TaxonConcept Ontology TaxonConcept Ontology txn http://lod.taxonconcept.org/ontology/txn.owl# 2013-05-19 0.976 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 conceptStatus The Links to the Status of the TaxonConcept testing taxonNameGroupID The URI to the Taxon Name Group String testing taxonNameGroupID_Of testing taxonNameID The URI to the Taxon Name String testing taxonNameID_Of The URI to the Taxon Name String testing acceptedNameID The URI to the Accepted Name String, should only be one. testing acceptedTaxonNameID_Of testing originalNameID The URI to the Original Name String testing originalNameID_Of testing altAcceptedNameID The URI to an Alternative Accepted Name String testing altAcceptedNameID_Of The URI to an Alternative Accepted Name String testing relatedTaxonNameID The URI to the Taxon Name String testing canonicalFormID The URI ID for the canonical form of the name i.e. Puma concolor or Felidae, for name to name mapping canonicalFormID Of The URI ID for the scientific name with authorship form of the name i.e. Puma concolor Linnaeus 1758, for name to name mapping synonymID The URI to a synonymID of the TaxonNameID testing heterochresonymID The URI to the Heterochresonym Name String testing heterotypicNameID The URI to the HeterotypicName Name String testing homotypicNameID The URI to the HomotypicName Name String testing orthochresonymID The URI to the Orthochresonym Name String testing areaHasIndividual Links an Area to an Individual testing areaHasObservedSpeciesConcept Links an Area to a Species Concept testing areaHasOccurrence Links an Area to an Occurrence testing areaInCounty Links an Area to Geonames County URI testing areaInStateProvince Links an Area to Geonames State/Province URI testing basisOfRecord Assumed to be equivalent to TDWG Basis of Record testing georeferenceProtocol The method used to determine the latitude, longitude as a URI testing georeferenceVerificationStatus Was this location verified, controlled choices URI testing hasExpectationOf 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. testing hasUnknownExpectationOf 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. testing isExpectedIn 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. testing isUnknownAboutIn Links a species concept to a Geonames URI where the relationship is unknown testing habitat associates a taxon with a habitat in which it may typically be found testing basisOfRecord Assumed to be equivalent to TDWG Basis of Record testing hasCollector The occurrence observer or specimen collector, hasCollector? testing hasCitation The range is a uniprot pubmed uri for example http://purl.uniprot.org/pubmed/1083304 testing hasADWPage The range is a page on the Animal Diversity Web site. testing hasDiscoverLifePage The range is a page on the Discover Life Web site. testing hasDLPage The range is a page on the DiscoverLife.org site. testing hasBBCPage The range is a page on the BBC site. testing hasBOLDPage A page at boldsystems.org testing hasDiscoverLifePage The range is a page on the http://www.discoverlife.org/ site. testing hasITISPage The range is a page on the ITIS.gov site. testing hasBioimagesPage The range is a page on the Bioimages site. testing isBioimagesPageOf testing hasBugGuidePage testing isBugGuidePageOf testing hasEOLPage The range is a page on the Encyclopedia of Life site. testing isEOLPageOf The range is a page on the Encyclopedia of Life site. testing hasEUNISPage testing hasEtypePage testing hasGBIFPage A page at GBIF.org testing hasWikispeciesArticle testing isWikispeciesArticleOf testing hasWikipediaArticle testing isWikipediaArticleOf testing hasWildObsPage testing hasUSDAPlantsPage testing hasImage Superproperty of all the links to images testing hasMapImage testing hasGBIFmap testing hasWikipediaMap testing identificationHasLabelImage The image of the identification label on a specimen testing identificationHasOcccurrence The link between an Identification and an Occurrence testing identificationHasSpeciesConcept The link between an Identification and Species Concept, redundant with identifiedAs testing identificationMethod Method used to identify the individual, as a URI testing identificationOfIndividual Links an identification to an individual testing identificationReference Links an identification to the URI for the reference used. testing identifiedBy Links an identification to the URI a human that made the identification as URI testing inCoLKingdom Links a species concept to a Catalog of Life Kingdom in an ontology testing inCoLPhylum Links a species concept to a Catalog of Life Phylum in an ontology testing inCoLClass Links a species concept to a Catalog of Life Class in an ontology testing inCoLFamily Links a species concept to a Catalog of Life Family in an ontology testing inCoLOrder Links a species concept to a Catalog of Life Order in an ontology testing inDBpediaClade Links a species concept to a clade in the DBpedia ontology testing inKingdom testing inPhylum testing inClass testing inSubclass testing inInfraclass testing inSuperorder testing inOrder testing inSuborder testing inSuperfamily testing inFamily testing inSubfamily testing inGenus testing uniprotKingdom uniprotPhylum uniprotClass uniprotOrder uniprotFamily uniprotGenus uniprotSpecies NCBI Genus Links to the most appropriate NCBI Genus testing NCBI Species Links to the most appropriate NCBI Species testing individualHasCurrrentIdentificationAssertion Links an individual to the most appropriate identification. Should be one. testing individualHasObservedArea Links an individual to an Area testing individualHasOccurrence Links an individual to an Occurrence, correct testing individualHasPreviousIdentificationAssertion Links an individual to the most appropriate identification. Zero to many testing individualHasSpeciesConcept Links an individual a Species Concept testing individualStatus Links from an individual to a controlled vocabulary of URI's for the current status of that individual testing individualhasImage Intended to link an individual to a image. Should be subproperty of foaf:depiction testing occurrenceHasArea Links an occurrence to an area testing occurrenceHasIndividual Links an occurrence to an individual testing occurrenceHasLabelImage The image of the occurrence label on a specimen testing occurrenceHasSpeciesConcept Links an occurrence to a species concept testing occurrenceInContinent Links an Occurrence to Geonames Continent URI testing occurrenceInCounty Links an Occurrence to Geonames County URI testing occurrenceInFeature testing occurrenceInStateProvince Links an Occurrence to Geonames StateProvince URI testing samplingProtocol Links an Occurrence to a standard vocabulary of sampling protocols as URI's testing sodHasTypeSpecimen Links an original description to a species type specimen testing speciesConceptBasedOn 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. testing speciesConceptHasObservedArea Links a species to an area. Should be speciesConcept? testing speciesConceptHasOcccurrence Links a species to an occurrence. Should be speciesConcept? testing speciesConcepthasVaritypeSpecimen Links a species concept to a varitype specimen testing thumbnail testing thumbnailOf testing typeSpecimenHasSod Links specimen to an original species description testing varitypeSpecimenHasSpeciesConcept Links a varitype specimen to a species concept testing areaWithInFeature This is used to connect geo areas to geoname features testing featureContainsArea This is used to link a geonames feature to a geo area. For example geo:44.86528100,-87.23147800;u=10 testing descYear This is the year of the description testing descYearOf testing yearBorn testing yearDied testing yearPub The year that document was pub testing pubYearOf The year that document was pub testing nameYear The year that a name was published testing nameYear Inverse of The year that a name was published testing firstAuthorID The URI to the First Author testing lastAuthorID The URI to the Last Author testing botany author abbreviation testing zoology author abbreviation testing behavioralNote testing scientificName testing binomial testing trinomial testing scientificNameWithAuthor testing hasOriginalName deprecated originalName testing commonName testing acceptedName testing hasAcceptedName deprecated synonymName testing surrogateName testing scientificNameAuthorship The author and year of the species description publication i.e (Baker, 1899) testing authority The author and year of the species description publication i.e (Baker, 1899) testing hasSpeciesConceptID This is for a string urn type identifier testing continent testing country testing countryCode testing county testing startDate testing endDate testing catalogCode testing collectionCode testing hasBOLD The Barcode of Life Integer ID testing hasEOL The Encyclopedia of Life Integer ID testing hasEbird eBird Species Code testing hasGBIF The Global Biodiversity Information Facility integer ID testing hasITIS The ITIS ID testing hasNCBI The NCBI Taxonomy ID testing hybrid testing identificationDate testing identificationNote testing institutionCode testing localityText testing locationName testing kingdom testing phylum testing class testing order testing family testing genus testing Specific epithet testing infraspecificEpithet testing stateProvince testing taxonRank testing yearDescribed The year that the species was originally described testing radius The radius in meters from a particular latitude, longitude point from within which a thing was observed or collected. Area testing Scientist Class for Scientist a foaf:Person testing Taxonomist Class for a Taxonomist a subclass of dbpedia-owl:Scientist testing ScientificAuthorPerson Someone who has authored a scientific article. testing ScientificCollectorPerson Someone who has collected a scientific sample or specimen. testing ScientificDataCuratorPerson Someone who has curated or entered data into a scientific data set. testing ScientificIdentifierPerson Someone who has identified a specimen. testing Taxonomist Class for a Taxonomist a subclass of dbpedia-owl:Scientist testing DataObject Year Class for the Concept Year testing Gallery testing Identification An identification action. The identification of a specimen. testing Image testing MapImage testing Occurrence testing testing testing OpenCycTaxon testing Sex testing SpeciesConcept testing SpeciesImageTag 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. testing SpeciesIndividual testing SpeciesIndividualTag 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. SpeciesModel testing SpeciesOriginalDescription testing SpeciesTaxonomyNCBI A tag like entity for the NCBI Taxonomic Classification. testing Specimen 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. testing TaxonConcept 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. testing TaxonNameID SurrogateNameID testing ScientificNameID testing MonomialNameID testing GenusNameID testing SubfamilyNameID testing FamilyNameID testing BinomialNameID testing TrinomialNameID testing ScientificNameWithAuthorID testing CommonNameID testing TaxonNameGroupID testing TaxonOntology testing TaxonRank testing female Female (♀) is the sex of an organism, or a part of an organism, which produces mobile ova (egg cells). testing hermaphrodite one organism having both male and female sexual characteristics and organs; at birth an unambiguous assignment of male or female cannot be made testing male Male (♂) refers to the sex of an organism, or part of an organism, which produces small mobile gametes, called spermatozoa. testing Sex Undetermined testing Sex Unknowable testing TDWG2010 BioBlitz Project testing TaxonConcept_Knowledge_Base_Project testing Rank Domain testing Rank Subdomain testing Rank Superkingdom testing Rank Kingdom testing Rank Subkingdom testing Rank Infrakingdom testing Rank Superphylum testing Rank Superdivision testing Rank Phylum testing Rank Division testing Rank Subphylum testing Rank Subdivision testing Rank Superclass testing Rank Class testing Rank Subclass testing Rank Infraclass testing Rank Superorder testing Rank Order testing Rank Suborder testing Rank Infraorder testing Rank Parvorder testing Rank Superfamily testing Rank Family testing Rank Subfamily testing Rank Tribe testing Rank Genus testing Rank Subgenus testing Rank Species testing Rank Subpecies testing Rank SubspecificAggregate testing Rank Variety testing Habitat testing TerrestrialHabitat testing FreshwaterHabitat testing FreshwaterHabitat testing TaxonConcept_Scheme testing Status_Testing testing Status_Preliminary testing