale NDDO:NDDO_00000095 Symbol Digit Modalities Datatype NDDO:NDDO_00000096 Semantic Fluency Assessment Scale 0.0 4.0 0.0 4.0 NDDO:NDDO_00000097 Semantic Fluency Datatype NDDO:NDDO_00000099 participant ID NDDO:NDDO_00000100 participant rooster ID NDDO:NDDO_00000101 site ID NDDO:NDDO_00000102 specification entity NDDO:NDDO_00000103 assessment scale NDDO:NDDO_00000105 visit specification NDDO:NDDO_00000106 person NDDO:NDDO_00000107 cohort NDDO:NDDO_00000108 Montreal Cognitive Assessment Questionnaire NDDO:NDDO_00000109 Semantic Fluency Assessment Questionnaire NDDO:NDDO_00000110 Symbol Digit Modalities Assessment Questionnaire NDDO:NDDO_00000111 Visit Code NDDO:NDDO_00000112 Visit Code Datatype NDDO:NDDO_00000113 cognitive assessment questionnaire NDDO:NDDO_00000114 study participant specification NDDO:NDDO_00000115 study participant occurence specification NDDO:NDDO_00000116 new study participant NDDO:NDDO_00000117 Age Datatype NDDO:NDDO_00000118 Marital Status Datatype NDDO:NDDO_00000119 Origin Protocol Datatype NDDO:NDDO_00000120 Race Datatype NDDO:NDDO_00000121 Sex Datatype NDDO:NDDO_00000160 adnigo lmci cohort NDDO:NDDO_00003000 vital signs data NDDO:NDDO_00003001 demographics data NDDO:NDDO_00003002 age data NDDO:NDDO_00003003 ethnicity data NDDO:NDDO_00003004 race data NDDO:NDDO_00003005 sex data NDDO:NDDO_00003006 education data NDDO:NDDO_00003007 personal history data NDDO:NDDO_00003008 marital status data NDDO:NDDO_00003014 cohort specification NDDO:NDDO_00003015 doctor NDDO:NDDO_10000007 follow-up study participant NDDO:NDDO_10000587 screening labs data NDDO:NDDO_10000605 medications data NDDO:NDDO_10000614 diagnostic summary data NDDO:NDDO_10000663 The goal of the ADNI study is to track the progression of the disease using biomarkers to assess the brain’s structure and function over the course of four disease states. ADNI1 study NDDO:NDDO_10000745 CN CN participants are the control subjects in the ADNI study. They show no signs of depression, mild cognitive impairment or dementia. Normal Aging or Cognitively Normal NDDO:NDDO_10000756 SMC SMC participants score within normal range for cognition (or CDR = 0) but indicate that they have a concern, and exhibit slight forgetfulness. The informant does not equate this as progressive memory impairment nor considers this as consistent forgetfulness. Significant Memory Concern NDDO:NDDO_10000767 EMCI Early Mild Cognitive Impairment (EMCI) NDDO:NDDO_10000792 LMCI http://purl.bioontology.org/ontology/RCTV2/28E3.00 http://purl.bioontology.org/ontology/SNOMEDCT/702955000 http://purl.obolibrary.org/obo/HP_0100543 Cognitive impairment (HPO) Cognitive impairment (RCTV2) Moderate cognitive impairment (SNOMEDCT) Late Mild Cognitive Impairment (LMCI) HPO RCTv2 SNOMEDCT NDDO:NDDO_10000854 study partner NDDO:NDDO_10000890 Participant ID Datatype NDDO:NDDO_10000925 Ethnicity Datatype NDDO:NDDO_10000971 ApoE4 http://purl.bioontology.org/ontology/SNOMEDCT/115519009 Apolipoprotein E4 NDDO:NDDO_10000978 Apolipoprotein E4 protein can have 0 alleles, which represent no risk of Alzheimer's desease up to two 2 alleles which represent severe risk of developing Alzheimer's desease. APOE4 Datatype NDDO:NDDO_10000994 Average FDG-PET of angular, temporal, and posterior cingulate NDDO:NDDO_10001003 Average PIB SUVR of frontal cortex, anterior cingulate, precuneus cortex, and parietal cortex NDDO:NDDO_10001012 Average AV45 SUVR of frontal, anterior cingulate, precuneus, and parietal cortex relative to the cerebellum NDDO:NDDO_10001021 CDR-SB http://scai.fraunhofer.de/AlzheimerOntology#clinical_dementia_rating http://www.semanticweb.org/ontologies/2012/0/Ontology1325521724189.owl#Clinical_Dementia_Rating_Scale-sum_of_boxes Clinical Dementia Rating Square of Boxes (CDR-SB) Assessment ADO CTO NDDO:NDDO_10001035 ADAS11 Alzheimers Disease Assessment (ADAS11) NDDO:NDDO_10001045 ADAS13 SNOMEDCT http://purl.bioontology.org/ontology/SNOMEDCT/714360001 Alzheimers Disease Assessment (ADAS13) NDDO:NDDO_10001057 MMSE http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C74982 A standardized and structured interview originally developed by Marshal Folstein, Susan Folstein and Paul McHugh (Journal of Psychiatric Research, 1975), which is used to evaluate an individual's cognitive function. Mini Mental State Exam (MMSE) National Cancer Institute Thesaurus NDDO:NDDO_10001070 RAVLT forgetting score NDDO:NDDO_10001073 Rey auditory verbal learning test (RAVLT) score NDDO:NDDO_10001077 RAVLT Forgetting Datatype NDDO:NDDO_10001085 RAVLT 5sum score NDDO:NDDO_10001092 RAVLT 5Sum Datatype NDDO:NDDO_10001100 FAQ http://purl.bioontology.org/ontology/SNOMEDCT/445885005 Functional Assessment SNOMEDCT NDDO:NDDO_10001122 ECog - Everyday Memory Score NDDO:NDDO_10001125 Everyday cognition (ECog) score NDDO:NDDO_10001129 ECog Memory Dataype NDDO:NDDO_10001137 ECog - Everyday Language Score NDDO:NDDO_10001144 ECog Language Datatype NDDO:NDDO_10001152 ECog - Everyday Visuospatial Ability Score NDDO:NDDO_10001159 ECog Visuospatial Ability Datatype NDDO:NDDO_10001167 ECog - Everyday Planing Score NDDO:NDDO_10001174 Ecog Planning Datatype NDDO:NDDO_10001182 ECog - Everyday Organization NDDO:NDDO_10001189 ECog Organization Datatype NDDO:NDDO_10001197 ECog - Everyday Divided Attention Score NDDO:NDDO_10001204 ECog Divided Attention Datatype NDDO:NDDO_10001212 ECog - Total Score NDDO:NDDO_10001219 ECog Total Datatype NDDO:NDDO_10001227 UCSF Ventricles NDDO:NDDO_10001236 UCSF Hippocampus NDDO:NDDO_10001245 UCSF WholeBrain NDDO:NDDO_10001254 UCSF Entorhinal NDDO:NDDO_10001263 UCSF Fusiform NDDO:NDDO_10001272 UCSF Med Temp NDDO:NDDO_10001281 UCSF ICV NDDO:NDDO_10001297 Exam Date Datatype NDDO:NDDO_10001312 Years From Baseline Datatype NDDO:NDDO_10001327 Months From Baseline Datatype NDDO:NDDO_10001362 RAVLT http://scai.fraunhofer.de/AlzheimerOntology#Rey_auditory_verbal_learning_test Rey Auditory Verbal Learning Test (RAVLT) ADO NDDO:NDDO_10001396 ECOG scale http://purl.bioontology.org/ontology/SNOMEDCT/273437007 Everyday Cognition questionnaire (assessment scale) everyday cognition scale Everyday Cognition questionnaire scale (ECOG scale) SNOMED CT NDDO:NDDO_10001410 http://purl.bioontology.org/ontology/SNOMEDCT/714338004 Everyday Cognition questionnaire score (observable entity) Everyday cognition (ECog) Assessment SNOMEDCT NDDO:NDDO_10001443 Rey Auditory Verbal Learning Test score scale (RAVLT scale) NDDO:NDDO_10001452 MMSE scale Mini-Mental State Exam Scale has positive integer values that range from 0 to 30. Mini Mental State Exam Scale (MMSE scale) NDDO:NDDO_10001463 Functional Assessment Questionnaire scale (FAQ scale) NDDO:NDDO_10001472 CDR scale http://purl.bioontology.org/ontology/SNOMEDCT/273367002 DRS - Clinical dementia rating scale Dementia rating scale CDR - Clinical dementia rating scale Clinical dementia rating scale (assessment scale) Clinical Dementia Rating Scale has real values that range from 0 to 1. Clinical dementia rating scale (CDR scale) SNOMED CT NDDO:NDDO_10001489 ADAS scale http://purl.bioontology.org/ontology/SNOMEDCT/273269001 ADAS - Alzheimer's disease assessment scale Alzheimer's disease assessment scale (assessment scale) Alzheimer disease assessment scale Alzheimers disease assessment scale (ADAS scale) SNOMED CT NDDO:NDDO_10001798 Alzheimers Disease assessment (ADAS13) score NDDO:NDDO_10001801 Alzheimers Disease assessment (ADAS) score NDDO:NDDO_10001805 ADAS 13 Datatype NDDO:NDDO_10001825 Alzheimers Disease assessment (ADAS11) score NDDO:NDDO_10001832 ADAS 11 Datatype 1.0 30.0 1.0 30.0 NDDO:NDDO_10001852 Mini mental state exam (MMSE) score NDDO:NDDO_10001859 MMSE Datatype NDDO:NDDO_10001963 functional and behavioral assesment score NDDO:NDDO_10001978 Clinical Dementia Rating Square of Boxes (CDR-SB) score NDDO:NDDO_10001985 CDSRB Datatype NDDO:NDDO_10002026 Functional Assessment Questionnaire (FAQ) score NDDO:NDDO_10002033 FAQ Datatype NDDO:NDDO_10002075 Education Datatype NDDO:NDDO_10002147 Participant Roster ID Datatype NDDO:NDDO_10002162 Site ID Datatype NDDO:NDDO_10002170 study phase role NDDO:NDDO_10002185 subject origin phase NDDO:NDDO_10002194 data collection phase NDDO:NDDO_10002218 ANART Scale http://purl.bioontology.org/ontology/SNOMEDCT/273640001 American National Reading Test NART - National adult reading test National adult reading test (assessment scale) American National Reading Test Scale (ANART Scale) SNOMED CT NDDO:NDDO_10002233 http://purl.bioontology.org/ontology/SNOMEDCT/273330005 Boston naming test (assessment scale) Boston Naming Test Boston Naming Test Scale SNOMED CT NDDO:NDDO_10002255 The scale for clock drawing assessment goes from 0 to 5 points. 