OBO Annotation Properties (BIRN derived)
type: Ontology
creator: The BIRN Ontology Task Force
date: 2006-10-07 (createdDate)
date: 2008-03-13 (modifiedDate)
version info: 1.3.0
comment: These are annotation properties the BIRN OTF expects will be shared by the community, not limited to the specific ontology development needs of BIRN. This current ontology is a proposal to be reviewed by the OBO Foundry participants and developers of other OBO Foundry ontologies - e.g., OBI, PaTO, GO, etc..
change note: Explicitly removed ALL rdfs:type=DatatypeProperty declarations automatigically added to these AnnotationProperties by Protege-OWL v3.3beta
change note: Now using a specific set of AnnotationProperties that link to specific Enumeration classes to specify annotations from a fixed list of values - e.g., ExternalSource, DefinitionSource. This is the second iteration of this mechanism (first was put in v1.2.2). This second version follows a patter recommended by Alan Ruttenberg which avoids using ObjectProperties as the Manchester design pattern for Value Partitions recommends, and instead sticks to AnnotationProperties only. Note this version of OBO_annotation_properties uses the same EnumerationClasses from v1.2.2, and still includes the related ObjectProperties, so as to be able to support XSLT-based translation of the BIRNLex files that used the v1.2.2 pattern. The next version of this file will eliminate the ObjectProperties and will rename the equivalent AnnotationProperties to remove the trailing '2' put in there to provide a unique name.
change note: Have 'cleansed' the file to be OWL-DL.
change note: v1.3.0 (2007-08-03) - Changed many things, but primarily: (1) removed rdf:datatype xsd:string specs for all AnnotationProperties, since they are now all untyped and should assume STRING as a the default; (2) added the typing of AnnotationProperties using annotationType which should aid in algorithmically processing.
change note: (2008-01-28) - fixed and annotationType that was missing the namespace prefix obo_annot.
change note: (2008-03-13) - finally added annotation prop for GO ID.
imports: skos-core-owl-dl.owl
imports: protege-dc.owl

EnumerationClass
type: Class
date: 2007-05-04 (createdDate)
date: 2007-05-04 (modifedDate)
scope note: A parent class for all enumerations used for class annotation.

AbbrevSource
type: Class
definition: The source authority for an externally derived class term abbreviation
subclass of: EnumerationClass

hasAbbrevSource
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#EnumerationClass
has validation method: sparql_verify_annotation_domain_and_range
annotation type: http://purl.org/dc/elements/1.1/relation

DefinitionSource
type: Class
subclass of: EnumerationClass
definition: The source authority for an externally derived definition
equivalent class: http://lodlaundromat.org/.well-known/genid/6c5ed3888b506cec8809a5d00b80ec3a#1

hasDefinitionSource
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#EnumerationClass
has validation method: sparql_verify_annotation_domain_and_range

ExternalSource
type: Class
subclass of: EnumerationClass
definition: Class derived from an external knowledge source
equivalent class: http://lodlaundromat.org/.well-known/genid/6c5ed3888b506cec8809a5d00b80ec3a#21

hasExternalSource
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#EnumerationClass
has validation method: sparql_verify_annotation_domain_and_range

pendingMereotopologicalRelationNote
type: AnnotationProperty
definition: A note describing a known mereotopological spatial relation in which this class participates that is beyond pure subsumptive is_a relation. Is a type of pending_object_relation_note.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#pendingActionNote

termDerviedFrom
type: AnnotationProperty
definition: Indicates a term derives from an external source but has been substantially altered from that source. Is a type of skos_history_note.
annotation type: http://www.w3.org/2004/02/skos/core#historyNote

oboDefinition
type: AnnotationProperty
definition: This is a class definition meeting the non-circular and Aristotelean requirements given by the OBO Foundry principles.
editorial note: It also will likely include the related Aristotelean genus-differentia approach to applying this manner of definition construction as used now (as of 2006) in The Gene Ontology.
annotation type: http://www.w3.org/2004/02/skos/core#definition

curator
type: AnnotationProperty
definition: contributed to the properties, assertions, and other content associated with this class.
annotation type: http://purl.org/dc/elements/1.1/contributor

antiquated
type: AnnotationProperty
definition: A synonym no longer in common use.
definition: A lexical variant carrying the same latent semantic value.
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

definingCitationID
type: AnnotationProperty
definition: A namespace-specified ID for a record in a citation database providing information fundamental to the definition of an ontology class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

definingCitationURI
type: AnnotationProperty
definition: A publically accessible URI for a record in a citation database providing information fundamental to the definition of an ontology class.
annotation type: http://purl.org/dc/elements/1.1/relation

externalSourceURI
type: AnnotationProperty
definition: A publically accessible URI other than a standard bibliographic citation to the specific external source from which the content of an ontology Class was derived.
annotation type: http://purl.org/dc/elements/1.1/relation

definingCitation
type: AnnotationProperty
definition: A literature a citation providing information fundamental to the definition of an ontology class.
usage note: This AnnotationProperty should only be used whether there is neither a publicly accessible URI nor a namespace-qualified ID which can be used to algorithmically construct a complete citation for use in a user interface or search system (e.g., the way one can use PMID and the NCBI PublMed webservices or HTTP services to automatically access citation information).

