BIRNLex_annotation_properties
type: Ontology
creator: xml:lang="en"The BIRN Ontology Task Force
created date: 2006-09-26
modified date: 2008-03-21
version info: 1.3.1
comment: These are OWL Annotation Properties created by the BIRN OTF for the purposes of better managing the curation of the BIRNLex ontology.
change note: v1.2 (2007-03-20): Changed all Class identifiers to rdf:ID properties. Some had previously been rdf:about properties. Since Protege-OWL automatically sets new class identifiers to rdf:ID, I'm changing these across the files, to help make it more deterministic when parsing the RDF/XML.
change note: Processed file with XSLT to remove the explicit DataTypeProperty declarations (v1.2.2)
change note: Have 'cleansed' the file to be OWL-DL (v1.2.2).
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: 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; (3) added ReferenceURLTemplate to linked IDs to aid in algorithmically constructing URLs from IDs. The reference URL template provides a URL template that includes a specification of how to combine it with the associated ID to build a putative URL for an external resource - putative in the sense that there is no guarantee the external curating authority will maintain this URL template; however, with these paired fields - ID and URL template template - it should be possible to update the template, when the authority changes their URL template - an updated that would then be algorithmicaly percollated to the use of that field across BIRNLex.
change note: v1.3.1 (2007-11-30) - Removed some UTF8 characters that dont translate well to other encodings (e.g., curly double quotes 0xE2809C).
change note: (2008-03-13) - finally added Template URLs for GO ID.
change note: (2008-03-21) - finally added ID property and Template URLs for ChEBI and PubChem CIDs.
imports: OBO annotation properties.owl

_birnlex_retired_class
type: Class
created date: 2007-06-06
modified date: 2007-06-06
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug
birnlex definition: These are classes for which the represented entities are now described using a different class. A class is deprecated if it's semantic meaning required alteration or its entity is now represented directly in an imported foundational ontology. Such obseleted classes are removed from the core subsumptive hierarchy and retired to this root branch of the tree for this ontology. Deprecated classes maintain their original identifiers, so as to provide support for previous applications making use of the class prior to its being deprecated.

_birnlex_limbo_class
type: Class
created date: 2007-03-05
modified date: 2007-03-05
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug
definition: class in limbo since major refactoring of foundational community ontologies (e.g., BFO, OBI, SKOS). (BB:2007-03-05).

CurationStatus
type: Class
equivalent class: Class
  one of: uncurated
  one of: curation complete
  one of: raw import
  one of: definition incomplete
  one of: graph position temporary
  one of: pending final vetting
scope note: The current range of values for this property are: (1) raw_import :== a class derived directly via import of an entity form an existing knowledge resource. Terms labeled as such has yet to receive any additional curation. As they do, their status is likely to change, though the link back to the original entity in the external resource is maintained; (2) definition_incomplete :== the curators recognize the definition of the class remains incomplete in someway. Many definitions are dervied from external sources (a fact tracked via an additional annotation property) and require considerable amending before they fully comply with the OBO Foundry Aristotelean genera/differentia & non-circular specification; (3) graph_position_temporary :== indicates the class may not be in its final preferred location within the ontology graph. This label can be particularly useful during early ontology creation, as for certain entities, it may not be obvious where precisely a given class should reside until a sufficiently large portion of the graph has been settled; (4) uncurated :== indicates a class has been created by curators but has received minimal review; (5) pending_final_vetting :== indicates the term is likely ready for promotion to "curation_complete" status, and only requires a final review by the curators responsible. A class may also be demoted to this status when a formerly "complete" class has been determined to require amendments. In accordance with the emerging best practices, such a term will be moved to an obsolete branch of the ontology, when the new replacement class has been fully vetted and marked as such; (6) curation_complete :== indicates a class has been fully vetted by the curation authorities and to the best of their ability determined to be ready for use.
definition: This provides specific info on the level of curation a given class has received and is specifically design to promote automated reporting on the status of classes in an ontology. It is likely some classes will require more than one instance of this property to fully describe their status. Is a type of skos_editorial_note.
subclass of: EnumerationClass

uncurated
type: CurationStatus
definition: indicates a class has been created by curators but has received minimal review.

