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 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 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 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). 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 part_of This property relates a TU to a node that represents it in a network. 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 has_Precision has_Point_Coordinate_Value has_Int_Value has_Support_Value has_Value has_Uncertainty_Factor has_Range_End_Value has_Float_Value has_Range_Start_Value 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. 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 TreeProcedure 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 JukesKantor 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 1 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 AlignmentProcedure 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 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 1 CDAO:0000140 Node CDAO:0000141 ContinuousCharDistanceLengthType IAO:0000027 data item IAO:0000030 information content entity 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: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 oboInOwl:DbXref oboInOwl:Definition oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Thing 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 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 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 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