UmlsCui
type: AnnotationProperty
editorial note: Is a type of obo_annot:obo_external_source_ID.
definition: This is the UMLS CUI ID for the concept associated with this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

MeshUid
type: AnnotationProperty
editorial note: Is a type of obo_annot:obo_external_source_ID.
definition: This is the Medical Subject Headings Unique ID for the concept associated with this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

GOid
type: AnnotationProperty
editorial note: Is a type of obo_annot:obo_external_source_ID.
definition: This is the Gene Ontology ID for the concept associated with this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

modifiedDate
type: AnnotationProperty
definition: the date when a class was last altered.
annotation type: http://purl.org/dc/elements/1.1/date

sourceIndirection
type: AnnotationProperty
definition: An indication of an external source from which this class is a direct subclass.
annotation type: http://www.w3.org/2004/02/skos/core#editorialNote

createdDate
type: AnnotationProperty
definition: The date when a class was added to the file.
annotation type: http://purl.org/dc/elements/1.1/date

externallySourcedDefinition
type: AnnotationProperty
definition: This is a class definition derived AS IS from an external, community knowledge resource.
annotation type: http://www.w3.org/2004/02/skos/core#definition

acronym
type: AnnotationProperty
definition: A synonym consisting of a sequence of letters typically taken from the beginning of words of which either the preferred label or another synonym are composed.
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

pendingFunctionalRelationNote
type: AnnotationProperty
definition: A note describing a known functional/process/occurant relation in which this class participates that is beyond pure subsumptive is_a relation. Is a type of pending_object_relation_note.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#pendingActionNote

misspelling
type: AnnotationProperty
definition: an incorrect spelling of either the preferred label or a synonym.
annotation type: http://www.w3.org/2004/02/skos/core#hiddenLabel

misnomer
type: AnnotationProperty
definition: incorrect term often found mistakenly used to refer to this class.
annotation type: http://www.w3.org/2004/02/skos/core#hiddenLabel

pendingObjectRelationNote
type: AnnotationProperty
definition: A note describing a known relation in which this class participates that is beyond pure subsumptive is_a relations.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#pendingActionNote

tempDefinition
type: AnnotationProperty
definition: a definition specifically declared to be temporary and in the midst of more detailed curation efforts.
annotation type: http://www.w3.org/2004/02/skos/core#definition

altDefinition
type: AnnotationProperty
definition: an additional, non-normative definition included while the curation status of a class is still pending.
editorial note: use of this property is discouraged. A well defined ontology class cannot allow for alternative definitions. This temporary_definition field should be used, when a definition is still pending full OBO definition status.
annotation type: http://www.w3.org/2004/02/skos/core#definition

taxonomicCommonName
type: AnnotationProperty
definition: This is the common name label frequently used to indicate a particular, species-level taxonomic group.
definition: The “common name” nametype is used for vernacular names associated with a particular taxon. These may be found at any level in the hierarchy; for example, “human”, “reptiles”, and “pale devil's-claw” are all used. Common names should be in lowercase letters, except where part of the name is derived from a proper noun, for example, “American butterfish” and “Robert's arbo- real rice rat”. The use of common names is inherently variable, regional, and often inconsistent. There is generally no authoritative reference that regulates the use of common names, and there is often not perfect correspondence between common names and formally described scientific taxa; therefore, there are some caveats to their use. For scientific discourse, there is no substitute for formal scientific names. Nevertheless, common names are invaluable for many indexing, retrieval, and display purposes. The combination “Oecomys roberti (Robert's arboreal rice rat)” conveys much more information than either name by itself. Issues raised by the variable, regional, and inexact use of common names are partly addressed by the “genbank common name” nametype (below) and the ability to customize names in the GenBank flatfile. (NCBI doc on NCBI Taxonomy, 2003).
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

externalSourceId
type: AnnotationProperty
definition: This field is to maintain the link back to an external source (see the externalSource property).
annotation type: http://purl.org/dc/elements/1.1/identifier

pendingActionNote
type: AnnotationProperty
definition: A note describing known tasks associate with a class that remain to be performed. This property should include a date in parenthesis to record when this pending action was first recognized as necessary.
alternative label: TODO
annotation type: http://www.w3.org/2004/02/skos/core#editorialNote

synonym
type: AnnotationProperty
definition: A lexical variant carrying the same latent semantic value.
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

abbrev
type: AnnotationProperty
definition: A lexical variant carrying the same latent semantic value.
definition: A synonym that is a shortened version of either the preferred lexical label of one of its synonyms
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

usageNote
type: AnnotationProperty
definition: A note providing guidance on the expected and appropriate usage of a given ontology class or relation. Note that a core:scopeNote is a type of usageNote where the specific range of classes, instances, or relations to which a given class or relation applies is constrained or scoped.

annotationType
type: AnnotationProperty
definition: A category designed to help data processing systems automatically determine how to process a given annotation.
scope note: The only valid values for this property are DC, SKOS, or BIRN AnnotationProperty URIs.
editorial note: The current use of this meta-property is to identify types of definitions (core:definition) and types of external source ID (dc:identifier) (BB: 2007-08-03.
editorial note: This is required, since sub-classing AnnotationProperties is not allowed in OWL-DL. Using this descriptive metadata AnnotationProperties, we can construct a chained code representation of a classification graph for AnnotationProperities very likely to be useful for information systems built to parse and process OWL content.
usage note: The legal cardinality range for annotationType applied to AnnotationProperties = 0...n - i.e., it is neither required, nor is it limited to a cardinality of 1, though it is recommend there be at least one annotationType for each AnnotationProperty, whenever there is an appropriate super-class available..

nifID
type: AnnotationProperty
definition: The ad-hoc ID created for entries in the Neuroscience Informatics Framework terminologies.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId