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