curation complete
type: CurationStatus
definition: indicates a class has been fully vetted by the curation authorities and to the best of their ability determined to be ready for use.

raw import
type: CurationStatus
definition: a class derived directly via import of an entity form an existing knowledge resource. Terms labeled as such has yet to receive any additional curation. As they do, their status is likely to change, though the link back to the original entity in the external resource is maintained.

definition incomplete
type: CurationStatus
definition: the curators recognize the definition of the class remains incomplete in someway. Many definitions are dervied from external sources (a fact tracked via an additional annotation property) and require considerable amending before they fully comply with the OBO Foundry Aristotelean genera/differentia & non-circular specification.

graph position temporary
type: CurationStatus
definition: indicates the class may not be in its final preferred location within the ontology graph. This label can be particularly useful during early ontology creation, as for certain entities, it may not be obvious where precisely a given class should reside until a sufficiently large portion of the graph has been settled.

pending final vetting
type: CurationStatus
definition: indicates the term is likely ready for promotion to "curation_complete" status, and only requires a final review by the curators responsible. A class may also be demoted to this status when a formerly "complete" class has been determined to require amendments. In accordance with the emerging best practices, such a term will be moved to an obsolete branch of the ontology, when the new replacement class has been fully vetted and marked as such.

hasCurationStatus
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#CurationStatus
has validation method: sparql_verify_annotation_domain_and_range
annotation type: http://www.w3.org/2004/02/skos/core#editorialNote

BirnlexExternalSource
type: Class
subclass of: EnumerationClass
definition: It indicates the external knowledge resource from which this class's definition derived.
equivalent class: Class
  one of: Brain Architecture Management System
  one of: Edinburgh Mouse Atlas Project
  one of: The BIRN BONFIRE terminology server
  one of: The BrainMap Project
  one of: Hof-et-al-mouse-2001
  one of: JAX-mouse-stock
  one of: MGI
  one of: IMSR
  one of: The NeuroNames Ontologies
  one of: Paxinos-Franklin-mouse-2001
  one of: PsychInfo Thesaurus
  one of: SAO
  one of: TacFarms
  one of: ATCC
  one of: SumsDB

Brain Architecture Management System
type: BirnlexExternalSource
source: http://brancusi.usc.edu/bkms/
publisher: Brain Architecture Center, University of Southern California, CA, USA

Edinburgh Mouse Atlas Project
type: BirnlexExternalSource
source: http://genex.hgu.mrc.ac.uk/
publisher: MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK

The BIRN BONFIRE terminology server
type: BirnlexExternalSource
publisher: The Biomedical Informatics Research Network (BIRN), NCRR, NIH

The BrainMap Project
type: BirnlexExternalSource
source: http://www.brainmap.org/
publisher: Research Imaging Center, University of Texas Health Science Center, San Antonio, TX, USA

The NeuroNames Ontologies
type: BirnlexExternalSource
source: http://braininfo.rprc.washington.edu/nnont.html
publisher: The BrainInfo Project, Washington National Primate Research Center, University of Washington, Seattle, WA, USA

BirnlexDefinitionSource
type: Class
subclass of: EnumerationClass
definition: It indicates the external knowledge resource from which this class's definition derived.
equivalent class: Class
  one of: BAMS defSource
  one of: BrainMap.org defSource
  one of: IMSR Glossary defSource
  one of: MGI defSource
  one of: NeuroNames defSource
  one of: The Sylvius Project defSource
  one of: ATCC defSource
  one of: ChEBI defSource

BirnlexCurator
type: Class
subclass of: EnumerationClass
definition: This property defines the BIRNLex ontology curators who've contributed to the definition of a class. More than one instance of this property is valid. In the case of multiple curators, the individual curator name may also be associated with the definition, if that person was primarily responsible for it.
equivalent class: Class
  one of: BIRN OTF
  one of: Carol Bean
  one of: Bill Bug
  one of: Christine Fennema-Notestine
  one of: Jeff Grethe
  one of: Amarnath Gupta
  one of: David Kennedy
  one of: Maryann Martone
  one of: Jessica Turner
  one of: Jyl Boline
  one of: Karen Crawford
  one of: Angie Laird
  one of: Allan MacKenzie-Graham
  one of: Brett Peterson
  one of: Rob Williams
  one of: Michele Diaz
  one of: Karl Helmer

hasBirnlexCurator
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#BirnlexCurator
has validation method: sparql_verify_annotation_domain_and_range

KnownApplicationUses
type: Class
subclass of: EnumerationClass
definition: A application where the class entity is known to currently be in use by annotators and users searching those annotations. Multiple instances of this property can be used to identify more than one current application.
scope note: This property is merely informative and not assumed to be an exhaustive list. Rather, it is just an list of examples known to the BIRNLex curators at the time the term was last modified.
equivalent class: Class
  one of: ABA app
  one of: BAMS app
  one of: BrainInfo.org app
  one of: BrainMaps.org app
  one of: BrainMap.org app
  one of: CoCoMac app
  one of: Franklin-Paxinos-mouse-2001 app
  one of: FreeSurfer app
  one of: GENSAT app
  one of: IATR app
  one of: MBAT app
  one of: SenseLab app

hasKnownApplicationUses
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#KnownApplicationUses
has validation method: sparql_verify_annotation_domain_and_range

ReferenceURLTemplate
type: Class
equivalent class: Class
  one of: ncbiTaxURLTemplate
  one of: gbifURLTemplate
  one of: gbifTaxonKeyURLTemplate
  one of: itisURLTemplate
  one of: jaxMiceURLTemplate
  one of: tacMiceURLTemplate
  one of: emapMouseStageDataURLTemplate
  one of: emapMouseStageDiagramURLTemplate
  one of: neuronamesURLTemplate
  one of: bamsURLTemplate
  one of: atccURLTemplate
  one of: meshURLTemplate
  one of: goURLTemplate
  one of: chebiURLTemplate
  one of: pubchemCicURLTemplate
usage note: The URL reference template is given exactly as posted in the form of a HTTP query, with the unique ID represented with the symbol '$$ID$$'
usage note: Note that each instance of ReferenceURLTemplate will be named using the template name of the matching ID AnnotationProperty. For example, the ReferenceURLTemplate ncbiTaxURLTemplate is linked to the ncbiTaxID AnnotationProperty, whose value can be combined algorithmically with this URL template to construct a working URL to the specific class reference. This is a far from perfect solution to some of the limitations of imposed on the use of AnnotationProperties - in particular, the inability to explicitly link one annotation property to another (e.g., explicitly relating ncbiTaxID ncbiTaxURLTemplate as applied to a specific owl:Class). However, this mechanism should suffice for now. It will not only support more complete automatic processing of this critical information, but can also be algorithmically translated to whatever better mechanims may become available in future versions of OWL.
subclass of: EnumerationClass

ncbiTaxURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a taxonomic category in NCBI Taxonomy
http query url template: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
web service url template: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#ncbiTaxID

gbifURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a taxonomic category in Global Biodiversity Information Facility taxonomic ,knowledgebase
http query url template: http://data.gbif.org/species/$$ID$$
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#gbifID

gbifTaxonKeyURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a taxonomy key in Global Biodiversity Information Facility taxonomic ,knowledgebase
http query url template: http://www.europe.gbif.net/portal/ecat_browser.jsp
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#gbifTaxonKeyID

itisURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a taxonomic category in the North American Integrated Taxonomic Information System (ITIS) taxonomic ,knowledgebase
http query url template: http://www.itis.gov/servlet/SingleRpt/SingleRpt
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#itisID

jaxMiceURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a mouse strain tracked in the Jackson Laboratory Mouse database
http query url template: http://jaxmice.jax.org/strain/$$ID$$.html
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#jaxMiceID

tacMiceURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a mouse strain tracked in the Taconic Farms Mouse database
http query url template: http://www.taconic.com/wmspage.cfm
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#tacMiceID

emapMouseStageDataURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for the data associated with a Theiler mouse prenatal development stage as given by the EMAP Project,
http query url template: http://genex.hgu.mrc.ac.uk/Databases/Anatomy/XML/$$ID$$.xml
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#emapMouseStageDataID

emapMouseStageDiagramURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for the diagram associated with a Theiler mouse prenatal development stage as given by the EMAP Project.
http query url template: http://genex.hgu.mrc.ac.uk/Databases/Anatomy/Diagrams/$$ID$$
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#emapMouseStageDiagramID

neuronamesURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for the main page in the BrainInfo.org portal for a NeuroNames neuroanatomical structure.
http query url template: http://braininfo.rprc.washington.edu/Scripts/hiercentraldirectory.aspx
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#neuronamesID

bamsURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for the main page in the Brain Architecture Management portal for a BAMS-defined neuroanatomical structure.
http query url template: http://brancusi.usc.edu/bkms/brain/show-braing2.php
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#bamsID

atccURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for a resource page at the American Type Culture Collection catalog.
http query url template: http://www.atcc.org/common/catalog/numSearch/numResults.cfm
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#atccID

meshURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for an NLM MeSH Browser page for a given MeSH heading.
http query url template: http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi
web service url template: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#MeshUid

goURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for an AmiGO Browser page for a given Gene Ontology term.
http query url template: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
web service url template: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#GOid

chebiURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for an Ontology Lookup Service Browser page for a given ChEBI term.
http query url template: http://www.ebi.ac.uk/ontology-lookup/
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#ChEBIid

pubchemCicURLTemplate
type: ReferenceURLTemplate
usage note: The URL reference template for an PubChem Browser page for a given PubChem CID term.
http query url template: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
url template linked ID: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#ChEBIid

hasReferenceURLTemplate
type: AnnotationProperty
annotation property domain: owl:Class
annotation property range: ReferenceURLTemplate
has validation method: sparql_verify_annotation_domain_and_range
usage note: A Class can be assigned more than one ReferenceURLTemplate assigned via distince hasReferenceURLTemplate properties
annotation type: http://purl.org/dc/elements/1.1/relation

PubChemCID
type: AnnotationProperty
definition: The ID from the NIH/NLM/NCBI PubChem chemical taxonomy corresponding to this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

ChEBIid
type: AnnotationProperty
definition: The ID from the Chemical Entities of Biological Interest (ChEBI) chemical taxonomy corresponding to this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

neuronamesID
type: AnnotationProperty
definition: The ID from the NeuroNames neuroanatomical thesaurus corresponding to this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

neuroNamesAncillaryTerm
type: AnnotationProperty
definition: "(NeuroNames) defines the brain in terms of about 550 primary structures to which all other structures, names, and synonyms are related. (It) provides standard English and Latin names for more than 850 unique structures including the primary structures, superstructures and related superficial features and shows hierarchical relations of each structure to its superstructures and substructures. NeuroNames also defines more than 1500 other neuroanatomical entities in terms of structures in the Hierarchy. The structure you name may not be part of the Brain Hierarchy. For example, it may represent a different way of subdividing the brain or it may exist only at the embryonic stage of brain development. Such items are referred to as 'ancillary structures' (http://braininfo.rprc.washington.edu/indexabout.html).
definition: This class was derived from a NeuroNames ancillary term, indicated the NeuroNames developers were unable to fit it into the core NN hierarchy.

animalModel
type: AnnotationProperty
definition: An organism providing a model system which mimics certain aspects of a particular human clinical syndrome or disease.

bamsID
type: AnnotationProperty
definition: The "aidi" ID from the Brain Architecture Management System (BAMS) corresponding to this class.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

birnlexPendingDifferentiaNote
type: AnnotationProperty
example: "Basal nucleus of Meynert" is used for labeling the Basal nucleus in humans. In a human specific neuroanatomical ontology layer, basal nucleus will receive the prefered lable "Basal nucleus of Meynert".
definition: This is a note describing a pending class sub-genera.
annotation type: http://www.w3.org/2004/02/skos/core#scopeNote
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#pendingActionNote

putativeClassExtension
type: AnnotationProperty
definition: This is a note describing possible class sub-genera.
annotation type: http://www.w3.org/2004/02/skos/core#scopeNote
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#pendingActionNote

birnlexDefinition
type: AnnotationProperty
definition: This is a type of OBO_definition that includes additional requirements specified by the BIRN OTF (additional requirements pending as of 2006-10-02).
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#oboDefinition

bonfireID
type: AnnotationProperty
definition: This ID is derived from the BIRN BONFIRE vocubulary management system
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

isReplacedByClass
type: AnnotationProperty
definition: This annotation property is used to link the new classes that now are used to represent the entities formerly represented by an obsoleted class. The value of this property will simply be the ontology ID for the replacement class(es).
annotation type: http://www.w3.org/2004/02/skos/core#historyNote
annotation type: http://purl.org/dc/elements/1.1/identifier

imsrStandardStrainName
type: AnnotationProperty
definition: This annotation property contains the approved strain name for an inbred mouse or rat as given by the International Mouse Strain Repository (IMSR).
annotation type: http://purl.org/dc/elements/1.1/identifier
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

hasFormerParentClass
type: AnnotationProperty
definition: This annotation property is used to link back to the original parent class for an obsoleted term. The value of this property will simply be the ontology ID for the parent class. An obsoleted asserted class should have one and only one former parent class.
annotation type: http://www.w3.org/2004/02/skos/core#historyNote
annotation type: http://purl.org/dc/elements/1.1/identifier

hasFormerChildClass
type: AnnotationProperty
definition: This annotation property is used to link back to an original child class for an obsoleted term. The value of this property will simply be the ontology ID for the child class. An obsoleted class can have greater than one former children..
annotation type: http://www.w3.org/2004/02/skos/core#historyNote
annotation type: http://purl.org/dc/elements/1.1/identifier

birnlexComment
type: AnnotationProperty
editorial note: Is there a use for a BIRN-specific comment independent of rdfs:comment?
annotation type: http://www.w3.org/2004/02/skos/core#editorialNote

birnlexRetiredDefinition
type: AnnotationProperty
definition: A former definition for a class. It is kept for the purposes of interpreting annotations made when this definition was in effect and to monitor the evolution of class definitions. Given this requirement, a "retiredDate" is added to the definition on the date of retirement.
annotation type: http://www.w3.org/2004/02/skos/core#definition

ncbiTaxGenbankCommonName
type: AnnotationProperty
definition: The "genbank common name" was introduced to provide a mechanism by which, when there is more than one common name associated with a particular node in the taxonomy, one of them could be designated to be the common name that should be used by default in the GenBank flat- files and other applications that are trying to find a common name to use for display (or other) purposes. This is not intended to confer any special status or blessing on this particular common name over any of the other common names that might be associated with the same node, and we have developed mechanisms to override this choice for a common name on a case-by-case basis if another name is more appropriate or desirable for a particular sequence entry. Each node may have at most one "genbank common name" (NCBI doc on NCBI Taxonomy, 2003).
usage note: The common taxonomic name assigned by NCBI Taxonomy and applied to GENBANK sequence records.
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

ncbiTaxBlastName
type: AnnotationProperty
definition: The "BLAST names" are a specially designated set of common names selected from the Taxonomy database. These were chosen to provide a pool of familiar names for large groups of organisms (such as "insects", "mammals", "fungi", and others) so that any particular species (which may not have an informative common name of its own) could inherit a meaningful collective common name from the Taxonomy database. This was originally developed for BLAST, because a list of BLAST results will typically include entries from many species identified by Latin binomials, which may not be familiar to all users. BLAST names may be nested; for example, "eukaryotes", "animals", "chordates", "mammals", and "primates" are all flagged as "blast names". Blast names are now used in several other applications, for example the Tax BLAST displays, the Summary view in Entrez Taxonomy, and in the Summary display of the Common Tree format (NCBI doc on NCBI Taxonomy, 2003).
usage note: The taxonomic name used in BLAST homology analysis given in NCBI Taxonomy
annotation type: http://www.w3.org/2004/02/skos/core#altLabel