1 point - Approximately circular face. 1 point - Symmetry of number placement. 1 point - Correctness of numbers. All numbers must be present and in the correct order, and inside the face of the clock. 1 point - Presence of two hands. Two hands (and only two hands) must be present on the clock face to receive credit for this item. 1 point - Presence of two hands set to ten after eleven. Total: 5 points. Clock Drawing Assessment Scale NDDO:NDDO_10002296 http://purl.bioontology.org/ontology/SNOMEDCT/273499007 Hachinski Ischemia Scale Hachinski Ischemia Scale NDDO:NDDO_10002307 Logical memory assessment scale has positive integer values that range from 0 to 25. Logical Memory Assessment Scale NDDO:NDDO_10002317 Depending on the frequence and severity, the NPI total score for each of the thirteen categories can have positive integer values ranging from 1 to 12. Neuropsychiatric Inventory Scale NDDO:NDDO_10002327 http://purl.bioontology.org/ontology/SNOMEDCT/273882000 Trail making test (assessment scale) TMT - Trail making test Trail Making Assessment Scale SNOMED CT NDDO:NDDO_10002340 Cell Immortalization Data NDDO:NDDO_10002355 RNA data NDDO:NDDO_10002382 American National Reading Test score NDDO:NDDO_10002389 ANART Datatype NDDO:NDDO_10002395 American National Reading Test 0.0 30.0 0.0 30.0 NDDO:NDDO_10002409 Boston Naming Test Score NDDO:NDDO_10002416 Boston Naming Test Datatype NDDO:NDDO_10002422 Boston Naming Test 0.0 5.0 0.0 5.0 NDDO:NDDO_10002535 Clock Drawing Assessment Score NDDO:NDDO_10002542 Clock Drawing Datatype NDDO:NDDO_10002548 http://www.cognitiveatlas.org/ontology/cogat.owl#CAO_01611 The participant is asked to draw a clock showing a specific time. The task is scored based on the number of features correctly drawn. Clock Drawing Assessment NDDO:NDDO_10002661 Trail Making Part A Score NDDO:NDDO_10002668 Trail Making Assessment Part A 0.0 25.0 0.0 25.0 NDDO:NDDO_10002682 Logical Memory Assessment Score NDDO:NDDO_10002689 Logical Memory Assessment NDDO:NDDO_10002739 Logical Memory II Score NDDO:NDDO_10002746 Logical Memory II Datatype NDDO:NDDO_10002752 Logical Memory Assessment II NDDO:NDDO_10002760 Logical Memory I Score NDDO:NDDO_10002767 Logical Memory I Datatype NDDO:NDDO_10002773 Logical Memory Assessment I NDDO:NDDO_10002781 Trail Making Part B Score NDDO:NDDO_10002788 Trail Making Assessment Part B 0 18 0 18 NDDO:NDDO_10002829 Hachinski Ischemia Score NDDO:NDDO_10002836 Hachinski Ischemia Datatype NDDO:NDDO_10002842 Hachinski assessment 0 5 0 5 1 3 1 3 1 12 1 12 1 4 1 4 NDDO:NDDO_10002892 Neuropsychiatric Inventory (NPI) score NDDO:NDDO_10003009 http://scai.fraunhofer.de/AlzheimerOntology#Neuropsychiatric_inventory NPI Neuropsychiatric Disturbance Neuropsychiatric Inventory Assessment NDDO:NDDO_10003053 NPI Datatype NDDO:NDDO_10003061 NPI Aberrant Motor Behaviour Score NDDO:NDDO_10003068 NPI Aberrant Motor Behaviour Datatype NDDO:NDDO_10003076 NPI Agitation Aggresion Score NDDO:NDDO_10003083 NPI Agitation Aggresion Datatype NDDO:NDDO_10003091 NPI Anxiety Score NDDO:NDDO_10003098 NPI Anxiety Datatype NDDO:NDDO_10003106 NPI Apathy Score NDDO:NDDO_10003113 NPI Apathy Datatype NDDO:NDDO_10003121 NPI Appetite And Eating Changes Score NDDO:NDDO_10003128 NPI Appetite and Eating Changes Datatype NDDO:NDDO_10003136 NPI Delusions Score NDDO:NDDO_10003143 NPI Delusions Datatype NDDO:NDDO_10003151 NPI Depression Score NDDO:NDDO_10003158 NPI Depression Datatype NDDO:NDDO_10003166 NPI Disinhibition Score NDDO:NDDO_10003173 NPI Disinhibition Datatype NDDO:NDDO_10003181 NPI Euphoria Score NDDO:NDDO_10003188 NPI Euphoria Datatype NDDO:NDDO_10003196 NPI Hallucinations Score NDDO:NDDO_10003203 NPI Euphoria Datatype NPI Hallucinations Datatype NDDO:NDDO_10003211 NPI Irritability Score NDDO:NDDO_10003218 NPI Irritability Datatype NDDO:NDDO_10003226 NPI Night Time Behaviour Score NDDO:NDDO_10003233 NPI Night Time Behaviour Datatype NDDO:NDDO_10003241 NPI Total Score NDDO:NDDO_10003248 NPI Total Datatype NDDO:NDDO_10003256 Diagnosis Datatype NDDO:NDDO_10003331 ADAS Datatype NDDO:NDDO_10003618 Logical Memory Datatype NDDO:NDDO_10003717 MRI Features Datatype NDDO:NDDO_10003726 UCSF Entorhinal Datatype NDDO:NDDO_10003741 UCSF Fusiform Datatype NDDO:NDDO_10003756 UCSF Hippocampus Datatype NDDO:NDDO_10003771 UCSF ICV Datatype NDDO:NDDO_10003786 UCSF Med Temp Datatype NDDO:NDDO_10003801 UCSF Ventricles Datatype NDDO:NDDO_10003816 UCSF Whole Brain Datatype NDDO:NDDO_10003846 RAVLT Datatype NDDO:NDDO_10004093 ECog Datatype NDDO:NDDO_10004251 PET Datatype NDDO:NDDO_10004260 AV45 Datatype NDDO:NDDO_10004275 FDG PET Datatype NDDO:NDDO_10004290 PIB SUVR Datatype NDDO:NDDO_10004433 Collection Protocol Datatype NDDO:NDDO_10004440 Collection Protocol Data NDDO:NDDO_10004455 Origin Protocol Data NDDO:NDDO_10004592 RAVLT learning score NDDO:NDDO_10004599 RAVLT Learning Datatype NDDO:NDDO_10004622 RAVLT Forgetting Percentage Datatype NDDO:NDDO_10004629 RAVLT Forgetting Percentage Score NDDO:NDDO_10020005 Functional Assessment Questionnaire NDDO:NDDO_10020006 Neuropsychiatric Inventory Assessment Questionnaire NDDO:NDDO_10020007 Alzheimer’s Disease Assessment (ADAS11) Questionnaire NDDO:NDDO_10020008 Alzheimer’s Disease Assessment (ADAS13) Questionnaire NDDO:NDDO_10020009 American National Reading Test Questionnaire NDDO:NDDO_10020010 Boston Naming Test Questionnaire NDDO:NDDO_10020011 Clock Drawing Assessment Questionnaire NDDO:NDDO_10020012 Logical Memory Assessment Questionnaire NDDO:NDDO_10020013 Logical Memory Assessment I Questionnaire NDDO:NDDO_10020014 Logical Memory Assessment II Questionnaire NDDO:NDDO_10020015 Mini Mental State Exam (MMSE) Questionnaire NDDO:NDDO_10020016 Rey Auditory Verbal Learning Test (RAVLT) Questionnaire NDDO:NDDO_10020017 Trail Making Assessment Questionnaire NDDO:NDDO_10020018 Trail Making Assessment Part A Questionnaire NDDO:NDDO_10020019 Trail Making Assessment Part B Questionnaire NDDO:NDDO_10020020 Hachinski Assessment Questionnaire NDDO:NDDO_10020021 Clinical Dementia Rating Square of Boxes (CDR-SB) Assessment Questionnaire NDDO:NDDO_10020022 Everyday cognition (ECog) Assessment Questionnaire NDDO:NDDO_10030086 medications assessement NDDO:NDDO_10030098 diagnostic summary assessment NDDO:NDDO_10030111 ADNI2 study NDDO:NDDO_10030112 ADNIGO study NDDO:NDDO_10030113 ADNI1 visit NDDO:NDDO_10030114 ADNIGO visit NDDO:NDDO_10030116 ADNI2 visit NDDO:NDDO_10030117 ADNI1 screen visit NDDO:NDDO_10030118 ADNI1 baseline visit NDDO:NDDO_10030119 ADNI1 month 6 visit NDDO:NDDO_10030120 ADNI1 month 12 visit NDDO:NDDO_10030121 ADNI1 month 18 visit NDDO:NDDO_10030122 ADNI1 month 24 visit NDDO:NDDO_10030123 ADNI1 month 30 visit NDDO:NDDO_10030124 ADNI1 month 36 visit NDDO:NDDO_10030125 ADNIGO new participant visit NDDO:NDDO_10030126 ADNIGO follow-up participant NDDO:NDDO_10030128 ADNIGO visit 1 follow-up participant NDDO:NDDO_10030129 ADNIGO visit 2 follow-up participant NDDO:NDDO_10030130 ADNIGO visit 3 follow-up participant NDDO:NDDO_10030131 ADNIGO visit 4 follow-up participant NDDO:NDDO_10030132 ADNIGO screen visit new participant NDDO:NDDO_10030133 ADNIGO baseline visit new participant NDDO:NDDO_10030134 ADNIGO month 3 visit new participant NDDO:NDDO_10030135 ADNIGO month 6 visit new participant NDDO:NDDO_10030136 ADNIGO month 12 visit new participant NDDO:NDDO_10030137 ANDIGO month 18 visit new participant NDDO:NDDO_10030138 ADNI2 new participant visit NDDO:NDDO_10030139 ADNI2 follow-up participant visit NDDO:NDDO_10030140 ADNI2 initial visit follow-up participant NDDO:NDDO_10030141 ADNI2 ongoing 6 month interim follow-up participant NDDO:NDDO_10030142 ADNI2 ongoing annual interim follow-up participant NDDO:NDDO_10030143 ADNI2 screen visit new participant NDDO:NDDO_10030145 ADNI2 baseline visit new participant NDDO:NDDO_10030146 ADNI2 month 3 visit new participant NDDO:NDDO_10030147 ADNI2 month 6 visit new participant NDDO:NDDO_10030148 ADNI2 month 12 visit new participant NDDO:NDDO_10030149 ADNI2 month 18 visit new participant NDDO:NDDO_10030150 ADNI2 month 24 visit new participant NDDO:NDDO_10030151 ADNI2 ongoing 6 month interim new participant NDDO:NDDO_10030152 ADNI2 ongoing annual interim new participant NDDO:NDDO_10030153 ADNI1 cohort NDDO:NDDO_10030154 adni1 cn cohort NDDO:NDDO_10030155 