TaxonConcept Ontology
Version 0.976 This is an ontology for dealing with data related to species including observations, specimens, images etc. Traditionally species have been identified by the combination of a genus and specific epithet, for example Puma concolor. However these names change frequently as new information moves a given species into a different genus etc. Most of the time the species concept itself is unchanged. This leads a lot of confusion and difficulty connecting data relating to a given species concept together. This ontology and the related TaxonConcept data set avoids this by minting identifiers that are tied to a specific species concept which can have several names and classifications. The RDF descriptions of each species concept provides some guide as to what is the best species concept for a given specimen or observation, and links together data sets containing additional information about that concept. Since some of these related data sets entail specific names or classifications they are loosely linked using skos:closeMatch etc. Depending on your particular needs, you might want to merge these in your own knowledge base as sameAs or simply merge those properties that you think are appropriate.
Version 0.976 Added additional GenusNameID, SubfamilyNameID and FamilyNameID for NLP project
The Links to the Status of the TaxonConcept
The URI to the Accepted Name String, should only be one.
The URI to an Alternative Accepted Name String
The URI ID for the canonical form of the name i.e. Puma concolor or Felidae, for name to name mapping
The URI ID for the scientific name with authorship form of the name i.e. Puma concolor Linnaeus 1758, for name to name mapping
The URI to a synonymID of the TaxonNameID
The URI to the Heterochresonym Name String
The URI to the HeterotypicName Name String
The URI to the HomotypicName Name String
The URI to the Orthochresonym Name String
Links an Area to Geonames State/Province URI
Assumed to be equivalent to TDWG Basis of Record
The method used to determine the latitude, longitude as a URI
Was this location verified, controlled choices URI
This is to link between a geographical area and a taxon-like entity. The doman and range are left blank so this can be used with different kinds of geographic vocabularies and different kinds of taxon concept vocabularies. It should not be used to indicate that a location has the expectation of a specific individual specimen, but to indicate that the location has an expectation of a specific class of organisms. For instance, it would be used to indicate that a geographic location has an expectation of a particular species. The use should approximate assertions similar to what one might find in a state or country checklist.
This is to link between a geographical area and a taxon-like entity. Where the association is not known. The doman and range are left blank so this can be used with different kinds of geographic vocabularies and different kinds of taxon concept vocabularies. It should not be used to indicate that a location has the expectation of a specific individual specimen, but to indicate that the location has an expectation of a specific class of organisms. For instance, it would be used to indicate that a geographic location has an expectation of a particular species. The use should approximate assertions similar to what one might find in a state or country checklist.
This is to link between a taxon-like entity and a geographical area. The doman and range are left blank so this can be used with different kinds of geographic vocabularies and different kinds of taxon concept vocabularies. It should not be used to indicate that a particular individual organism is expecten in a geographical area, but to indicate that the species etc. is expected in a particular geographical area. For instance, it would be used to indicate that a species is expected in a particular state or province. The use should approximate assertions similar to what one might find in a state or country checklist.
Links a species concept to a Geonames URI where the relationship is unknown
associates a taxon with a habitat in which it may typically be found
The occurrence observer or specimen collector, hasCollector?
The range is a uniprot pubmed uri for example http://purl.uniprot.org/pubmed/1083304
The range is a page on the Animal Diversity Web site.
The range is a page on the Discover Life Web site.
The range is a page on the DiscoverLife.org site.
A page at boldsystems.org
The range is a page on the http://www.discoverlife.org/ site.
The range is a page on the ITIS.gov site.
The range is a page on the Bioimages site.
The range is a page on the Encyclopedia of Life site.
A page at GBIF.org
Superproperty of all the links to images
The image of the identification label on a specimen
The link between an Identification and an Occurrence
The link between an Identification and Species Concept, redundant with identifiedAs
Method used to identify the individual, as a URI
Links an identification to an individual
Links an identification to the URI for the reference used.