ncbiInPartName
type: AnnotationProperty
definition: The "in-part" nametype is included for retrieval terms that have a broader range of application than the taxon or taxa at which they appear. For example, we list reptiles and Reptilia as in-part nametypes at our nodes Testudines (the turtles), Lepidosauria (the lizards and snakes), and Crocodylidae (the crocodilians). (NCBI doc on NCBI Taxonomy, 2003).
annotation type: http://www.w3.org/2004/02/skos/core#scopeNote

ncbiIncludesName
type: AnnotationProperty
definition: The "includes" nametype is the opposite of the in-part nametype and is included for retrieval terms that have a narrower scope of application than the taxon at which they appear. For example, we could list "reptiles" as an "includes" nametype for the Amniota (or at any higher node in the lineage) (NCBI doc on NCBI Taxonomy, 2003).
annotation type: http://www.w3.org/2004/02/skos/core#scopeNote

itisID
type: AnnotationProperty
definition: The unique ID for this taxonomic category in the North American Integrated Taxonomic Information System (ITIS) taxonomic ,knowledgebase
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

gbifID
type: AnnotationProperty
definition: The unique ID for this taxonomic category in Global Biodiversity Information Facility taxonomic ,knowledgebase
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

gbifTaxonKeyID
type: AnnotationProperty
definition: The unique ID for this taxonomy key in Global Biodiversity Information Facility taxonomic ,knowledgebase
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

ncbiTaxID
type: AnnotationProperty
definition: The unique ID for this taxonomic category in the NCBI Taxonomy database
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

ncbiTaxScientificName
type: AnnotationProperty
definition: The preferred label for this taxonomic category in the NCBI Taxonomy database
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#synonym

jaxMiceID
type: AnnotationProperty
definition: The unique ID for a mouse strain distributed by and tracked in the Jackson Laboratory Mouse database.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

tacMiceID
type: AnnotationProperty
definition: The unique ID for a mouse strain distributed by and tracked in the Taconic Farms Mouse database.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

atccID
type: AnnotationProperty
definition: The unique ID for a biological material - typically a cell line - from the American Type Culture Collection database.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

emapMouseStageDataID
type: AnnotationProperty
definition: The unique ID for a Theiler mouse prenatal development stage as given by the EMAP Project.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

emapMouseStageDiagramID
type: AnnotationProperty
definition: The unique ID type linked to a partiular URL Template. An instance of this ID type can be combined algorithmically with a URL template ('$$ID$$') placeholder literal is replaced by an ID value to create a URL that links to the curated info associated with that ID.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

urlTemplateLinkedID
type: AnnotationProperty
definition: This is a template for constructing an HTTP-based dynamic query using an associated source ID.
usage note: This URL constructed this way will typically return a well-formed HTML page for viewing in a web browser, so long as the curating authority doesn't changed their HTTP Query template.
annotation type: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#externalSourceId

httpQueryUrlTemplate
type: AnnotationProperty
definition: This is a template for constructing an HTTP-based dynamic query using an associated source ID.
usage note: This URL will typically return a well-formed HTML page for viewing in a web browser, so long as the curating authority doesn't changed their HTTP Query template.
annotation type: http://purl.org/dc/elements/1.1/relation

webServiceUrlTemplate
type: AnnotationProperty
definition: This is the HTTP or WSDL URL with which a query can be constructed to return a data fragment describing the associated source ID.
usage note: This is merely information and is designed to be associated with an ExternalSource, when a service is available to access related resource information using an External ID tracked in the ontology.
annotation type: http://purl.org/dc/elements/1.1/relation