adni1 mci cohort NDDO:NDDO_10030156 adni1 ad cohort NDDO:NDDO_10030157 ADNIGO cohort NDDO:NDDO_10030158 adnigo cn cohort NDDO:NDDO_10030159 adnigo emci cohort NDDO:NDDO_10030161 adnigo ad cohort NDDO:NDDO_10030162 ADNI2 cohort NDDO:NDDO_10030163 adni2 cn cohort NDDO:NDDO_10030164 adni2 smc cohort NDDO:NDDO_10030165 adni2 emci cohort NDDO:NDDO_10030166 adni2 lmci cohort NDDO:NDDO_10030167 adni2 ad cohort NDDO:NDDO_200002422 MDS-UPDRS Part III Positive Integer Datatype NDDO:NDDO_200002424 VMAT-2 PET image data score NDDO:NDDO_200002425 DaT SPECT image data score NDDO:NDDO_200002427 Florbetaben PET image data score NDDO:NDDO_200002428 Diffusion Tensor image data score NDDO:NDDO_20000362 Unified Parkinson's Disease Rating Scale Questionnaire (UPDRS) MDS-UPDRS A standardized rating scale originally developed by S. Fahn, R. Elton, and other members of the UPDRS Development Committee in 1987 which is used to evaluate the status of a patient's Parkinson's disease. This instrument is made up of 6 parts consisting of a mental, behavior and mood section, an activities of daily living section, a motor examination, and questions concerning any complications with the patient's current therapy as well as modified versions of the Hoehn and Yahr Staging assessment and the Schwab and England Activities of Daily Living Scale. Each question is either scored with a 0 for a 'no' response and 1 for a 'yes' response or with a 0-4 point scale. (NCIT) NCIT Unified Parkinsons Disease Rating Scale (UPRDS) Assessment NDDO:NDDO_20000376 Modified Schwab & England Activities of Daily Living (ADL) NDDO:NDDO_20000385 The University of Pennsylvania Smell Test 0 40 0 40 NDDO:NDDO_200003850 The University of Pennsylvania Smell Test Datatype NDDO:NDDO_20000403 Range from 0-40 The University of Pennsylvania Smell Test Scale NDDO:NDDO_20000407 The University of Pennsylvania Smell Test Score NDDO:NDDO_20000433 Clinical Diagnosis and Management Assessment NDDO:NDDO_20000442 Diagnostic assessment NDDO:NDDO_20000451 This scale is recommended to assess daytime sleepiness. PDO there are 8 different situations rated from 0-3. Total score from 0-24. Epworth Sleepiness Scale (ESS scale) NDDO:NDDO_20000479 WMS-III Letter-Number Sequencing Test NDDO:NDDO_20000488 An assessment tool to ascertain verbal learning and memory skills that is well tolerated by those with moderate to severe dementia. (NCIT) NCIT Hopkins Verbal Learning Test-Revised (HVLT-R) NDDO:NDDO_20000500 http://purl.bioontology.org/ontology/SNMI/P9-01400 Benton visual behaviour test (CTV3) Benton visual retention test (SNOMED CT) Psychologic test, Benton visual retention test (SNMI) Benton Judgment of Line Orientation Test NDDO:NDDO_20000527 An instrument for measuring anxiety. It is designed to differentiate between temporary "state anxiety" and general, long-standing "trait anxiety". (Copyright Mind Garden, Inc.) (NCIT) State-Trait Anxiety Inventory (STAI-Y) NDDO:NDDO_20000538 REM Sleep Behavior Disorder Screening (RBDSQ) NDDO:NDDO_20000547 Impulsive-Compulsive Disorder (QUIP-S) Assessment NDDO:NDDO_20000556 Cognitive Categorization assessment NDDO:NDDO_20000565 Physical Activity Scale for the Elderly (PASE) Assessment NDDO:NDDO_20000574 medical history data NDDO:NDDO_20000583 family history data NDDO:NDDO_20000624 MDS-UPDRS Part I Positive Integer Datatype NDDO:NDDO_20000627 MDS-UPDRS Positive Integer Datatype NDDO:NDDO_20000633 MDS-UPDRS Part II Positive Integer Datatype NDDO:NDDO_20000642 clinical laboratory assesment NDDO:NDDO_20000657 Dopamine Transporter (DaT) SPECT Imaging NDDO:NDDO_20000666 VMAT-2 PET imaging NDDO:NDDO_20000675 Florbetaben PET imaging NDDO:NDDO_20000700 Structural MRI image score NDDO:NDDO_20000707 Structural MRI image NDDO:NDDO_20000715 Parkinson disease (PD) NDDO:NDDO_20000718 participant stage NDDO:NDDO_20000724 SWEDD NDDO:NDDO_20000733 healthy control (HC) NDDO:NDDO_20000742 Prodromal NDDO:NDDO_20000751 genetic cohort NDDO:NDDO_20000760 PD patient with LRRK2 mutation (LRRK2+) NDDO:NDDO_20000769 unaffected individual NDDO:NDDO_20000778 PD patient with GBA mutation (GBA+) NDDO:NDDO_20000841 unclassified NDDO:NDDO_20000847 genetic registry NDDO:NDDO_20000865 Pain and other sensations Score NDDO:NDDO_20000868 MDS-UPDRS Part I Assessment Score NDDO:NDDO_20000872 http://www.semanticweb.org/ontologies/2011/1/Ontology1296772722296.owl#MDS-UPDRS PDON Range from 0-4 0: Normal 1: Slight 2: Mild 3: Moderate 4: Severe MDS-UPDRS Scale NDDO:NDDO_20000943 brain volume regions NDDO:NDDO_20000952 3rd_Ventricle NDDO:NDDO_20000961 4th_Ventricle NDDO:NDDO_20000970 Right_Accumbens_Area NDDO:NDDO_20000979 Left_Accumbens_Area NDDO:NDDO_20000988 Right_Amygdala NDDO:NDDO_20000997 Left_Amygdala NDDO:NDDO_20001006 Brain_Stem NDDO:NDDO_20001015 Right_Caudate NDDO:NDDO_20001024 Left_Caudate NDDO:NDDO_20001033 Right_Cerebellum_Exterior NDDO:NDDO_20001042 Left_Cerebellum_Exterior NDDO:NDDO_20001051 Right_Cerebellum_White_Matter NDDO:NDDO_20001060 Left_Cerebellum_White_Matter NDDO:NDDO_20001069 Right_Cerebral_White_Matter NDDO:NDDO_20001078 Left_Cerebral_White_Matter NDDO:NDDO_20001087 CSF NDDO:NDDO_20001096 Right_Hippocampus NDDO:NDDO_20001105 Left_Hippocampus NDDO:NDDO_20001114 Right_Inf_Lat_Vent NDDO:NDDO_20001123 Left_Inf_Lat_Vent NDDO:NDDO_20001132 Right_Lateral_Ventricle NDDO:NDDO_20001141 Left_Lateral_Ventricle NDDO:NDDO_20001150 Right_Pallidum NDDO:NDDO_20001159 Left_Pallidum NDDO:NDDO_20001168 Right_Putamen NDDO:NDDO_20001177 Left_Putamen NDDO:NDDO_20001186 Right_Thalamus_Proper NDDO:NDDO_20001195 Left_Thalamus_Proper NDDO:NDDO_20001204 Right_Ventral_DC NDDO:NDDO_20001213 Left_Ventral_DC NDDO:NDDO_20001222 Optic_Chiasm NDDO:NDDO_20001231 Cerebellar_Vermal_Lobules_I-V NDDO:NDDO_20001240 Cerebellar_Vermal_Lobules_VI-VII NDDO:NDDO_20001249 Cerebellar_Vermal_Lobules_VIII-X NDDO:NDDO_20001258 Left_Basal_Forebrain NDDO:NDDO_20001267 Right_Basal_Forebrain NDDO:NDDO_20001276 Right_ACgG_anterior_cingulate_gyrus NDDO:NDDO_20001285 Left_ACgG_anterior_cingulate_gyrus NDDO:NDDO_20001294 Right_AIns_anterior_insula NDDO:NDDO_20001303 Left_AIns_anterior_insula NDDO:NDDO_20001312 Right_AOrG_anterior_orbital_gyrus NDDO:NDDO_20001321 Left_AOrG_anterior_orbital_gyrus NDDO:NDDO_20001330 Right_AnG_angular_gyrus NDDO:NDDO_20001339 Left_AnG_angular_gyrus NDDO:NDDO_20001348 Right_Calc_calcarine_cortex NDDO:NDDO_20001357 Left_Calc_calcarine_cortex NDDO:NDDO_20001366 Right_CO_central_operculum NDDO:NDDO_20001375 Left_CO_central_operculum NDDO:NDDO_20001384 Right_Cun_cuneus NDDO:NDDO_20001393 Left_Cun_cuneus NDDO:NDDO_20001402 Right_Ent_entorhinal_area NDDO:NDDO_20001411 Left_Ent_entorhinal_area NDDO:NDDO_20001420 Right_FO_frontal_operculum NDDO:NDDO_20001429 Left_FO_frontal_operculum NDDO:NDDO_20001438 Right_FRP_frontal_pole NDDO:NDDO_20001447 Left_FRP_frontal_pole NDDO:NDDO_20001456 Right_FuG_fusiform_gyrus NDDO:NDDO_20001465 Left_FuG_fusiform_gyrus NDDO:NDDO_20001474 Right_GRe_gyrus_rectus NDDO:NDDO_20001483 Left_GRe_gyrus_rectus NDDO:NDDO_20001492 Right_IOG_inferior_occipital_gyrus NDDO:NDDO_20001501 Left_IOG_inferior_occipital_gyrus NDDO:NDDO_20001510 Right_ITG_inferior_temporal_gyrus NDDO:NDDO_20001519 Left_ITG_inferior_temporal_gyrus NDDO:NDDO_20001528 Right_LiG_lingual_gyrus NDDO:NDDO_20001537 Left_LiG_lingual_gyrus NDDO:NDDO_20001546 Right_LOrG_lateral_orbital_gyrus NDDO:NDDO_20001555 Left_LOrG_lateral_orbital_gyrus NDDO:NDDO_20001564 Right_MCgG_middle_cingulate_gyrus NDDO:NDDO_20001573 Left_MCgG_middle_cingulate_gyrus NDDO:NDDO_20001582 Right_MFC_medial_frontal_cortex NDDO:NDDO_20001591 Left_MFC_medial_frontal_cortex NDDO:NDDO_20001600 Right_MFG_middle_frontal_gyrus NDDO:NDDO_20001609 Left_MFG_middle_frontal_gyrus NDDO:NDDO_20001618 Right_MOG_middle_occipital_gyrus NDDO:NDDO_20001627 Left_MOG_middle_occipital_gyrus NDDO:NDDO_20001636 Right_MOrG_medial_orbital_gyrus NDDO:NDDO_20001645 Left_MOrG_medial_orbital_gyrus NDDO:NDDO_20001654 Right_MPoG_postcentral_gyrus_medial_segment NDDO:NDDO_20001663 Left_MPoG_postcentral_gyrus_medial_segment NDDO:NDDO_20001672 Right_MPrG_precentral_gyrus_medial_segment NDDO:NDDO_20001681 Left_MPrG_precentral_gyrus_medial_segment NDDO:NDDO_20001690 Right_MSFG_superior_frontal_gyrus_medial_segment NDDO:NDDO_20001699 Left_MSFG_superior_frontal_gyrus_medial_segment NDDO:NDDO_20001708 Right_MTG_middle_temporal_gyrus NDDO:NDDO_20001717 Left_MTG_middle_temporal_gyrus NDDO:NDDO_20001726 Right_OCP_occipital_pole NDDO:NDDO_20001735 Left_OCP_occipital_pole NDDO:NDDO_20001744 Right_OFuG_occipital_fusiform_gyrus NDDO:NDDO_20001753 Left_OFuG_occipital_fusiform_gyrus NDDO:NDDO_20001762 Right_OpIFG_opercular_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20001771 Left_OpIFG_opercular_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20001780 Right_OrIFG_orbital_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20001789 Left_OrIFG_orbital_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20001798 Right_PCgG_posterior_cingulate_gyrus NDDO:NDDO_20001807 Left_PCgG_posterior_cingulate_gyrus NDDO:NDDO_20001816 Right_PCu_precuneus NDDO:NDDO_20001825 Left_PCu_precuneus NDDO:NDDO_20001834 Right_PHG_parahippocampal_gyrus NDDO:NDDO_20001843 Left_PHG_parahippocampal_gyrus NDDO:NDDO_20001852 Right_PIns_posterior_insula NDDO:NDDO_20001861 Left_PIns_posterior_insula NDDO:NDDO_20001870 Right_PO_parietal_operculum NDDO:NDDO_20001879 Left_PO_parietal_operculum NDDO:NDDO_20001888 Right_PoG_postcentral_gyrus NDDO:NDDO_20001897 Left_PoG_postcentral_gyrus NDDO:NDDO_20001906 Right_POrG_posterior_orbital_gyrus NDDO:NDDO_20001915 Left_POrG_posterior_orbital_gyrus NDDO:NDDO_20001924 Right_PP_planum_polare NDDO:NDDO_20001933 Left_PP_planum_polare NDDO:NDDO_20001942 Right_PrG_precentral_gyrus NDDO:NDDO_20001951 Left_PrG_precentral_gyrus NDDO:NDDO_20001960 Right_PT_planum_temporale NDDO:NDDO_20001969 Left_PT_planum_temporale NDDO:NDDO_20001978 Right_SCA_subcallosal_area NDDO:NDDO_20001987 Left_SCA_subcallosal_area NDDO:NDDO_20001996 Right_SFG_superior_frontal_gyrus NDDO:NDDO_20002005 Left_SFG_superior_frontal_gyrus NDDO:NDDO_20002014 Right_SMC_supplementary_motor_cortex NDDO:NDDO_20002023 Left_SMC_supplementary_motor_cortex NDDO:NDDO_20002032 Right_SMG_supramarginal_gyrus NDDO:NDDO_20002041 Left_SMG_supramarginal_gyrus NDDO:NDDO_20002050 Right_SOG_superior_occipital_gyrus NDDO:NDDO_20002059 Left_SOG_superior_occipital_gyrus NDDO:NDDO_20002068 Right_SPL_superior_parietal_lobule NDDO:NDDO_20002077 Left_SPL_superior_parietal_lobule NDDO:NDDO_20002086 Right_STG_superior_temporal_gyrus NDDO:NDDO_20002095 Left_STG_superior_temporal_gyrus NDDO:NDDO_20002104 Right_TMP_temporal_pole NDDO:NDDO_20002113 Left_TMP_temporal_pole NDDO:NDDO_20002122 Right_TrIFG_triangular_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20002131 Left_TrIFG_triangular_part_of_the_inferior_frontal_gyrus NDDO:NDDO_20002140 Right_TTG_transverse_temporal_gyrus NDDO:NDDO_20002149 Left_TTG_transverse_temporal_gyrus NDDO:NDDO_20002158 CAUDATE_R NDDO:NDDO_20002167 CAUDATE_L NDDO:NDDO_20002176 PUTAMEN_R NDDO:NDDO_20002185 PUTAMEN_L NDDO:NDDO_20002194 MCATOT NDDO:NDDO_20002203 AGG_RIGIDITY NDDO:NDDO_20002212 AGG_TREMOR NDDO:NDDO_20002221 SUM_LEFT NDDO:NDDO_20002230 SUM_RIGHT NDDO:NDDO_20002239 gait assessment NDDO:NDDO_20002318 A standardized rating scale used to assess an individual's general level of daytime sleepiness. (NCIT) NCIT Epworth sleepingness scale assessment (ESS) NDDO:NDDO_20002341 MDS-UPDRS Part IV NDDO:NDDO_20002344 MDS-UPDRS NDDO:NDDO_20002359 MDS-UPDRS Part III NDDO:NDDO_20002368 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C121298 A rating scale included in the Behavior Assessment System for Children that measures the subject's ability to follow through or complete simple daily tasks. (NCIT) NCIT Range from 0%-100% activities of daily living scale NDDO:NDDO_20002400 http://purl.bioontology.org/ontology/MESH/D056324 DTI Diffusion Tensor Imaging (DTI) http://doe-generated-ontology.com/OntoAD#C1537007 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Diffusion_Tensor_Imaging NDDO:NDDO_20002434 The mission of PPMI is to identify one or more biomarkers of Parkinson’s disease (PD) progression, a critical next step in the development of new and better treatments for PD. PPMI will establish a comprehensive, standardized, longitudinal PD data and biological sample repository that will be made available to the research community. PPMI study NDDO:NDDO_20002479 urine sampling NDDO:NDDO_20002499 structural MR imaging http://doe-generated-ontology.com/OntoAD#AD000411 NDDO:NDDO_20002517 Scales for Outcomes in Parkinsons Disease Assessment SCOPA-AUT NDDO:NDDO_20002526 skin biopsy NDDO:NDDO_20002556 Diffusion Tensor image NDDO:NDDO_20002571 Florbetaben PET image NDDO:NDDO_20002603 DaT SPECT image NDDO:NDDO_20002618 VMAT-2 PET image NDDO:NDDO_20002690 Epworth Sleepiness (ESS) Score NDDO:NDDO_20002711 Modified Schwab & England Activities of Daily Living Score NDDO:NDDO_20002816 physical state data NDDO:NDDO_20002831 biological sample NDDO:NDDO_20002855 Time spent with dyskinesias Score NDDO:NDDO_20002858 MDS-UPDRS Part IV Assessment Score NDDO:NDDO_20002870 Functional impact of dyskinesias Score NDDO:NDDO_20002885 http://purl.bioontology.org/ontology/RCD/X7ABI RCD/X7ABI urine sample NDDO:NDDO_20002902 http://purl.bioontology.org/ontology/RCD/X7AAG RCD/X7AAG skin sample NDDO:NDDO_20002919 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17610 http://purl.bioontology.org/ontology/RCD/X7ADl NCIT RCD/X7ADl blood sample NDDO:NDDO_20002932 Time spent in the off state Score NDDO:NDDO_20002956 WMS-III Letter-Number Sequencing Test Score NDDO:NDDO_20002977 range from 0-21 WMS-III Letter-Number Sequencing Test Scale NDDO:NDDO_20003032 MDS-UPDRS Part IV Positive Integer Datatype NDDO:NDDO_20003041 Rigidity - Neck Score NDDO:NDDO_20003050 MDS-UPDRS Part III Assessment Score 0 4 NDDO:NDDO_20003056 Functional impact of dyskinesias Datatype 0 4 NDDO:NDDO_20003095 Pain and other sensations Datatype 0 4 NDDO:NDDO_20003134 Complexity of motor fluctuations Datatype NDDO:NDDO_20003147 Complexity of motor fluctations Score 0 4 NDDO:NDDO_20003173 Time spent in the OFF state Datatype 0 4 NDDO:NDDO_20003212 Painful OFF-state dystonia Datatype NDDO:NDDO_20003225 Painful off-state dystonia Score 0 4 NDDO:NDDO_20003251 Functional impact of fluctuations Datatype NDDO:NDDO_20003264 Functional imapct of fluctations Score 0 4 NDDO:NDDO_20003290 Speech Part II Datatype NDDO:NDDO_20003303 Speech Part II Score 0 4 NDDO:NDDO_20003329 Sleep problems Datatype NDDO:NDDO_20003342 Sleep problems Score 0 4 NDDO:NDDO_20003368 Daytime sleepiness Datatype NDDO:NDDO_20003381 Daytime sleepiness Score 0 4 NDDO:NDDO_20003407 Hallucinations and psychosis Datatype NDDO:NDDO_20003420 Hallucinations and psychosis Score 0 4 NDDO:NDDO_20003446 Depressed mood Datatype NDDO:NDDO_20003459 Depressed mood Score 0 4 NDDO:NDDO_20003485 Handwriting Datatype NDDO:NDDO_20003498 Handwriting Score 0 4 NDDO:NDDO_20003524 Doing hobbies and other activities Datatype NDDO:NDDO_20003537 Doing hobbies and other activities Score 0 4 NDDO:NDDO_20003563 Time spent with dyskinesias Datatype 0 4 NDDO:NDDO_20003602 Freezing Datatype NDDO:NDDO_20003615 Freezing Score NDDO:NDDO_20003641 Who is filling out questionnaire Datatype NDDO:NDDO_20003650 Who is filling out questionnaire Score 0 4 NDDO:NDDO_20003664 Light headedness on standing Datatype NDDO:NDDO_20003677 Light headedness on standing Score 0 4 NDDO:NDDO_20003703 Apathy Datatype NDDO:NDDO_20003716 Apathy Score 0 4 NDDO:NDDO_20003742 Features of DDS Datatype NDDO:NDDO_20003755 Features of DDS Score 0 4 NDDO:NDDO_20003781 Walking and balance Datatype NDDO:NDDO_20003794 Walking and balance Score 0 4 NDDO:NDDO_20003820 Turning in bed Datatype NDDO:NDDO_20003833 Turning in bed Score 0 4 NDDO:NDDO_20003859 Anxious mood Datatype NDDO:NDDO_20003872 Anxious mood Score 0 4 NDDO:NDDO_20003898 Tremor Datatype NDDO:NDDO_20003911 Tremor Score 0 4 NDDO:NDDO_20003937 Getting out of bed Datatype NDDO:NDDO_20003950 Getting out of bed Score NDDO:NDDO_20003976 Source of information Datatype NDDO:NDDO_20003985 Source of information Score 0 4 NDDO:NDDO_20003999 Cognitive impairment Datatype NDDO:NDDO_20004012 Cognitive impairment Score 0 4 NDDO:NDDO_20004038 Saliva and drooling Datatype NDDO:NDDO_20004051 Saliva and drooling Score 0 4 NDDO:NDDO_20004077 Eating tasks Datatype NDDO:NDDO_20004090 Eating tasks Score 0 4 NDDO:NDDO_20004116 Chewing and swallowing Datatype NDDO:NDDO_20004129 Chewing and swallowing Score 0 4 NDDO:NDDO_20004155 Dressing Datatype NDDO:NDDO_20004168 Dressing Score 0 4 NDDO:NDDO_20004194 Hygiene Datatype NDDO:NDDO_20004207 Hygiene Score 0 4 NDDO:NDDO_20004233 Constipation problems Datatype NDDO:NDDO_20004246 Constipation problems Score 0 4 NDDO:NDDO_20004272 Urinary problems Datatype NDDO:NDDO_20004285 Urinary problems Score 0 4 NDDO:NDDO_20004311 Fatigue Datatype NDDO:NDDO_20004324 Fatigue Score NDDO:NDDO_20004359 Brain region volume Datatype 0 4 NDDO:NDDO_20004368 Rest tremor amplitude - LLE Datatype NDDO:NDDO_20004401 Rest tremor amplitude - LLE Score 0 4 NDDO:NDDO_20004411 Rigidity - Neck Datatype 0 4 NDDO:NDDO_20004454 Posture Datatype NDDO:NDDO_20004487 Posture Score 0 4 NDDO:NDDO_20004497 Global spontaneity of movement Datatype NDDO:NDDO_20004530 Global spontaneity of movement Score 0 4 NDDO:NDDO_20004540 Postural stability Datatype NDDO:NDDO_20004573 Postural stability Score 0 5 NDDO:NDDO_20004583 Hoehn and Yahr Stage Datatype NDDO:NDDO_20004592 http://www.semanticweb.org/ontologies/2011/1/Ontology1296772722296.owl#Hoehn_and_Yahr_stage_scale PDON Range from 0-5 0: Asymptomatic. 1: Unilateral involvement only. 2: Bilateral involvement without impairment of balance. 3: Mile to moderate involvement; some postural instability but physically independent; needs assistance to recover from pull test. 4: Severe disability; still able to walk or stand unassisted. 5: Wheelchair bound or bedridden unless aided. Hoehn and Yahr Stage Scale NDDO:NDDO_20004596 MDS-UPDRS Hoehn and Yahr Stage Assessment Score 0 4 NDDO:NDDO_20004622 Freezing of gait Datatype NDDO:NDDO_20004655 Freezing of gait Score 0 4 NDDO:NDDO_20004665 Rigidity - RLE Datatype NDDO:NDDO_20004698 Rigidity - RLE Score 0 4 NDDO:NDDO_20004708 Rigidity - LUE Datatype NDDO:NDDO_20004741 Rigidity - LUE Score 0 4 NDDO:NDDO_20004751 Finger Tapping Left Hand Datatype NDDO:NDDO_20004784 Finger Tapping Left Hand Score 0 4 NDDO:NDDO_20004794 Finger Tapping Right Hand Datatype NDDO:NDDO_20004827 Finger Tapping Right Hand Score 0 4 NDDO:NDDO_20004837 Leg agility - Right leg Datatype NDDO:NDDO_20004870 Leg agility - Right leg Score 0 4 NDDO:NDDO_20004880 Toe tapping - Left foot Datatype NDDO:NDDO_20004913 Toe tapping - Left foot Score 0 4 NDDO:NDDO_20004923 Constancy of rest Datatype NDDO:NDDO_20004956 Constancy of rest Score 0 4 NDDO:NDDO_20004966 Rest tremor amplitude - Lip/jaw Datatype NDDO:NDDO_20004999 Rest tremor amplitude - Lip/jaw Score 0 4 NDDO:NDDO_20005009 Pronation - Supination Movements - Left Hand Datatype NDDO:NDDO_20005042 Pronation - Supination Movements - Left Hand Score 0 4 NDDO:NDDO_20005052 Pronation - Supination Movements - Right Hand Datatype NDDO:NDDO_20005085 Pronation - Supination Movements - Right Hand Score 0 4 NDDO:NDDO_20005095 Postural tremor - Right hand Datatype NDDO:NDDO_20005128 Postural tremor - Right hand Score 0 4 NDDO:NDDO_20005138 Rigidity - LLE Datatype NDDO:NDDO_20005171 Rigidity - LLE Score 0 4 NDDO:NDDO_20005181 Rigidity - RUE Datatype NDDO:NDDO_20005214 Rigidity - RUE Score 0 4 NDDO:NDDO_20005224 Leg agility - Left leg Datatype NDDO:NDDO_20005257 Leg agility - Left leg Score 0 4 NDDO:NDDO_20005267 Toe tapping - Right foot Datatype NDDO:NDDO_20005300 Toe tapping - Right foot Score 0 4 NDDO:NDDO_20005310 Facial expression Datatype NDDO:NDDO_20005343 Facial expression Score 0 4 NDDO:NDDO_20005353 Gait Datatype NDDO:NDDO_20005386 Gait Score 0 4 NDDO:NDDO_20005396 Arising from chair Datatype NDDO:NDDO_20005429 Arising from chair Score 0 4 NDDO:NDDO_20005439 Hand movements - Left Hand Datatype NDDO:NDDO_20005472 Hand movements - Left Hand Score 0 4 NDDO:NDDO_20005482 Hand movements - Right Hand Datatype NDDO:NDDO_20005515 Hand movements - Right Hand Score 0 4 NDDO:NDDO_20005525 Rest tremor amplitude - LUE Datatype NDDO:NDDO_20005558 Rest tremor amplitude - LUE Score 0 4 NDDO:NDDO_20005568 Kinetic tremor - Left hand Datatype NDDO:NDDO_20005601 Kinetic tremor - Left hand Score 0 4 NDDO:NDDO_20005611 Rest tremor amplitude - RUE Datatype NDDO:NDDO_20005644 Rest tremor amplitude - RUE Score 0 4 NDDO:NDDO_20005654 Kinetic tremor - Right hand Datatype NDDO:NDDO_20005687 Kinetic tremor - Right hand Score 0 4 NDDO:NDDO_20005697 Postural tremor - Left hand Datatype NDDO:NDDO_20005730 Postural tremor - Left hand Score 0 4 NDDO:NDDO_20005740 Rest tremor amplitude - RLE Datatype NDDO:NDDO_20005773 Rest tremor amplitude - RLE Score 0 1 NDDO:NDDO_20005783 MDS-UPDRS Part III Boolean Datatype NDDO:NDDO_20005810 Interference of movements with ratings Datatype NDDO:NDDO_20005817 Did these movements interfere with ratings Score NDDO:NDDO_20005825 Presence of dyskinesias Datatype NDDO:NDDO_20005832 Were dyskinesias present Score 0 4 NDDO:NDDO_20005840 Speech Part III Datatype NDDO:NDDO_20005873 Speech Part III Score NDDO:NDDO_20006433 MDS-UPDRS Assassment Score NDDO:NDDO_20006448 3rd_Ventricle Datatype NDDO:NDDO_20006455 3rd_Ventricle Score NDDO:NDDO_20006463 4th_Ventricle Datatype NDDO:NDDO_20006470 4th_Ventricle Score NDDO:NDDO_20006478 Right_Accumbens_Area Datatype NDDO:NDDO_20006485 Right_Accumbens_Area Score NDDO:NDDO_20006493 Left_Accumbens_Area Datatype NDDO:NDDO_20006500 Left_Accumbens_Area Score NDDO:NDDO_20006508 Right_Amygdala Datatype NDDO:NDDO_20006515 Right_Amygdala Score NDDO:NDDO_20006523 Left_Amygdala Datatype NDDO:NDDO_20006530 Left_Amygdala Score NDDO:NDDO_20006538 Brain_Stem Datatype NDDO:NDDO_20006545 Brain_Stem Score NDDO:NDDO_20006553 Right_Caudate Datatype NDDO:NDDO_20006560 Right_Caudate Score NDDO:NDDO_20006568 Left_Caudate Datatype NDDO:NDDO_20006575 Left_Caudate Score NDDO:NDDO_20006583 Right_Cerebellum_Exterior Datatype NDDO:NDDO_20006590 Right_Cerebellum_Exterior Score NDDO:NDDO_20006598 Left_Cerebellum_Exterior Datatype NDDO:NDDO_20006605 Left_Cerebellum_Exterior Score NDDO:NDDO_20006613 Right_Cerebellum_White_Matter Datatype NDDO:NDDO_20006620 Right_Cerebellum_White_Matter Score NDDO:NDDO_20006628 Left_Cerebellum_White_Matter Datatype NDDO:NDDO_20006635 Left_Cerebellum_White_Matter Score NDDO:NDDO_20006643 Right_Cerebral_White_Matter Datatype NDDO:NDDO_20006650 Right_Cerebral_White_Matter Score NDDO:NDDO_20006658 Left_Cerebral_White_Matter Datatype NDDO:NDDO_20006665 Left_Cerebral_White_Matter Score NDDO:NDDO_20006673 CSF Datatype NDDO:NDDO_20006680 CSF Score NDDO:NDDO_20006688 Right_Hippocampus Datatype NDDO:NDDO_20006695 Right_Hippocampus Score NDDO:NDDO_20006703 Left_Hippocampus Datatype NDDO:NDDO_20006710 Left_Hippocampus Score NDDO:NDDO_20006718 Right_Inf_Lat_Vent Datatype NDDO:NDDO_20006725 Right_Inf_Lat_Vent Score NDDO:NDDO_20006733 Left_Inf_Lat_Vent Datatype NDDO:NDDO_20006740 Left_Inf_Lat_Vent Score NDDO:NDDO_20006748 Right_Lateral_Ventricle Datatype NDDO:NDDO_20006755 Right_Lateral_Ventricle Score NDDO:NDDO_20006763 Left_Lateral_Ventricle Datatype NDDO:NDDO_20006770 Left_Lateral_Ventricle Score NDDO:NDDO_20006778 Right_Pallidum Datatype NDDO:NDDO_20006785 Right_Pallidum Score NDDO:NDDO_20006793 Left_Pallidum Datatype NDDO:NDDO_20006800 Left_Pallidum Score NDDO:NDDO_20006808 Right_Putamen Datatype NDDO:NDDO_20006815 Right_Putamen Score NDDO:NDDO_20006823 Left_Putamen Datatype NDDO:NDDO_20006830 Left_Putamen Score NDDO:NDDO_20006838 Right_Thalamus_Proper Datatype NDDO:NDDO_20006845 Right_Thalamus_Proper Score NDDO:NDDO_20006853 Left_Thalamus_Proper Datatype NDDO:NDDO_20006860 Left_Thalamus_Proper Score NDDO:NDDO_20006868 Right_Ventral_DC Datatype NDDO:NDDO_20006875 Right_Ventral_DC Score NDDO:NDDO_20006883 Left_Ventral_DC Datatype NDDO:NDDO_20006890 Left_Ventral_DC Score NDDO:NDDO_20006898 Optic_Chiasm Datatype NDDO:NDDO_20006905 Optic_Chiasm Score NDDO:NDDO_20006913 Cerebellar_Vermal_Lobules_I-V Datatype NDDO:NDDO_20006920 Cerebellar_Vermal_Lobules_I-V Score NDDO:NDDO_20006928 Cerebellar_Vermal_Lobules_VI-VII Datatype NDDO:NDDO_20006935 Cerebellar_Vermal_Lobules_VI-VII Score NDDO:NDDO_20006943 Cerebellar_Vermal_Lobules_VIII-X Datatype NDDO:NDDO_20006950 Cerebellar_Vermal_Lobules_VIII-X Score NDDO:NDDO_20006958 Left_Basal_Forebrain Datatype NDDO:NDDO_20006965 Left_Basal_Forebrain Score NDDO:NDDO_20006973 Right_Basal_Forebrain Datatype NDDO:NDDO_20006980 Right_Basal_Forebrain Score NDDO:NDDO_20006988 Right_ACgG_anterior_cingulate_gyrus Datatype NDDO:NDDO_20006995 Right_ACgG_anterior_cingulate_gyrus Score NDDO:NDDO_20007003 Left_ACgG_anterior_cingulate_gyrus Datatype NDDO:NDDO_20007010 Left_ACgG_anterior_cingulate_gyrus Score NDDO:NDDO_20007018 Right_AIns_anterior_insula Datatype NDDO:NDDO_20007025 Right_AIns_anterior_insula Score NDDO:NDDO_20007033 Right_AOrG_anterior_orbital_gyrus Datatype NDDO:NDDO_20007040 Right_AOrG_anterior_orbital_gyrus Score NDDO:NDDO_20007048 Left_AIns_anterior_insula Datatype NDDO:NDDO_20007055 Left_AIns_anterior_insula Score NDDO:NDDO_20007063 Left_AOrG_anterior_orbital_gyrus Datatype NDDO:NDDO_20007070 Left_AOrG_anterior_orbital_gyrus Score NDDO:NDDO_20007078 Right_AnG_angular_gyrus Datatype NDDO:NDDO_20007085 Right_AnG_angular_gyrus Score NDDO:NDDO_20007093 Left_AnG_angular_gyrus Datatype NDDO:NDDO_20007100 Left_AnG_angular_gyrus Score NDDO:NDDO_20007108 Right_Calc_calcarine_cortex Datatype NDDO:NDDO_20007115 Right_Calc_calcarine_cortex Score NDDO:NDDO_20007123 Left_Calc_calcarine_cortex Datatype NDDO:NDDO_20007130 Left_Calc_calcarine_cortex Score NDDO:NDDO_20007138 Right_CO_central_operculum Datatype NDDO:NDDO_20007145 Right_CO_central_operculum Score NDDO:NDDO_20007153 Left_CO_central_operculum Datatype NDDO:NDDO_20007160 Left_CO_central_operculum Score NDDO:NDDO_20007168 Right_Cun_cuneus Datatype NDDO:NDDO_20007175 Right_Cun_cuneus Score NDDO:NDDO_20007183 Left_Cun_cuneus Datatype NDDO:NDDO_20007190 Left_Cun_cuneus Score NDDO:NDDO_20007198 Right_Ent_entorhinal_area Datatype NDDO:NDDO_20007205 Right_Ent_entorhinal_area Score NDDO:NDDO_20007213 Left_Ent_entorhinal_area Datatype NDDO:NDDO_20007220 Left_Ent_entorhinal_area Score NDDO:NDDO_20007228 Right_FO_frontal_operculum Datatype NDDO:NDDO_20007235 Right_FO_frontal_operculum Score NDDO:NDDO_20007243 Left_FO_frontal_operculum Datatype NDDO:NDDO_20007250 Left_FO_frontal_operculum Score NDDO:NDDO_20007258 Right_FRP_frontal_pole Datatype NDDO:NDDO_20007265 Right_FRP_frontal_pole Score NDDO:NDDO_20007273 Left_FRP_frontal_pole Datatype NDDO:NDDO_20007280 Left_FRP_frontal_pole Score NDDO:NDDO_20007288 Right_FuG_fusiform_gyrus Datatype NDDO:NDDO_20007295 Right_FuG_fusiform_gyrus Score NDDO:NDDO_20007303 Left_FuG_fusiform_gyrus Datatype NDDO:NDDO_20007310 Left_FuG_fusiform_gyrus Score NDDO:NDDO_20007318 Right_GRe_gyrus_rectus Datatype NDDO:NDDO_20007325 Right_GRe_gyrus_rectus Score NDDO:NDDO_20007333 Left_GRe_gyrus_rectus Datatype NDDO:NDDO_20007340 Left_GRe_gyrus_rectus Score NDDO:NDDO_20007348 Right_IOG_inferior_occipital_gyrus Datatype NDDO:NDDO_20007355 Right_IOG_inferior_occipital_gyrus Score NDDO:NDDO_20007363 Left_IOG_inferior_occipital_gyrus Datatype NDDO:NDDO_20007370 Left_IOG_inferior_occipital_gyrus Score NDDO:NDDO_20007378 Right_ITG_inferior_temporal_gyrus Datatype NDDO:NDDO_20007385 Right_ITG_inferior_temporal_gyrus Score NDDO:NDDO_20007393 Left_ITG_inferior_temporal_gyrus Datatype NDDO:NDDO_20007400 Left_ITG_inferior_temporal_gyrus Score NDDO:NDDO_20007408 Right_LiG_lingual_gyrus Datatype NDDO:NDDO_20007415 Right_LiG_lingual_gyrus Score NDDO:NDDO_20007423 Left_LiG_lingual_gyrus Datatype NDDO:NDDO_20007430 Left_LiG_lingual_gyrus Score NDDO:NDDO_20007438 Right_LOrG_lateral_orbital_gyrus Datatype NDDO:NDDO_20007445 Right_LOrG_lateral_orbital_gyrus Score NDDO:NDDO_20007453 Left_LOrG_lateral_orbital_gyrus Datatype NDDO:NDDO_20007460 Left_LOrG_lateral_orbital_gyrus Score NDDO:NDDO_20007468 Right_MCgG_middle_cingulate_gyrus Datatype NDDO:NDDO_20007475 Right_MCgG_middle_cingulate_gyrus Score NDDO:NDDO_20007483 Left_MCgG_middle_cingulate_gyrus Datatype NDDO:NDDO_20007490 Left_MCgG_middle_cingulate_gyrus Score NDDO:NDDO_20007498 Right_MFC_medial_frontal_cortex Datatype NDDO:NDDO_20007505 Right_MFC_medial_frontal_cortex Score NDDO:NDDO_20007513 Left_MFC_medial_frontal_cortex Datatype NDDO:NDDO_20007520 Left_MFC_medial_frontal_cortex Score NDDO:NDDO_20007528 Right_MFG_middle_frontal_gyrus Datatype NDDO:NDDO_20007535 Right_MFG_middle_frontal_gyrus Score NDDO:NDDO_20007543 Left_MFG_middle_frontal_gyrus Datatype NDDO:NDDO_20007550 Left_MFG_middle_frontal_gyrus Score NDDO:NDDO_20007558 Right_MOG_middle_occipital_gyrus Datatype NDDO:NDDO_20007565 Right_MOG_middle_occipital_gyrus Score NDDO:NDDO_20007573 Left_MOG_middle_occipital_gyrus Datatype NDDO:NDDO_20007580 Left_MOG_middle_occipital_gyrus Score NDDO:NDDO_20007588 Right_MOrG_medial_orbital_gyrus Datatype NDDO:NDDO_20007595 Right_MOrG_medial_orbital_gyrus Score NDDO:NDDO_20007603 Left_MOrG_medial_orbital_gyrus Datatype NDDO:NDDO_20007610 Left_MOrG_medial_orbital_gyrus Score NDDO:NDDO_20007618 Right_MPoG_postcentral_gyrus_medial_segment Datatype NDDO:NDDO_20007625 Right_MPoG_postcentral_gyrus_medial_segment Score NDDO:NDDO_20007633 Left_MPoG_postcentral_gyrus_medial_segment Datatype NDDO:NDDO_20007640 Left_MPoG_postcentral_gyrus_medial_segment Score NDDO:NDDO_20007648 Right_MPrG_precentral_gyrus_medial_segment Datatype NDDO:NDDO_20007655 Right_MPrG_precentral_gyrus_medial_segment Score NDDO:NDDO_20007663 Left_MPrG_precentral_gyrus_medial_segment Datatype NDDO:NDDO_20007670 Left_MPrG_precentral_gyrus_medial_segment Score NDDO:NDDO_20007678 Right_MSFG_superior_frontal_gyrus_medial_segment Datatype NDDO:NDDO_20007685 Right_MSFG_superior_frontal_gyrus_medial_segment Score NDDO:NDDO_20007693 Left_MSFG_superior_frontal_gyrus_medial_segment Datatype NDDO:NDDO_20007700 Left_MSFG_superior_frontal_gyrus_medial_segment Score NDDO:NDDO_20007708 Right_MTG_middle_temporal_gyrus Datatype NDDO:NDDO_20007715 Right_MTG_middle_temporal_gyrus Score NDDO:NDDO_20007723 Left_MTG_middle_temporal_gyrus Datatype NDDO:NDDO_20007730 Left_MTG_middle_temporal_gyrus Score NDDO:NDDO_20007738 Right_OCP_occipital_pole Datatype NDDO:NDDO_20007745 Right_OCP_occipital_pole Score NDDO:NDDO_20007753 Left_OCP_occipital_pole Datatype NDDO:NDDO_20007760 Left_OCP_occipital_pole Score NDDO:NDDO_20007768 Right_OFuG_occipital_fusiform_gyrus Datatype NDDO:NDDO_20007775 Right_OFuG_occipital_fusiform_gyrus Score NDDO:NDDO_20007783 Left_OFuG_occipital_fusiform_gyrus Datatype NDDO:NDDO_20007790 Left_OFuG_occipital_fusiform_gyrus Score NDDO:NDDO_20007798 Right_OpIFG_opercular_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20007805 Right_OpIFG_opercular_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20007813 Left_OpIFG_opercular_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20007820 Left_OpIFG_opercular_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20007828 Right_OrIFG_orbital_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20007835 Right_OrIFG_orbital_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20007843 Left_OrIFG_orbital_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20007850 Left_OrIFG_orbital_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20007858 Right_PCgG_posterior_cingulate_gyrus Datatype NDDO:NDDO_20007865 Right_PCgG_posterior_cingulate_gyrus Score NDDO:NDDO_20007873 Left_PCgG_posterior_cingulate_gyrus Datatype NDDO:NDDO_20007880 Left_PCgG_posterior_cingulate_gyrus Score NDDO:NDDO_20007888 Right_PCu_precuneus Datatype NDDO:NDDO_20007895 Right_PCu_precuneus Score NDDO:NDDO_20007903 Left_PCu_precuneus Datatype NDDO:NDDO_20007910 Left_PCu_precuneus Score NDDO:NDDO_20007918 Right_PHG_parahippocampal_gyrus Datatype NDDO:NDDO_20007925 Right_PHG_parahippocampal_gyrus Score NDDO:NDDO_20007933 Left_PHG_parahippocampal_gyrus Datatype NDDO:NDDO_20007940 Left_PHG_parahippocampal_gyrus Score NDDO:NDDO_20007948 Right_PIns_posterior_insula Datatype NDDO:NDDO_20007955 Right_PIns_posterior_insula Score NDDO:NDDO_20007963 Left_PIns_posterior_insula Datatype NDDO:NDDO_20007970 Left_PIns_posterior_insula Score NDDO:NDDO_20007978 Right_PO_parietal_operculum Datatype NDDO:NDDO_20007985 Right_PO_parietal_operculum Score NDDO:NDDO_20007993 Left_PO_parietal_operculum Datatype NDDO:NDDO_20008000 Left_PO_parietal_operculum Score NDDO:NDDO_20008008 Right_PoG_postcentral_gyrus Datatype NDDO:NDDO_20008015 Right_PoG_postcentral_gyrus Score NDDO:NDDO_20008023 Left_PoG_postcentral_gyrus Datatype NDDO:NDDO_20008030 Left_PoG_postcentral_gyrus Score NDDO:NDDO_20008038 Right_POrG_posterior_orbital_gyrus Datatype NDDO:NDDO_20008045 Right_POrG_posterior_orbital_gyrus Score NDDO:NDDO_20008053 Left_POrG_posterior_orbital_gyrus Datatype NDDO:NDDO_20008060 Left_POrG_posterior_orbital_gyrus Score NDDO:NDDO_20008068 Right_PP_planum_polare Datatype NDDO:NDDO_20008075 Right_PP_planum_polare Score NDDO:NDDO_20008083 Left_PP_planum_polare Datatype NDDO:NDDO_20008090 Left_PP_planum_polare Score NDDO:NDDO_20008098 Right_PrG_precentral_gyrus Datatype NDDO:NDDO_20008105 Right_PrG_precentral_gyrus Score NDDO:NDDO_20008113 Left_PrG_precentral_gyrus Datatype NDDO:NDDO_20008120 Left_PrG_precentral_gyrus Score NDDO:NDDO_20008128 Right_PT_planum_temporale Datatype NDDO:NDDO_20008135 Right_PT_planum_temporale Score NDDO:NDDO_20008143 Left_PT_planum_temporale Datatype NDDO:NDDO_20008150 Left_PT_planum_temporale Score NDDO:NDDO_20008158 Right_SCA_subcallosal_area Datatype NDDO:NDDO_20008165 Right_SCA_subcallosal_area Score NDDO:NDDO_20008173 Left_SCA_subcallosal_area Datatype NDDO:NDDO_20008180 Left_SCA_subcallosal_area Score