Links an identification to the URI a human that made the identification as URI
Links a species concept to a Catalog of Life Kingdom in an ontology
Links a species concept to a Catalog of Life Phylum in an ontology
Links a species concept to a Catalog of Life Class in an ontology
Links a species concept to a Catalog of Life Family in an ontology
Links a species concept to a Catalog of Life Order in an ontology
Links a species concept to a clade in the DBpedia ontology
uniprotKingdom
uniprotPhylum
uniprotClass
uniprotOrder
uniprotFamily
uniprotGenus
uniprotSpecies
Links to the most appropriate NCBI Genus
Links to the most appropriate NCBI Species
Links an individual to the most appropriate identification. Should be one.
Links an individual to an Occurrence, correct
Links an individual to the most appropriate identification. Zero to many
Links from an individual to a controlled vocabulary of URI's for the current status of that individual
Intended to link an individual to a image. Should be subproperty of foaf:depiction
The image of the occurrence label on a specimen
Links an occurrence to a species concept
Links an Occurrence to Geonames Continent URI
Links an Occurrence to Geonames County URI
Links an Occurrence to Geonames StateProvince URI
Links an Occurrence to a standard vocabulary of sampling protocols as URI's
Links an original description to a species type specimen
This describes the theoretical models behind the species concept. All species concepts are at least based on an Objective Model. In addition the may also be based on a Biological Species Model and or a Phylogenetic Species Model. A species concept could be based on all three of these. This is to reflect that there are several criteria used to support a species concept. It also allows one to create a species concept for the domestic cat that is separate from its wild relative. If one followed a strict phylogentic species model, than the domestic cat would be considered to be a subclass of the species Felis sylvestris. This would result in observations or references about the domestic cat being interpreted as observations or references of the African Wildcat Felis sylvestris.
Links a species to an area. Should be speciesConcept?
Links a species to an occurrence. Should be speciesConcept?
Links a species concept to a varitype specimen
Links specimen to an original species description
Links a varitype specimen to a species concept
This is used to connect geo areas to geoname features
This is used to link a geonames feature to a geo area. For example geo:44.86528100,-87.23147800;u=10
yearPub
pubYearOf
nameYear
Inverse of The year that a name was published
The author and year of the species description publication i.e (Baker, 1899)
This is for a string urn type identifier
The Global Biodiversity Information Facility integer ID
The year that the species was originally described
The radius in meters from a particular latitude, longitude point from within which a thing was observed or collected.
Scientist
Class for Scientist a foaf:Person
Taxonomist
Class for a Taxonomist a subclass of dbpedia-owl:Scientist
Someone who has authored a scientific article.
Someone who has collected a scientific sample or specimen.
Someone who has curated or entered data into a scientific data set.
DataObject
Year
Class for the Concept Year
An identification action. The identification of a specimen.
A tag like entity that can be used to indicate that an image is associated with a specific species concept. Instances of SpeciesImageTag take the form of the species concept URI with the fragment of #Image rather than #Species.
A tag like entity that can be used to indicate that an individual organism is an associated with a particular species concept. Instances of SpeciesIndividualTag take the form of the species concept URI with the fragment of #Individual rather than #Species.
A tag like entity for the NCBI Taxonomic Classification.
A organismal specimen that is related to a specific organism, parts of an individual organism, or a collection of these from several organisms. It should be used for the smallest entity in a specimen database. Ideally there should be at least one specimen per individual organism. Specimens consisting of multiple individuals or multiple species often complicate analysis. If one photo contains multiple entities, document these as separate specimens all linked to the same photo.
A particular taxonomic concept. Currently only species concepts are implemented, however theoretically there could be additional subclasses of GenusConcepts, FamilyConcepts etc. A SubspeciesConcept and lower are considered to be subclasses of SpeciesConcepts, but one persons subspecies is often anothers species. My current thinking is to represent individuals and observations of subspecies as individuals and observations of the larger species concept. It has yet to be implemented but I am considering recording these as observations and individuals of a given species "in the form of" their subspecies indentifier or name.
female
Female (♀) is the sex of an organism, or a part of an organism, which produces mobile ova (egg cells).
hermaphrodite
one organism having both male and female sexual characteristics and organs; at birth an unambiguous assignment of male or female cannot be made
male
Male (♂) refers to the sex of an organism, or part of an organism, which produces small mobile gametes, called spermatozoa.