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 Hilmar Lapp Phylotastic Tree Annotation Team The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA. http://creativecommons.org/publicdomain/zero/1.0/ Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology Comparison of two or more biological entities of the same class when the similarities and differences of the entities are treated explicitly as the product of an evolutionary process of descent with modification. CDAO Team The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics Comparative Data Analysis Ontology This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome. W3C PROVenance Interchange Ontology (PROV-O) Recommendation version 2013-04-30 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 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 term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative 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 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 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 A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB 2018-09-21T16:43:39Z Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after 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 Classify prov-o terms into three categories, including 'starting-point', 'qualifed', and 'extended'. This classification is used by the prov-o html document to gently introduce prov-o terms to its users. Classify prov-o terms into six components according to prov-dm, including 'agents-responsibility', 'alternate', 'annotations', 'collections', 'derivations', and 'entities-activities'. This classification is used so that readers of prov-o specification can find its correspondence with the prov-dm specification. A reference to the principal section of the PROV-CONSTRAINTS document that describes this concept. A definition quoted from PROV-DM or PROV-CONSTRAINTS that describes the concept expressed with this OWL term. A reference to the principal section of the PROV-DM document that describes this concept. A note by the OWL development team about how this term expresses the PROV-DM concept, or how it should be used in context of semantic web or linked data. When the prov-o term does not have a definition drawn from prov-dm, and the prov-o editor provides one. PROV-O does not define all property inverses. The directionalities defined in PROV-O should be given preference over those not defined. However, if users wish to name the inverse of a PROV-O property, the local name given by prov:inverse should be used. A reference to the principal section of the PROV-DM document that describes this concept. The position that this OWL term should be listed within documentation. The scope of the documentation (e.g., among all terms, among terms within a prov:category, among properties applying to a particular class, etc.) is unspecified. This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. Example annotation: prov:wasGeneratedBy prov:qualifiedForm prov:qualifiedGeneration, prov:Generation . Then this unqualified assertion: :entity1 prov:wasGeneratedBy :activity1 . can be qualified by adding: :entity1 prov:qualifiedGeneration :entity1Gen . :entity1Gen a prov:Generation, prov:Influence; prov:activity :activity1; :customValue 1337 . Note how the value of the unqualified influence (prov:wasGeneratedBy :activity1) is mirrored as the value of the prov:activity (or prov:entity, or prov:agent) property on the influence class. Classes and properties used to qualify relationships are annotated with prov:unqualifiedForm to indicate the property used to assert an unqualified provenance relation. The property links a Node to the Edge it belongs to in the child position. belongs_to_Edge_as_Child The property links a node to any of the other nodes that are its ancestors in a rooted tree. has_Ancestor This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states. has_Nucleotide_State The property links a Node to one of the edges that are incident on such node. belongs_to_Edge belongs_to_Character_State_Data_Matrix The property links a rooted tree to the specific node that represents the unique root of the tree. has_Root The property links a node to a node that is an immediate descendant in the tree. has_Child The property that relates a coordinate list to the first item in the list. has_First_Coordinate_Item has_Coordinate belongs_to_Continuous_Character has_Standard_Datum This property associates a amino acid character-state instance with a state value from the domain of amino acid states. has_Amino_Acid_State is_annotation_of has_RNA_Datum This property relates a transformation to a 'left' state (the state associated with the 'left' node). has_Left_State precedes exclude Property that associates to each Edge the Nodes it connects. has_Node nca_node_of Associates a TU to some external taxonomy reference. has_External_Reference This property links a coordinate to the coordinate system it references. has_Coordinate_System belongs_to_Nucleotide_Character connects_to This property relates a type of evolutionary change (an Edge_Transformation) to the character that undergoes the change. The change is a transformation_of the affected character. hereditary_change_of has_Descendants reconciliation_of belongs_to_Amino_Acid_Character This property associates a character-state instance with a state value on a continuous numeric scale. has_Continuous_State The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root). belongs_to_Edge_as_Parent The property that links a node to its unique parent in a rooted tree. has_Parent belongs_to_Compound_Character This propery relates different instances of the same character, including the case when the states of the character differ (e.g., large_beak of beak_size_character of TU A is homologous_to small_beak of beak_size_character of TU B). homologous_to This property relates a transformation to the components that compose it. has_Change_Component has_Categorical_Datum This property associates a character-state instance with its state value, e.g., a state value expressed in terms of an imported domain ontology. has_State This property relates a transformation to a 'left' node (the node that has the 'left' state). has_Left_Node This property relates a transformation to a 'right' state (the state associated with the 'right' node). has_Right_State This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree). For MIAPA reporting, this property (and/or its inverse) should be used to establish the relationship between rows of the data matrix and nodes in the tree(s). represents_TU This property associates a compound character-state instance with its compound state value. has_Compound_State This property relates a character-state datum to its TU. belongs_to_TU belongs_to_Network obsolete part_of true This property relates a TU to a node that represents it in a network. For MIAPA reporting, recommended to be used for referencing the corresponding tree (tip) node(s) from a data matrix row represented_by_Node The property that relates a coordinate list to the item in the list beyond the first item. has_Remaining_Coordinate_List has_Element belongs_to_Tree Associates to a Directed Edge the Node that is in the parent position in the edge (i.e., the node touched by the edge and closer to the root of the tree) has_Parent_Node belongs_to_Tree_as_Root has_Hereditary_Change belongs_to_Character has_Molecular_Datum The property associates to a Directed Edge the Node that is in the child position in the edge, i.e., the node touched by the edge and closer to the leaves of the tree. has_Child_Node This property relates a transformation to a 'right' node (the node that has the 'right' state). has_Right_Node This object property is one way for providing MIAPA-compliant edge lengths. The object is an instance of the appropriate cdao:EdgeLength subclass, which its value described by cdao:has_Value. The alternative is to use the miapa:'has edge length' data property or one of its subproperties. edgeLength For MIAPA reporting, recommended for referencing sequence and other identifiers for a TU as applicable. :otu1 a cdao:TU ; dsw:derivedFrom [ a dsw:Specimen ; dwc:institutionCode "MVZ" ; dwc:collectionCode "Birds" ; dwc:catalogNumber "35287" ; ] . For MIAPA reporting, recommended to associate the taxonomic unit to a specimen. Use a unique identifier for the specimen, or create an instance of type dsw:Specimen described by the "Darwin Core triplet" (dwc:institutionCode, dwc:collectionCode, dwc:catalogNumber). For MIAPA reporting, recommended as the property relating an OTU to a taxonomic concept (an entry in a taxonomy, such as an NCBI taxonomy reference) that has been obtained through taxonomic name or other kinds of name resolution or reconciliation procedures. implements is implemented by has version For MIAPA reporting, recommended as the property for indicating a spatial location for OTUs and/or specimens. An exact location can be described using geo:lat, geo:long, and geo:alt. These are the same terms DBpedia uses (see http://wiki.dbpedia.org/Datasets#h18-17). Inexact locations known by name can be described using dc:description. An object property to express the accountability of an agent towards another agent. The subordinate agent acted on behalf of the responsible agent in an actual activity. actedOnBehalfOf starting-point agents-responsibility hadDelegate activity qualified This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple. The prov:activity property references an prov:Activity which influenced a resource. This property applies to an prov:ActivityInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent. activityOfInfluence agent qualified This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple. The prov:agent property references an prov:Agent which influenced a resource. This property applies to an prov:AgentInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent. agentOfInfluence alternateOf expanded alternate http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Two alternate entities present aspects of the same thing. These aspects may be the same or different, and the alternate entities may or may not overlap in time. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-alternate alternateOf http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-alternate The Location of any resource. This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>. atLocation expanded The naming of prov:atLocation parallels prov:atTime, and is not named prov:hadLocation to avoid conflicting with the convention that prov:had* properties are used on prov:Influence classes. This property is not functional because the many values could be at a variety of granularies (In this building, in this room, in that chair). locationOf entity qualified This property behaves in spirit like rdf:object; it references the object of a prov:wasInfluencedBy triple. The prov:entity property references an prov:Entity which influenced a resource. This property applies to an prov:EntityInfluence, which is given by a subproperty of prov:qualifiedInfluence from the influenced prov:Entity, prov:Activity or prov:Agent. entityOfInfluence generated expanded entities-activities prov:generated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions. wasGeneratedBy The _optional_ Activity of an Influence, which used, generated, invalidated, or was the responsibility of some Entity. This property is _not_ used by ActivityInfluence (use prov:activity instead). This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>. hadActivity qualified derivations The multiple rdfs:domain assertions are intended. One is simpler and works for OWL-RL, the union is more specific but is not recognized by OWL-RL. wasActivityOfInfluence The _optional_ Generation involved in an Entity's Derivation. hadGeneration qualified derivations generatedAsDerivation hadMember expanded expanded wasMemberOf A collection is an entity that provides a structure to some constituents, which are themselves entities. These constituents are said to be member of the collections. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-collection The _optional_ Plan adopted by an Agent in Association with some Activity. Plan specifications are out of the scope of this specification. hadPlan qualified agents-responsibility wasPlanOf hadPrimarySource expanded derivations wasPrimarySourceOf hadPrimarySource property is a particular case of wasDerivedFrom (see http://www.w3.org/TR/prov-dm/#term-original-source) that aims to give credit to the source that originated some information. The _optional_ Role that an Entity assumed in the context of an Activity. For example, :baking prov:used :spoon; prov:qualified [ a prov:Usage; prov:entity :spoon; prov:hadRole roles:mixing_implement ]. This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>. hadRole qualified agents-responsibility prov:hadRole references the Role (i.e. the function of an entity with respect to an activity), in the context of an instantaneous usage, generation, association, start, and end. wasRoleIn The _optional_ Usage involved in an Entity's Derivation. hadUsage qualified derivations wasUsedInDerivation influenced expanded agents-responsibility wasInfluencedBy Subproperties of prov:influencer are used to cite the object of an unqualified PROV-O triple whose predicate is a subproperty of prov:wasInfluencedBy (e.g. prov:used, prov:wasGeneratedBy). prov:influencer is used much like rdf:object is used. influencer qualified http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence This property and its subproperties are used in the same way as the rdf:object property, i.e. to reference the object of an unqualified prov:wasInfluencedBy or prov:influenced triple. This property is used as part of the qualified influence pattern. Subclasses of prov:Influence use these subproperties to reference the resource (Entity, Agent, or Activity) whose influence is being qualified. hadInfluence invalidated expanded entities-activities prov:invalidated is one of few inverse property defined, to allow Activity-oriented assertions in addition to Entity-oriented assertions. wasInvalidatedBy If this Activity prov:wasAssociatedWith Agent :ag, then it can qualify the Association using prov:qualifiedAssociation [ a prov:Association; prov:agent :ag; :foo :bar ]. qualifiedAssociation qualified agents-responsibility qualifiedAssociationOf If this Entity prov:wasAttributedTo Agent :ag, then it can qualify how it was influenced using prov:qualifiedAttribution [ a prov:Attribution; prov:agent :ag; :foo :bar ]. qualifiedAttribution qualified agents-responsibility qualifiedAttributionOf If this Activity prov:wasInformedBy Activity :a, then it can qualify how it was influenced using prov:qualifiedCommunication [ a prov:Communication; prov:activity :a; :foo :bar ]. qualifiedCommunication qualified entities-activities qualifiedCommunicationOf If this Agent prov:actedOnBehalfOf Agent :ag, then it can qualify how with prov:qualifiedResponsibility [ a prov:Responsibility; prov:agent :ag; :foo :bar ]. qualifiedDelegation qualified agents-responsibility qualifiedDelegationOf If this Entity prov:wasDerivedFrom Entity :e, then it can qualify how it was derived using prov:qualifiedDerivation [ a prov:Derivation; prov:entity :e; :foo :bar ]. qualifiedDerivation qualified derivations qualifiedDerivationOf If this Activity prov:wasEndedBy Entity :e1, then it can qualify how it was ended using prov:qualifiedEnd [ a prov:End; prov:entity :e1; :foo :bar ]. qualifiedEnd qualified entities-activities qualifiedEndOf If this Activity prov:generated Entity :e, then it can qualify how it performed the Generation using prov:qualifiedGeneration [ a prov:Generation; prov:entity :e; :foo :bar ]. qualifiedGeneration qualified entities-activities qualifiedGenerationOf Because prov:qualifiedInfluence is a broad relation, the more specific relations (qualifiedCommunication, qualifiedDelegation, qualifiedEnd, etc.) should be used when applicable. qualifiedInfluence qualified derivations qualifiedInfluenceOf If this Entity prov:wasInvalidatedBy Activity :a, then it can qualify how it was invalidated using prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity :a; :foo :bar ]. qualifiedInvalidation qualified entities-activities qualifiedInvalidationOf If this Entity prov:hadPrimarySource Entity :e, then it can qualify how using prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity :e; :foo :bar ]. qualifiedPrimarySource qualified derivations qualifiedSourceOf If this Entity prov:wasQuotedFrom Entity :e, then it can qualify how using prov:qualifiedQuotation [ a prov:Quotation; prov:entity :e; :foo :bar ]. qualifiedQuotation qualified derivations qualifiedQuotationOf If this Entity prov:wasRevisionOf Entity :e, then it can qualify how it was revised using prov:qualifiedRevision [ a prov:Revision; prov:entity :e; :foo :bar ]. qualifiedRevision qualified derivations revisedEntity If this Activity prov:wasStartedBy Entity :e1, then it can qualify how it was started using prov:qualifiedStart [ a prov:Start; prov:entity :e1; :foo :bar ]. qualifiedStart qualified entities-activities qualifiedStartOf If this Activity prov:used Entity :e, then it can qualify how it used it using prov:qualifiedUsage [ a prov:Usage; prov:entity :e; :foo :bar ]. qualifiedUsage qualified entities-activities qualifiedUsingActivity A prov:Entity that was used by this prov:Activity. For example, :baking prov:used :spoon, :egg, :oven . For provenance reporting in MIAPA, the property linking an activity that generated an output (such as a tree inference procedure involving software) to the parameter specification that was the plan for executing the software. used starting-point entities-activities wasUsedBy An prov:Agent that had some (unspecified) responsibility for the occurrence of this prov:Activity. For provenance reporting in MIAPA, the property linking the activity that generated an output to the agent that was involved in (responsible for) it. For software procedures, this will be a SoftwareAgent, and for manual procedures it will be a Person. wasAssociatedWith starting-point agents-responsibility wasAssociateFor Attribution is the ascribing of an entity to an agent. wasAttributedTo starting-point agents-responsibility Attribution is the ascribing of an entity to an agent. contributed Attribution is a particular case of trace (see http://www.w3.org/TR/prov-dm/#concept-trace), in the sense that it links an entity to the agent that ascribed it. IF wasAttributedTo(e2,ag1,aAttr) holds, THEN wasInfluencedBy(e2,ag1) also holds. For MIAPA reporting, recommended as the property relating a phylogenetic tree to the data matrix (or matrices) from which it was derived. The more specific subproperties of prov:wasDerivedFrom (i.e., prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource) should be used when applicable. wasDerivedFrom starting-point derivations A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. hadDerivation Derivation is a particular case of trace (see http://www.w3.org/TR/prov-dm/#term-trace), since it links an entity to another entity that contributed to its existence. End is when an activity is deemed to have ended. An end may refer to an entity, known as trigger, that terminated the activity. wasEndedBy expanded entities-activities ended For provenance reporting in MIAPA, the property linking the tree or the data matrix to the activity that generated it. wasGeneratedBy starting-point entities-activities generated Because prov:wasInfluencedBy is a broad relation, its more specific subproperties (e.g. prov:wasInformedBy, prov:actedOnBehalfOf, prov:wasEndedBy, etc.) should be used when applicable. This property has multiple RDFS domains to suit multiple OWL Profiles. See <a href="#owl-profile">PROV-O OWL Profile</a>. wasInfluencedBy qualified agents-responsibility The sub-properties of prov:wasInfluencedBy can be elaborated in more detail using the Qualification Pattern. For example, the binary relation :baking prov:used :spoon can be qualified by asserting :baking prov:qualifiedUsage [ a prov:Usage; prov:entity :spoon; prov:atLocation :kitchen ] . Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. prov:wasInfluencedBy should not be used without also using one of its subproperties. influenced influencee: an identifier (o2) for an entity, activity, or agent; http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence influencer: an identifier (o1) for an ancestor entity, activity, or agent that the former depends on; http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence An activity a2 is dependent on or informed by another activity a1, by way of some unspecified entity that is generated by a1 and used by a2. wasInformedBy starting-point entities-activities informed wasInvalidatedBy expanded entities-activities invalidated An entity is derived from an original entity by copying, or 'quoting', some or all of it. wasQuotedFrom expanded derivations quotedAs Quotation is a particular case of derivation (see http://www.w3.org/TR/prov-dm/#term-quotation) in which an entity is derived from an original entity by copying, or "quoting", some or all of it. Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.' Start is when an activity is deemed to have started. A start may refer to an entity, known as trigger, that initiated the activity. wasStartedBy expanded entities-activities started has_Precision has_Point_Coordinate_Value has_Int_Value has_Support_Value In MIAPA-compliant reporting, can be used to provide the value for instances of cdao:EdgeLength (or one of its subclasses) used for annotating edges with lengths. has_Value has_Uncertainty_Factor has_Range_End_Value has_Float_Value has_Range_Start_Value This data property is one way for providing MIAPA-compliant edge lengths, in this case branch lengths. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value. branch length This data property is one way for providing MIAPA-compliant edge lengths, in this case bootstrap values. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value. bootstrap value This data property is one way for providing MIAPA-compliant edge lengths, in this case posterior probabilities. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value. posterior probability has edge length The time at which an InstantaneousEvent occurred, in the form of xsd:dateTime. atTime qualified entities-activities The time at which an activity ended. See also prov:startedAtTime. endedAtTime starting-point entities-activities It is the intent that the property chain holds: (prov:qualifiedEnd o prov:atTime) rdfs:subPropertyOf prov:endedAtTime. The time at which an entity was completely created and is available for use. generatedAtTime expanded entities-activities It is the intent that the property chain holds: (prov:qualifiedGeneration o prov:atTime) rdfs:subPropertyOf prov:generatedAtTime. The time at which an entity was invalidated (i.e., no longer usable). invalidatedAtTime expanded entities-activities It is the intent that the property chain holds: (prov:qualifiedInvalidation o prov:atTime) rdfs:subPropertyOf prov:invalidatedAtTime. The time at which an activity started. See also prov:endedAtTime. startedAtTime starting-point entities-activities It is the intent that the property chain holds: (prov:qualifiedStart o prov:atTime) rdfs:subPropertyOf prov:startedAtTime. For provenance reporting in MIAPA, the property for giving the literal value of a provenance entity, specifically the value of parameter specifications (which are instances of prov:Plan, a subclass of prov:Entity). value expanded entities-activities Provides a value that is a direct representation of an entity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-value The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values'). edam:operation_0004 For the purposes of MIAPA annotation and cross-ontology interoperability, instances of edam:Operation are instances of a prov:Activity. They need to be further classified as to whether they are maipa:'Manual procedure' or miapa:'Software procedure' instances. Operation edam:operation_0323 Phylogenetic tree construction edam:operation_0539 Phylogenetic tree construction (method centric) edam:operation_2928 Alignment construction BFO:0000031 CDAO:0000002 DesoxiRibonucleotideResidueStateDatum CDAO:0000003 CoordinatePoint CDAO:0000004 Lineage CDAO:0000005 Phylo4Tree CDAO:0000006 Network CDAO:0000007 Description of a model of transformations. For MIAPA-compliant reporting, the model description is a kind of miapa:'Parameter specification', and this a kind of prov:Plan. Alternatively, we could model this as dc:isPartOf some prov:Plan. This is a non-computible description of a model, not the fully specified mathematical model, which typically relates the probability of a transformation to various parameters. ModelDescription CDAO:0000008 StandardStateDatum CDAO:0000009 ContinuousCharacterLengthType CDAO:0000010 ContinuousCharBayesianLengthType CDAO:0000011 NEXUSTreeBlock 1 CDAO:0000012 RootedTree CDAO:0000013 Kimura2Parameters CDAO:0000014 A procedure that generates the tree. For provenance annotation in MIAPA, the activity that generated the tree should be asserted as an instance of cdao:TreeProcedure. TreeProcedure See https://github.com/miapa/miapa/issues/5 CDAO:0000015 This concept is tied to the verbally ambiguous 'gap' concept and to the use of a gap character (often the en dash '-') in text representations of sequence alignments. In general, this represents the absence of any positively diagnosed Character-State. As such, the gap may be interpreted as an additional Character-State, as the absence of the Character, or as an unknown value. In some cases it is helpful to separate these. This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing. Generic_State CDAO:0000016 UnrootedSubtree CDAO:0000017 UnresolvedTree CDAO:0000018 BifurcatingTree CDAO:0000019 ContinuousStateDatum CDAO:0000020 SubstitutionModel CDAO:0000021 JukesCantor 1 CDAO:0000022 A positional coordinate giving the source of a character state, used for molecular sequences. drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on DatumCoordinate CDAO:0000023 UnresolvedRootedTree CDAO:0000024 'Branch' is the domain-specific synonym for an edge of a (Phylogenetic) Tree or Network. Branches may have properties such as length and degree of support. Branch CDAO:0000025 Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment. CharacterStateDataMatrixAnnotation CDAO:0000026 AncestralNode CDAO:0000027 UnresolvedUnrootedTree CDAO:0000029 UncertainStateDomain 2 CDAO:0000030 ReconcileTree 1 CDAO:0000031 This class describes a continuous value. The link to the actual float value is through the property has_Value. It could have also other properties attached (e.g., has_Precision). Continuous CDAO:0000032 A procedure that generates the alignment. For provenance annotation in MIAPA, the activity that generated the alignment should be asserted as an instance of cdao:AlignmentProcedure. AlignmentProcedure https://github.com/miapa/miapa/issues/5 CDAO:0000033 Dichotomy CDAO:0000034 Molecular CDAO:0000035 ContinuousCharParsimonyLengthType CDAO:0000039 Categorical CDAO:0000040 The base class of annotations in CDAO. Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists. CDAOAnnotation CDAO:0000041 originationEvent 3 CDAO:0000042 Polytomy 1.0 CDAO:0000043 PolymorphicStateDomain CDAO:0000044 TreeAnnotation CDAO:0000045 Standard CDAO:0000046 The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character. Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data. EdgeLength To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete. CDAO:0000047 RibonucleotideResidue CDAO:0000048 Clade CDAO:0000049 DiscreteCharParsimonyLengthType CDAO:0000050 MolecularStateDatum CDAO:0000051 PolyphyleticGroup CDAO:0000052 NexusDataBlock 2 CDAO:0000053 BranchingNode CDAO:0000055 Compound CDAO:0000056 A matrix of character-state data, typically containing observed data, though in some cases the states in the matrix might be simulated or hypothetical. Synonyms: character Data matrix, character-state matrix CharacterStateDataMatrix CDAO:0000057 RibonucleotideResidueStateDatum CDAO:0000058 TimeCalibratedLengthType CDAO:0000059 SetOfNodes 1 CDAO:0000060 MRCANode CDAO:0000061 FASTADataMatrix 1 1 1 CDAO:0000062 evolutionaryTransition CDAO:0000063 EdgeLengthType CDAO:0000064 cladogeneticChange CDAO:0000065 anageneticChange CDAO:0000066 TUAnnotation CDAO:0000067 PhyloTree CDAO:0000068 ContinuousCharacter CDAO:0000069 PHYLIPTree CDAO:0000070 Subtree CDAO:0000071 Traits shown to be relevant for phylogenetic classification Character CDAO:0000072 GalledTree CDAO:0000073 SpeciesTree CDAO:0000074 TreeFormat CDAO:0000075 StandardCharacter CDAO:0000076 This class will be declared equivalent ot the amino acid class description imported AminoAcidResidue CDAO:0000077 geneDuplication CDAO:0000078 A character that could be divided into separate characters but is not due to the non-independence of changes that would result, e.g., as in the case of a subsequence that is either present or absent as a block. CompoundCharacter CDAO:0000079 SIMMAPTree CDAO:0000080 CommonAncestralNode CDAO:0000081 NewickTree CDAO:0000082 TimeProportionalLengthType CDAO:0000083 DiscreteCharDistanceLengthType CDAO:0000084 StarTree CDAO:0000085 FullyResolvedUnrootedTree CDAO:0000086 ParaphyleticGroup CDAO:0000087 geneticEvent CDAO:0000088 UnrootedTree CDAO:0000089 CategoricalStateDatum CDAO:0000090 DiscreteCharLikelihoodLengthType CDAO:0000091 The universe of possible states for a particular type of character, e.g., the states of an