NDDO:NDDO_20008188 Right_SFG_superior_frontal_gyrus Datatype NDDO:NDDO_20008195 Right_SFG_superior_frontal_gyrus Score NDDO:NDDO_20008203 Left_SFG_superior_frontal_gyrus Datatype NDDO:NDDO_20008210 Left_SFG_superior_frontal_gyrus Score NDDO:NDDO_20008218 Right_SMC_supplementary_motor_cortex Datatype NDDO:NDDO_20008225 Right_SMC_supplementary_motor_cortex Score NDDO:NDDO_20008233 Left_SMC_supplementary_motor_cortex Datatype NDDO:NDDO_20008240 Left_SMC_supplementary_motor_cortex Score NDDO:NDDO_20008248 Right_SMG_supramarginal_gyrus Datatype NDDO:NDDO_20008255 Right_SMG_supramarginal_gyrus Score NDDO:NDDO_20008263 Left_SMG_supramarginal_gyrus Datatype NDDO:NDDO_20008270 Left_SMG_supramarginal_gyrus Score NDDO:NDDO_20008278 Right_SOG_superior_occipital_gyrus Datatype NDDO:NDDO_20008285 Right_SOG_superior_occipital_gyrus Score NDDO:NDDO_20008293 Left_SOG_superior_occipital_gyrus Datatype NDDO:NDDO_20008300 Left_SOG_superior_occipital_gyrus Score NDDO:NDDO_20008308 Right_SPL_superior_parietal_lobule Datatype NDDO:NDDO_20008315 Right_SPL_superior_parietal_lobule Score NDDO:NDDO_20008323 Left_SPL_superior_parietal_lobule Datatype NDDO:NDDO_20008330 Left_SPL_superior_parietal_lobule Score NDDO:NDDO_20008338 Right_STG_superior_temporal_gyrus Datatype NDDO:NDDO_20008345 Right_STG_superior_temporal_gyrus Score NDDO:NDDO_20008353 Left_STG_superior_temporal_gyrus Datatype NDDO:NDDO_20008360 Left_STG_superior_temporal_gyrus Score NDDO:NDDO_20008368 Right_TMP_temporal_pole Datatype NDDO:NDDO_20008375 Right_TMP_temporal_pole Score NDDO:NDDO_20008383 Left_TMP_temporal_pole Datatype NDDO:NDDO_20008390 Left_TMP_temporal_pole Score NDDO:NDDO_20008398 Right_TrIFG_triangular_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20008405 Right_TrIFG_triangular_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20008413 Left_TrIFG_triangular_part_of_the_inferior_frontal_gyrus Datatype NDDO:NDDO_20008420 Left_TrIFG_triangular_part_of_the_inferior_frontal_gyrus Score NDDO:NDDO_20008428 Right_TTG_transverse_temporal_gyrus Datatype NDDO:NDDO_20008435 Right_TTG_transverse_temporal_gyrus Score NDDO:NDDO_20008443 Left_TTG_transverse_temporal_gyrus Datatype NDDO:NDDO_20008450 Left_TTG_transverse_temporal_gyrus Score NDDO:NDDO_20008458 CAUDATE_R Datatype NDDO:NDDO_20008465 CAUDATE_R Score NDDO:NDDO_20008473 CAUDATE_L Datatype NDDO:NDDO_20008480 CAUDATE_L Score NDDO:NDDO_20008488 PUTAMEN_R Datatype NDDO:NDDO_20008495 PUTAMEN_R Score NDDO:NDDO_20008503 PUTAMEN_L Datatype NDDO:NDDO_20008510 PUTAMEN_L Score NDDO:NDDO_20008518 image assessment score is another possible label Brain region volume score NDDO:NDDO_20009809 PPMI baseline visit NDDO:NDDO_20009818 PPMI premature withdrawal NDDO:NDDO_20009827 PPMI screening visit NDDO:NDDO_20009836 PPMI sympthomatic therapy NDDO:NDDO_20009845 PPMI visit v01 NDDO:NDDO_20009854 PPMI visit v02 NDDO:NDDO_20009863 PPMI visit v03 NDDO:NDDO_20009872 PPMI visit v04 NDDO:NDDO_20009881 PPMI visit v05 NDDO:NDDO_20009890 PPMI visit v06 NDDO:NDDO_20009899 PPMI visit v07 NDDO:NDDO_20009908 PPMI visit v08 NDDO:NDDO_20009917 PPMI visit v09 NDDO:NDDO_20009926 PPMI visit v10 NDDO:NDDO_20009935 PPMI visit v11 NDDO:NDDO_20009944 PPMI visit v12 NDDO:NDDO_20009953 PPMI visit v13 NDDO:NDDO_20009962 PPMI visit v14 NDDO:NDDO_20009971 PPMI visit v15 NDDO:NDDO_20010040 Clinical Diagnosis and Management Datatype NDDO:NDDO_20010041 clinical laboratory Datatype NDDO:NDDO_20010042 Benton Judgment of Line Orientation Test Datatype NDDO:NDDO_20010043 Cognitive Categorization Datatype NDDO:NDDO_20010044 Hopkins Verbal Learning Test-Revised (HVLT-R) Datatype NDDO:NDDO_20010045 Diagnostic Assessment Datatype NDDO:NDDO_20010046 Brain region volume scale NDDO:NDDO_20010047 Impulsive-Compulsive Disorders (QUIP-S) Score NDDO:NDDO_20010048 Impulsive-Compulsive Disorders (QUIP-S) Datatype NDDO:NDDO_20010049 Physical Activity Scale for the Elderly (PASE) Datatype NDDO:NDDO_20010050 REM Sleep Behavior Disorder Screening Questionnaire (RBDSQ) Datatype NDDO:NDDO_20010051 SCOPA-AUT Datatype NDDO:NDDO_20010052 Unified Parkinsons Disease Rating Scale (UPRDS) Datatype NDDO:NDDO_20010115 CSF fluid sample NDDO:NDDO_20010116 SWEDD Cohort NDDO:NDDO_20010117 Predormal Cohort NDDO:NDDO_20010118 Genetic Cohort NDDO:NDDO_20010119 Genetic Registry Cohort NDDO:NDDO_20010122 Benton Judgment of Line Orientation Test Questionnaire NDDO:NDDO_20010123 Cognitive Categorization Questionnaire NDDO:NDDO_20010124 Hopkins Verbal Learning Test-Revised (HVLT-R) Questionnaire NDDO:NDDO_20010126 WMS-III Letter-Number Sequencing Test Questionnaire NDDO:NDDO_20010127 Clinical Diagnosis and Management Questionnaire NDDO:NDDO_20010128 clinical laboratory questionnaire NDDO:NDDO_20010129 Diagnostic Questionnaire NDDO:NDDO_20010130 family history assessment NDDO:NDDO_20010131 Epworth sleepingness scale questionnaire (ESS) NDDO:NDDO_20010132 MDS-UPDRS questionnaire NDDO:NDDO_20010133 MDS-UPDRS - Hoehn and Yahr Stage questionnaire NDDO:NDDO_20010134 MDS-UPDRS Part I questionnaire NDDO:NDDO_20010135 MDS-UPDRS Part II questionnaire NDDO:NDDO_20010136 MDS-UPDRS Part III questionnaire NDDO:NDDO_20010137 MDS-UPDRS Part IV questionnaire NDDO:NDDO_20010138 Modified Schwab & England Activities of Daily Living (ADL) Questionnaire NDDO:NDDO_20010139 MDS-UPDRS Part II NDDO:NDDO_20010140 Physical Activity Scale for the Elderly (PASE) Questionnaire NDDO:NDDO_20010141 Questionnaire for Impulsive-Compulsive Disorders (QUIP-S) NDDO:NDDO_20010143 REM Sleep Behavior Disorder Screening Questionnaire (RBDSQ) NDDO:NDDO_20010144 Scales for Outcomes in Parkinsons Disease Questionnaire SCOPA-AUT NDDO:NDDO_20010145 State-Trait Anxiety Inventory Questionnaire (STAI-Y) NDDO:NDDO_20010146 The University of Pennsylvania Smell Test Questionnaire NDDO:NDDO_20010147 Unified Parkinsons Disease Rating Scale Questionnaire (UPRDS) NDDO:NDDO_20010148 MDS-UPDRS Part I NDDO:NDDO_20010149 Benton Judgment of Line Orientation Test Score NDDO:NDDO_20010150 Cognitive Categorization Score NDDO:NDDO_20010151 Hopkins Verbal Learning Test-Revised (HVLT-R) Score NDDO:NDDO_20010152 clinical laboratory score NDDO:NDDO_20010153 Diagnostic assessment score NDDO:NDDO_20010154 Physical Activity Scale for the Elderly (PASE) Score NDDO:NDDO_20010155 Unified Parkinsons Disease Rating Scale (UPRDS) Score NDDO:NDDO_20010156 Clinical Diagnosis and Management Scale NDDO:NDDO_20010157 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100535 The Movement Disorder Society version of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) Hoehn and Yahr Stage. (NCIT) MDS-UPDRS - Hoehn and Yahr Stage NDDO:NDDO_20010160 clinical laboratory scale NDDO:NDDO_20010161 Diagnostic assessment scale NDDO:NDDO_20010163 Physical Activity Scale for the Elderly (PASE) Scale NDDO:NDDO_20010164 Impulsive-Compulsive Disorders (QUIP-S) Scale NDDO:NDDO_20010165 REM Sleep Behavior Disorder Screening Scale NDDO:NDDO_20010166 SCOPA-AUT Scale NDDO:NDDO_20010167 UPRDS Scale NDDO:NDDO_20010168 Benton Judgment of Line Orientation Scale NDDO:NDDO_20010169 Cognitive Categorization Scale NDDO:NDDO_20010170 Hopkins Verbal Learning Test-Revised (HVLT-R) Scale 0 100 0 100 NDDO:NDDO_20010189 Modified Schwab & England Activities of Daily Living Datatype NDDO:NDDO_20010243 Clinical Diagnosis and Management Score 0.0 24.0 0.0 24.0 NDDO:NDDO_20010258 Epworth Sleepiness (ESS) Datatype 0 21 0 21 NDDO:NDDO_20010336 WMS-III Letter-Number Sequencing Datatype NDDO:NDDO_20010445 range from 20-80 State-Trait Anxiety Inventory (STAI-Y) Scale NDDO:NDDO_20010455 State-Trait Anxiety Inventory (STAI-Y) Score 20 80 20 80 NDDO:NDDO_20010476 State-Trait Anxiety Inventory (STAI-Y) Datatype NDDO:NDDO_20010515 REM Sleep Behavior Disorder Screening Questionnaire (RBDSQ) Score NDDO:NDDO_20010545 Scales for Outcomes in Parkinsons Disease Assessment SCOPA-AUT Score NDDO:NDDO_20010575 http://scai.fraunhofer.de/AlzheimerOntology#fcMRI fcMRI rsfMRI ADO Resting State Functional MR imaging (rsfMRI) NDDO:NDDO_20010588 Resting State Functional MRI image score NDDO:NDDO_20010595 Resting State Functional MRI image NDDO:NDDO_20010694 MDS-UPDRS Part II Assessment Score NDDO:NDDO_20011144 gait data NDDO:NDDO_20011177 skin sample data NDDO:NDDO_20011186 urine sample data NDDO:NDDO_20044000 PPMI cohort NDDO:NDDO_20044001 Magnetic Resonance Imaging (MRI) design NDDO:NDDO_20044002 Positron Emission Tomography (PET) design NDDO:NDDO_21000114 De Novo PD Cohort NDDO:NDDO_21000115 Control Cohort NDDO:Semantic_Fluency_Assessment_design