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