Amino_Acid character come from the Amino_Acid domain. CharacterStateDomain CDAO:0000092 CoordinateList CDAO:0000093 GammaDistribution CDAO:0000094 DesoxiRibonucleotideResidueCharacter CDAO:0000095 CoordinateRange CDAO:0000096 ReticulateEvolution 1 1 1 CDAO:0000097 hereditaryChange 1 1 CDAO:0000098 The instance of a given character for a given TU. Its state is an object property drawn from a particular character state domain, e.g., the state of an Amino_Acid_State_Datum is an object property drawn from the domain Amino_Acid. CharacterStateDatum 2 CDAO:0000099 An edge connecting two nodes in a (Phylogenetic) Tree or Network, also known as a 'branch'. Edges may have attributes such as length, degree of support, and direction. An edge can be a surrogate for a 'split' or bipartition, since each edge in a tree divides the terminal nodes into two sets. Edge CDAO:0000100 DiscreteCharacterLengthType CDAO:0000101 EdgeAnnotation CDAO:0000102 FullyResolvedRootedTree CDAO:0000103 GrafenLengthType CDAO:0000104 A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system. CoordinateSystem CDAO:0000105 GenBankDataMatrix CDAO:0000107 DataMatrixFormat CDAO:0000108 TerminalNode CDAO:0000109 RibonucleotideResidueCharacter CDAO:0000110 Tree CDAO:0000111 CategoricalCharacter CDAO:0000112 AminoAcidResidueStateDatum CDAO:0000113 PHYLIPDataMatrix CDAO:0000114 ContinuousCharLikelihoodLengthType CDAO:0000115 MolecularCharacter CDAO:0000116 hereditaryPersistance CDAO:0000117 SetOfCharacters CDAO:0000118 The class is used to describe colletions of phylogenetic data elements. Examples include sets of trees for annotating consensus tree provenance, and sets of characters or higher order grouping (e.g., groups of groups of characters) that extends the CharSet block of NEXUS. SetOfThings 1 CDAO:0000120 A set of ordered states, typically the residues in a macromolecular sequence. Sequence CDAO:0000121 speciation CDAO:0000122 cladogenesis 2 CDAO:0000124 Bifurcation CDAO:0000125 DiscreteCharBayesianLengthType CDAO:0000126 Link to an externally defined taxonomic hierarchy. TaxonomicLink CDAO:0000127 MonophyleticGroup CDAO:0000128 molecularRecombination CDAO:0000129 HolophyleticGroup CDAO:0000130 FullyResolvedTree CDAO:0000131 AminoAcidResidueCharacter CDAO:0000132 recombination CDAO:0000133 DesoxiRibonucleotideResidue CDAO:0000134 RootedSubtree CDAO:0000136 CompoundStateDatum CDAO:0000137 GapCost CDAO:0000138 A unit of analysis that may be tied to a node in a tree and to a row in a character matrix. It subsumes the traditional concepts of 'OTU' and 'HTU'. TU 1 1 CDAO:0000139 A directed edge. Rooted trees have directed edges. The direction is specified by way of the parent and child relationships of nodes that the edge connects. DirectedEdge 1 CDAO:0000140 Node CDAO:0000141 ContinuousCharDistanceLengthType IAO:0000010 software IAO:0000027 data item IAO:0000028 symbol IAO:0000030 information content entity IAO:0000033 directive information entity IAO:0000064 algorithm IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO: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 IAO:0000129 version number 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: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:8000000 I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. cjm 2018-05-20T20:55:03Z ontology module IAO:8000001 An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. cjm 2018-05-20T20:55:30Z base ontology module IAO:8000002 An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module cjm 2018-05-20T20:55:47Z editors ontology module IAO:8000003 An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module cjm 2018-05-20T20:56:13Z main release ontology module IAO:8000004 An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. cjm 2018-05-20T20:56:23Z bridge ontology module IAO:8000005 A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file cjm 2018-05-20T20:56:47Z import ontology module IAO:8000006 An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology cjm 2018-05-20T20:58:11Z subset ontology module IAO:8000007 A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. cjm 2018-05-20T20:58:38Z curation subset ontology module IAO:8000008 An ontology module that is intended for usage in analysis or discovery applications. cjm 2018-05-20T20:58:49Z analysis subset ontology module IAO:8000009 A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset cjm 2018-05-20T20:59:19Z single layer subset ontology module IAO:8000010 A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim cjm 2018-05-20T20:59:57Z exclusion subset ontology module IAO:8000011 An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import cjm 2018-05-20T21:00:14Z external import ontology module IAO:8000012 A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset cjm 2018-05-20T21:14:16Z species subset ontology module IAO:8000013 An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. cjm 2018-05-20T21:20:33Z reasoned ontology module IAO:8000014 An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process cjm 2018-05-20T21:21:12Z generated ontology module IAO:8000015 An ontology module that is automatically generated from a template specification and fillers for slots in that template. cjm 2018-05-20T21:21:21Z template generated ontology module IAO:8000016 cjm 2018-05-20T21:28:15Z taxonomic bridge ontology module IAO:8000017 cjm 2018-05-22T04:15:54Z ontology module subsetted by expressivity IAO:8000018 A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports cjm 2018-05-22T04:16:10Z obo basic subset ontology module IAO:8000019 cjm 2018-05-22T04:16:28Z ontology module subsetted by OWL profile IAO:8000020 cjm 2018-05-22T04:16:48Z EL++ ontology module MIAPA:0000001 Gene tree MIAPA:0000002 Consensus tree MIAPA:0000003 A procedure (a type of prov:Activity) that involves running software to generate the output, and is therefore associated with a piece of software, and uses a parameter specification as the plan for running the software. Software procedure MIAPA:0000009 A procedure (a type of prov:Activity) that involves a person making manual manipulations to data, such as manually editing an alignment. An alignment procedure can involve both running software and manual editing to generate the output, and therefore ManualProcedure and SoftwareProcedure are not disjoint. Manual procedure MIAPA:0000010 Parameter specification MIAPA:0000015 Should be pushed down to SWO. Maximum likelihood method MIAPA:0000016 Should be pushed down to SWO. RAxML MIAPA:0000020 Should be pushed down to SWO. MAFFT MIAPA:0000022 Should be pushed down to SWO. SINA MIAPA:0000024 Should be pushed down to SWO. PRANK MIAPA:0000025 Should be pushed down to SWO. PAUP* MIAPA:0000026 Should be pushed down to SWO. TNT MIAPA:0000027 Should be pushed down to SWO. PhyML MIAPA:0000028 Should be pushed down to SWO. AMPHORA MIAPA:0000032 GTR+GAMMA MIAPA:0000033 GTR+CAT MIAPA:0000034 WAG MIAPA:0000037 A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the "maximum parsimony tree") is the phylogenetic tree that minimizes evolutionary transitions over all characters. Should be pushed down to SWO. Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/ https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method Parsimony method MIAPA:0000038 Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree. Should be pushed down to SWO. Hilmar Lapp Phylogenetic tree construction (pruning and grafting) MIAPA:0000039 To be pushed down to CDAO. This would retain though in MIAPA the equivalence to "prov:Collection and provhadMember only cdao:Network". SetOfNetworks MIAPA:0000040 To be pushed down to CDAO. This would retain though in MIAPA the equivalence to "prov:Collection and provhadMember only cdao:Network". SetOfTrees MIAPA:0000041 Should be pushed down to SWO. MrBayes MIAPA:0000044 Should be pushed down to SWO. BEAST dcterms:Location dsw:Specimen swo2:SWO_0000592 Likelihood method swo:SWO_0000060 MUSCLE oboInOwl:DbXref oboInOwl:Definition oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Thing Activity prov:Activity For provenance annotation in MIAPA, instances of prov:Activity (or one of its subclasses) generate parts of the data such as the alignment and the tree. They are linked to tree or alignment through the property prov:wasGeneratedBy. Activity starting-point entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Activity http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Activity 0 ActivityInfluence ActivityInfluence provides additional descriptions of an Activity's binary influence upon any other kind of resource. Instances of ActivityInfluence use the prov:activity property to cite the influencing Activity. It is not recommended that the type ActivityInfluence be asserted without also asserting one of its more specific subclasses. ActivityInfluence qualified ActivitiyInfluence is the capacity of an activity to have an effect on the character, development, or behavior of another by means of generation, invalidation, communication, or other. Agent prov:Agent For provenance annotation in MIAPA, instances of prov:Agent, or more specifically an instance of prov:Person and/or prov:SoftwareAgent, are involved in (associated with, responsible for) the prov:Activity that generated a certain piece of the data (such as an alignment, or a tree). Agent starting-point agents-responsibility An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Agent AgentInfluence AgentInfluence provides additional descriptions of an Agent's binary influence upon any other kind of resource. Instances of AgentInfluence use the prov:agent property to cite the influencing Agent. It is not recommended that the type AgentInfluence be asserted without also asserting one of its more specific subclasses. AgentInfluence qualified AgentInfluence is the capacity of an agent to have an effect on the character, development, or behavior of another by means of attribution, association, delegation, or other. Association An instance of prov:Association provides additional descriptions about the binary prov:wasAssociatedWith relation from an prov:Activity to some prov:Agent that had some responsiblity for it. For example, :baking prov:wasAssociatedWith :baker; prov:qualifiedAssociation [ a prov:Association; prov:agent :baker; :foo :bar ]. Association qualified agents-responsibility An activity association is an assignment of responsibility to an agent for an activity, indicating that the agent had a role in the activity. It further allows for a plan to be specified, which is the plan intended by the agent to achieve some goals in the context of this activity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Association http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Association Attribution An instance of prov:Attribution provides additional descriptions about the binary prov:wasAttributedTo relation from an prov:Entity to some prov:Agent that had some responsible for it. For example, :cake prov:wasAttributedTo :baker; prov:qualifiedAttribution [ a prov:Attribution; prov:entity :baker; :foo :bar ]. Attribution qualified agents-responsibility http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Attribution is the ascribing of an entity to an agent. When an entity e is attributed to agent ag, entity e was generated by some unspecified activity that in turn was associated to agent ag. Thus, this relation is useful when the activity is not known, or irrelevant. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribution http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribution Bundle Note that there are kinds of bundles (e.g. handwritten letters, audio recordings, etc.) that are not expressed in PROV-O, but can be still be described by PROV-O. Bundle expanded A bundle is a named set of provenance descriptions, and is itself an Entity, so allowing provenance of provenance to be expressed. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-bundle-entity http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-bundle-declaration Collection prov:Collection Collection expanded collections A collection is an entity that provides a structure to some constituents, which are themselves entities. These constituents are said to be member of the collections. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-collection Communication An instance of prov:Communication provides additional descriptions about the binary prov:wasInformedBy relation from an informed prov:Activity to the prov:Activity that informed it. For example, :you_jumping_off_bridge prov:wasInformedBy :everyone_else_jumping_off_bridge; prov:qualifiedCommunication [ a prov:Communication; prov:activity :everyone_else_jumping_off_bridge; :foo :bar ]. Communication qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Communication is the exchange of an entity by two activities, one activity using the entity generated by the other. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Communication http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-wasInformedBy Delegation An instance of prov:Delegation provides additional descriptions about the binary prov:actedOnBehalfOf relation from a performing prov:Agent to some prov:Agent for whom it was performed. For example, :mixing prov:wasAssociatedWith :toddler . :toddler prov:actedOnBehalfOf :mother; prov:qualifiedDelegation [ a prov:Delegation; prov:entity :mother; :foo :bar ]. Delegation qualified agents-responsibility Delegation is the assignment of authority and responsibility to an agent (by itself or by another agent) to carry out a specific activity as a delegate or representative, while the agent it acts on behalf of retains some responsibility for the outcome of the delegated work. For example, a student acted on behalf of his supervisor, who acted on behalf of the department chair, who acted on behalf of the university; all those agents are responsible in some way for the activity that took place but we do not say explicitly who bears responsibility and to what degree. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-delegation http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-delegation Derivation An instance of prov:Derivation provides additional descriptions about the binary prov:wasDerivedFrom relation from some derived prov:Entity to another prov:Entity from which it was derived. For example, :chewed_bubble_gum prov:wasDerivedFrom :unwrapped_bubble_gum; prov:qualifiedDerivation [ a prov:Derivation; prov:entity :unwrapped_bubble_gum; :foo :bar ]. The more specific forms of prov:Derivation (i.e., prov:Revision, prov:Quotation, prov:PrimarySource) should be asserted if they apply. Derivation qualified derivations http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Derivation http://www.w3.org/TR/2013/REC-prov-n-20130430/#Derivation-Relation End An instance of prov:End provides additional descriptions about the binary prov:wasEndedBy relation from some ended prov:Activity to an prov:Entity that ended it. For example, :ball_game prov:wasEndedBy :buzzer; prov:qualifiedEnd [ a prov:End; prov:entity :buzzer; :foo :bar; prov:atTime '2012-03-09T08:05:08-05:00'^^xsd:dateTime ]. End qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig End is when an activity is deemed to have been ended by an entity, known as trigger. The activity no longer exists after its end. Any usage, generation, or invalidation involving an activity precedes the activity's end. An end may refer to a trigger entity that terminated the activity, or to an activity, known as ender that generated the trigger. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-End http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-End Entity prov:Entity For provenance annotation in MIAPA, the instances of a tree and of an alignment are entities for which provenance information (how they were generated) is required to be tracked (and thus annotated). Entity starting-point entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-entity http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Entity EntityInfluence EntityInfluence provides additional descriptions of an Entity's binary influence upon any other kind of resource. Instances of EntityInfluence use the prov:entity property to cite the influencing Entity. It is not recommended that the type EntityInfluence be asserted without also asserting one of its more specific subclasses. EntityInfluence qualified EntityInfluence is the capacity of an entity to have an effect on the character, development, or behavior of another by means of usage, start, end, derivation, or other. Generation An instance of prov:Generation provides additional descriptions about the binary prov:wasGeneratedBy relation from a generated prov:Entity to the prov:Activity that generated it. For example, :cake prov:wasGeneratedBy :baking; prov:qualifiedGeneration [ a prov:Generation; prov:activity :baking; :foo :bar ]. Generation qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Generation is the completion of production of a new entity by an activity. This entity did not exist before generation and becomes available for usage after this generation. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Generation http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Generation Influence An instance of prov:Influence provides additional descriptions about the binary prov:wasInfluencedBy relation from some influenced Activity, Entity, or Agent to the influencing Activity, Entity, or Agent. For example, :stomach_ache prov:wasInfluencedBy :spoon; prov:qualifiedInfluence [ a prov:Influence; prov:entity :spoon; :foo :bar ] . Because prov:Influence is a broad relation, the more specific relations (Communication, Delegation, End, etc.) should be used when applicable. Because prov:Influence is a broad relation, its most specific subclasses (e.g. prov:Communication, prov:Delegation, prov:End, prov:Revision, etc.) should be used when applicable. Influence qualified derivations Influence is the capacity of an entity, activity, or agent to have an effect on the character, development, or behavior of another by means of usage, start, end, generation, invalidation, communication, derivation, attribution, association, or delegation. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-influence http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-influence InstantaneousEvent An instantaneous event, or event for short, happens in the world and marks a change in the world, in its activities and in its entities. The term 'event' is commonly used in process algebra with a similar meaning. Events represent communications or interactions; they are assumed to be atomic and instantaneous. InstantaneousEvent qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#dfn-event The PROV data model is implicitly based on a notion of instantaneous events (or just events), that mark transitions in the world. Events include generation, usage, or invalidation of entities, as well as starting or ending of activities. This notion of event is not first-class in the data model, but it is useful for explaining its other concepts and its semantics. Invalidation An instance of prov:Invalidation provides additional descriptions about the binary prov:wasInvalidatedBy relation from an invalidated prov:Entity to the prov:Activity that invalidated it. For example, :uncracked_egg prov:wasInvalidatedBy :baking; prov:qualifiedInvalidation [ a prov:Invalidation; prov:activity :baking; :foo :bar ]. Invalidation qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Invalidation is the start of the destruction, cessation, or expiry of an existing entity by an activity. The entity is no longer available for use (or further invalidation) after invalidation. Any generation or usage of an entity precedes its invalidation. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Invalidation http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Invalidation Location Location expanded A location can be an identifiable geographic place (ISO 19112), but it can also be a non-geographic place such as a directory, row, or column. As such, there are numerous ways in which location can be expressed, such as by a coordinate, address, landmark, and so forth. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-location http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribute Organization Organization expanded agents-responsibility An organization is a social or legal institution such as a company, society, etc. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types Person prov:Person Person expanded agents-responsibility Person agents are people. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types Plan prov:Plan There exist no prescriptive requirement on the nature of plans, their representation, the actions or steps they consist of, or their intended goals. Since plans may evolve over time, it may become necessary to track their provenance, so plans themselves are entities. Representing the plan explicitly in the provenance can be useful for various tasks: for example, to validate the execution as represented in the provenance record, to manage expectation failures, or to provide explanations. Plan expanded qualified agents-responsibility A plan is an entity that represents a set of actions or steps intended by one or more agents to achieve some goals. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Association http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Association PrimarySource An instance of prov:PrimarySource provides additional descriptions about the binary prov:hadPrimarySource relation from some secondary prov:Entity to an earlier, primary prov:Entity. For example, :blog prov:hadPrimarySource :newsArticle; prov:qualifiedPrimarySource [ a prov:PrimarySource; prov:entity :newsArticle; :foo :bar ] . PrimarySource qualified derivations A primary source for a topic refers to something produced by some agent with direct experience and knowledge about the topic, at the time of the topic's study, without benefit from hindsight. Because of the directness of primary sources, they 'speak for themselves' in ways that cannot be captured through the filter of secondary sources. As such, it is important for secondary sources to reference those primary sources from which they were derived, so that their reliability can be investigated. A primary source relation is a particular case of derivation of secondary materials from their primary sources. It is recognized that the determination of primary sources can be up to interpretation, and should be done according to conventions accepted within the application's domain. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-primary-source http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-original-source Quotation An instance of prov:Quotation provides additional descriptions about the binary prov:wasQuotedFrom relation from some taken prov:Entity from an earlier, larger prov:Entity. For example, :here_is_looking_at_you_kid prov:wasQuotedFrom :casablanca_script; prov:qualifiedQuotation [ a prov:Quotation; prov:entity :casablanca_script; :foo :bar ]. Quotation qualified derivations A quotation is the repeat of (some or all of) an entity, such as text or image, by someone who may or may not be its original author. Quotation is a particular case of derivation. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-quotation http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-quotation Revision An instance of prov:Revision provides additional descriptions about the binary prov:wasRevisionOf relation from some newer prov:Entity to an earlier prov:Entity. For example, :draft_2 prov:wasRevisionOf :draft_1; prov:qualifiedRevision [ a prov:Revision; prov:entity :draft_1; :foo :bar ]. Revision qualified derivations A revision is a derivation for which the resulting entity is a revised version of some original. The implication here is that the resulting entity contains substantial content from the original. Revision is a particular case of derivation. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-revision http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Revision Role Role qualified agents-responsibility A role is the function of an entity or agent with respect to an activity, in the context of a usage, generation, invalidation, association, start, and end. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-attribute-role http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-attribute SoftwareAgent prov:SoftwareAgent SoftwareAgent expanded agents-responsibility A software agent is running software. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types Start An instance of prov:Start provides additional descriptions about the binary prov:wasStartedBy relation from some started prov:Activity to an prov:Entity that started it. For example, :foot_race prov:wasStartedBy :bang; prov:qualifiedStart [ a prov:Start; prov:entity :bang; :foo :bar; prov:atTime '2012-03-09T08:05:08-05:00'^^xsd:dateTime ] . Start qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Start is when an activity is deemed to have been started by an entity, known as trigger. The activity did not exist before its start. Any usage, generation, or invalidation involving an activity follows the activity's start. A start may refer to a trigger entity that set off the activity, or to an activity, known as starter, that generated the trigger. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Start http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Start Usage An instance of prov:Usage provides additional descriptions about the binary prov:used relation from some prov:Activity to an prov:Entity that it used. For example, :keynote prov:used :podium; prov:qualifiedUsage [ a prov:Usage; prov:entity :podium; :foo :bar ]. Usage qualified entities-activities http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig Usage is the beginning of utilizing an entity by an activity. Before usage, the activity had not begun to utilize this entity and could not have been affected by the entity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-Usage http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Usage dA absent unknown gap dG rU dC dT 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 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 It is possible that this really should be a class instead of an individual, namely the class of all default parameter specifications (which would then have instances specific to programs). default parameters unspecified parameters 7.2.8 3.7 6.712b 4.0b10 7.2.7 10 7.2.6, Pthreads-based and SSE3-vectorized 3.2 1.5.1 This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome. W3C PROVenance Interchange Ontology (PROV-O) Recommendation version 2013-04-30 This property associates a character data matrix with a character (a column) represented in the matrix. has_Character This property relates a character to a state datum for the character. has_Datum This property links two networks where the latter is a substructure of the former subtree_of This property relates an amino acid character (a column in a protein sequence alignment) to a state datum for the character (an individual cell in the alignment column). has_Amino_Acid_Datum This property relates a compound character (a character with some states that are subdividable) to a state datum for the character. has_Compound_Datum A property that links a node to any of its descendants in a rooted tree. has_Descendant has_Type Generic 'has' property. has exclude_Node Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of. belongs_to For providing MIAPA-compliant edge lengths, one should normally use its subproperty miapa:edgeLength. The alternative is to use the miapa:'has edge length' data property or one of its subproperties. has_Annotation This property relates a nucleotide character (a column in a nucleotide alignment) to a state datum for the character (an individual cell in the alignment column). has_Nucleotide_Datum exclude_Subtree has_Lineage_node This property relates a continuous character to a state datum for the character. has_Continuous_Datum This property associates a character data matrix with a TU (a row) represented in the matrix. has_TU Comparison of two or more biological entities of the same class when the similarities and differences of the entities are treated explicitly as the product of an evolutionary process of descent with modification. CDAO Team The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics Comparative Data Analysis Ontology Hilmar Lapp Phylotastic Tree Annotation Team The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA. http://creativecommons.org/publicdomain/zero/1.0/ Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology 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 EmptyCollection EmptyCollection expanded collections An empty collection is a collection without members. specializationOf expanded alternate http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig An entity that is a specialization of another shares all aspects of the latter, and additionally presents more specific aspects of the same thing as the latter. In particular, the lifetime of the entity being specialized contains that of any specialization. Examples of aspects include a time period, an abstraction, and a context associated with the entity. http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-specialization generalizationOf http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-specialization A revision is a derivation that revises an entity into a revised version. wasRevisionOf expanded derivations hadRevision