Semantic Fluency Assessment design NDDO:adverse_events_assessment_design adverse events assessment design NDDO:biomarker_assessment_design biomarker assessment design NDDO:biospecimen_collection_design biospecimen collection design NDDO:clinical_history_taking_design clinical history taking design NDDO:demographic_assessment_design demographic assessment design NDDO:education_asessment_design education assessment design NDDO:neurological_assessment_design neurological assessment design NDDO:personal_history_assessment_design personal history assessment design NDDO:screening_labs_assessment_design screening labs assessment design NDDO:vital_signs_assessment_design vital signs assessment design Montreal Cognitive Assessment (MoCA) design Symbol Digit Modalities Test (SDMT) design American_National_Reading_Test_design American National Reading Test design Boston_Naming_Test_design Boston Naming Test design Clock_Drawing_Assessment_design Clock Drawing Assessment design Functional_Assessment_Questionnaire_design Functional Assessment Questionnaire (FAQ) design Functional_assessment_design Functional assessment design Hachinski_assessment_design Hachinski assessment design Logical_Memory_Assessment_II_design Logical Memory Assessment II design Logical_Memory_Assessment_I_design Logical Memory Assessment I design Logical_Memory_Assessment_design Logical Memory Assessment design Neuropsychiatric_Inventory_Assessment_design Neuropsychiatric Inventory Assessment design Neuropsychiatric_Inventory_assessment_design Neuropsychiatric Inventory (NPI) Assessment design Rey_Auditory_Verbal_Learning_Test_design Rey Auditory Verbal Learning Test (RAVLT) design Trail_Making_Assessment_A_design Trail Making Assessment A design Trail_Making_Assessment_B_design Trail Making Assessment B design Trail_Making_Assessment_design Trail Making Assessment design medications_assessment_design medications assessment design Clinical Dementia Rating Square of Boxes (CDR-SB) Assessment design Alzheimers Disease Assessment (ADAS11) design Alzheimers Disease Assessment (ADAS13) design Clinical Dementia Rating Square of Boxes (CDR-SB) Assessment design Everyday Cognition (ECog) Assessment design Mini Mental State Exam (MMSE) design http://purl.bioontology.org/ontology/MESH/D014145 The subject's ability to connect 25 numbered and lettered circles in sequence in a specific length of time. A score of 12 or below is suggestive of organic brain damage. Making Tests, Trail Making Test, Trail Test, Trail Making Trail Making Tests Tests, Trail Making Trail Making Assessment OntoDT OntoDT: identifier Ontology of Biomedical Investigations OBI: data representational model Benton_Judgment_of_Line_Orientation_Test_design Benton Judgment of Line Orientation Test design Clinical_Diagnosis_and_Management_Assessment_Design Clinical Diagnosis and Management Assessment design Cognitive_Categorization_assessment_design Cognitive Categorization assessment design Diagnostic_assessment_design Diagnostic assessment design Florbetaben_PET_imaging_design Florbetaben PET imaging design MDS-UPDRS_-_Hoehn_and_Yahr_Stage_design MDS-UPDRS - Hoehn and Yahr Stage design MDS-UPDRS_Part_III_design MDS-UPDRS Part III design MDS-UPDRS_Part_II_design MDS-UPDRS Part II design MDS-UPDRS_Part_IV_design MDS-UPDRS Part IV design MDS-UPDRS_Part_I_design MDS-UPDRS Part I design MDS-UPDRS_design MDS-UPDRS design Scales_for_Outcomes_in_Parkinsons_Disease_Assessment_SCOPA-AUT_design Scales for Outcomes in Parkinsons Disease Assessment SCOPA-AUT design The_University_of_Pennsylvania_Smell_Test_design The University of Pennsylvania Smell Test design VMAT-2_PET_imaging_design VMAT-2 PET imaging design WMS-III_Letter-Number_Sequencing_Test_design WMS-III Letter-Number Sequencing Test design clinical_laboratory_assessment_design clinical laboratory assessment design family_history_assessment_design family history assessment design gait_assessment_design gait assessment design structural_MR_imaging_design structural MR imaging design Diffusion Tensor Imaging (DTI) design Dopamine Transporter (DaT) SPECT Imaging design Epworth sleepingness scale assessment (ESS) design Hopkins Verbal Learning Test-Revised (HVLT-R) design Impulsive-Compulsive Disorder (QUIP-S) Assessment design Modified Schwab & England Activities of Daily Living (ADL) design Physical Activity Scale for the Elderly (PASE) Assessment design REM Sleep Behavior Disorder Screening (RBDSQ) design Resting State Functional MR imaging (rsfMRI) design State-Trait Anxiety Inventory (STAI-Y) design Unified Parkinsons Disease Rating Scale (UPRDS) Assessment design owl:Thing example to be eventually removed 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 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 term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 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 This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true 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 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 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 Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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 ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument en Adam Goldstein Alan Ruttenberg Albert Goldfain Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn James A. Overton James Malone Jennifer Fostel Jie Zheng Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki Satya Sahoo Sivaram Arabandi Werner Ceusters William Duncan William Hogan Yongqun (Oliver) He http://creativecommons.org/licenses/by/4.0/ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any 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. For more information see http://www.obofoundry.org/docs/Citation.html This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner Person:Alan Ruttenberg 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 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 hasPart hasPart 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 realizes https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl has material basis at all times https://raw.githubusercontent.com/BFO-ontology/BFO/master/docs/OWL-TIME/tests/bfo_tr.owl material basis of at some time To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) has measurement unit label This document is about information artifacts and their representations is_about is 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 isAbout A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of has_specified_input see is_input_of example_of_usage 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. 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 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output inheres in this fragility inheres in this vase this red color inheres in this apple 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 inheres in has participant 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) 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://www.obofoundry.org/ro/#OBO_REL:has_participant has participant hasParticipant hasParticipant 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 role of roleOf Alan Ruttenberg Albert Goldfain Anand Kumar Barry Smith Bill Hogan Cornelius Rosse Daniel Merico Lindsay Cowell Richard Scheuermann Sivaram Arabandi Werner Ceusters 2009-08-07 The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to albertgoldfain@gmail.com. Be sure to include a google-account username with your request (this will be the username associated with a gmail address). This ontology is in early development. Expect it to change. 2011-09-20 IAO_0021000-IAO_0021999 IAO_0020000-IAO_0020999 Ana Kostovska Ilin Tolovski Pance Panov Pance Panov OWL https://creativecommons.org/licenses/by/4.0/ Ontology for describing data on neurodegenerative diseases in patients Ontology Foundational model of anatomy Information Artefact Ontology NCBI Taxonomy of living organisms Neurological Disease Ontology Ontology for General Medical Science Ontology of Biomedical Investigations Protein Ontology Ana Kostovska Ilin Tolovski Pance Panov External classes to be imported by the NDDO ontology rdf:Alt rdf:Bag rdf:List rdf:Property rdf:Seq rdf:Statement rdf:XMLLiteral rdfs:Class rdfs:Container rdfs:ContainerMembershipProperty rdfs:Datatype rdfs:Literal rdfs:Resource owl:DatatypeProperty owl:ObjectProperty