Species Products Discovery Objects

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The Species Product Discovery Service is the main service realising the Biodiversity Access facilities in gCube. This service aims at offering an unifying view over the data offered by diverse data sources. In order to do that, the service makes available two typologies of objects:

  • TaxonomyItem, i.e. a characterisation of species taxa;
  • Occurrence, i.e. a characterisation of a dataset of species occurrence records;

by interacting with the diverse data sources.

This page describes the fields characterising every typology of object produced by the Species Product Discovery Service and how these fields are populated by using the information produced by every data source.

TaxonomyItem

The Fields

A TaxonomyItem object is characterised by the following fields: scientificNameAuthorship, citation, commonNames, credits, id, lsid, modified, parent, properties, rank, scientificName, and status.

commonNames, properties and status are compound objects and the fields characterising them are described in dedicated sections respectively, i.e. commonNames Fields, ElementProperty Fields, and TaxonomyStatus Fields.

The semantic of these fields is inherited from Darwin Core Terms. A quick guide here.

scientificNameAuthorship
Description The authorship information for the scientificName represented by the TaxonomyItem. If the authority is known and can be separated from the rest of the scientific name, the authority string should also be placed in the ‘author’ field.
Example (Schltdl.) Crins
Darwin Core Term scientificNameAuthorship
Data Type string
Mandatory false
citation
Description Citation information specified by the data publisher.
Example Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=105838 on 2012-11-27
Darwin Core Term nameAccordingTo
Data Type string
Mandatory false
commonNames
Description A common or vernacular name.
Example see commonName fields.
Darwin Core Term vernacularName
Data Type List <CommonName>
Mandatory false
credits
Description Citation information specified by the data publisher.
Example This information object has been generated via the Species Product Discovery service on 2012-11-26 by interfacing with speciesLink (http://splink.cria.org.br/)
Darwin Core Term bibliographicCitation
Data Type string
Mandatory true
id
Description The unique identifier used for a name or taxon reference in the core data file.
Example "37829"
Darwin Core Term taxonID
Data Type string
Mandatory true
lsid
Description An identifier for the nomenclatural (not taxonomic) details of a TaxonomyItem. It is exclusively used to reference an external and resolvable identifier that returns nomenclatural (not taxonomic) details of a name. Use taxonID to refer to taxa. Use to explicitly refer to an external nomenclatural record.
Example “urn:lsid:ipni.org:names:37829-1:1.3”
Darwin Core Term scientificNameID
Data Type string
Mandatory false
modified
Description Date when the record the TaxonomyItem is representing was last updated.
Example “2009-08-21”
Darwin Core Term modified
Data Type calendar
Mandatory false
parent
Description The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).
Example
Darwin Core Term n/a
Data Type TaxonomyItem
Mandatory false
properties
Description Any property besides the others that is worth to associate with the TaxonomyItem. These properties might include comments or notes about the taxon or name or data sources.
Example n/a
Darwin Core Term n/a
Data Type List <ElementProperty>
Mandatory false
rank
Description The taxonomic rank of the most specific name in the scientificName.
Recommended vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml
Example "subspecies", "varietas", "forma", "species", "genus"
Darwin Core Term taxonRank
Data Type string
Mandatory true
scientificName
Description The scientific name of taxon with or without authorship information depending on the format of the source database.
Example "Coleoptera" , "Vespertilionidae”, "Manis" , "Ctenomys sociabilis", "Ambystoma tigrinum diaboli", "Quercus agrifolia var. oxyadenia (Torr.)"
Darwin Core Term scientificName
Data Type string
Mandatory true
status
Description The status of the taxon represented by the TaxonomiItem.
Example "invalid", "misapplied", "homotypic synonym", "accepted"
Darwin Core Term taxonomicStatus
Data Type TaxonomyStatus
Mandatory true

CommonName Fields

A CommonName is characterised by the following fields: language and name.

language
Description The language of the resource.
Example
Darwin Core Term language
Data Type string
Mandatory true
name
Description A common or vernacular name.
Example
Darwin Core Term vernacularName
Data Type string
Mandatory false

ElementProperty Fields

An ElementProperty is characterised by the following fields: name and value.

name
Description Key used to identify comments or notes.
Example “Reference”, “Source”
Darwin Core Term n/a
Data Type string
Mandatory false
value
Description The value of the given property.
Example “Compagno, L.J.V.1999Checklist of living elasmobranchs.p. 471-498. In W.C. Hamlett (ed.) Sharks, skates, and rays: the biology of elasmobranch fishes. John Hopkins University Press, Maryland.”, “DatabaseFishBase”
Darwin Core Term n/a
Data Type string
Mandatory false

TaxonomyStatus Fields

A TaxonomyStatus is characterised by the following fields: status, refId, and statusAsString.

status
Description The status of the use of the scientificName as a label for a taxon.
Controlled vocabulary: "accepted", "invalid", "misapplied", "provisional", “synonym”, “unknown”, “valid”.
Example
Darwin Core Term taxonomicStatus
Data Type string
Mandatory true
refId
Description This value points to the record representing the valid (zoological) or accepted (botanical) name using the taxonID of that record as the “pointer”.
Example
Darwin Core Term acceptedNameUsageID
Data Type string
Mandatory false
statusAsString
Description Comments or notes about the taxon or name.
Example “Type consists of a skull and skeletal fragments”.
Darwin Core Term taxonRemarks
Data Type string
Mandatory false

TaxonomyItem Compilation

In the table below there is the list of compiled fields by data source. A detailed description of the compilation policy is given in the related sections, i.e.

TaxonomyItem Field FloraDoBrasil CoL IRMNG ITIS OBIS NCBI WoRMS
author Compiled Compiled Compiled Compiled Compiled Compiled
citation Compiled Compiled Compiled
commonNames Compiled Compiled Compiled Compiled Compiled
credits Compiled
id Compiled Compiled Compiled Compiled Compiled Compiled Compiled
lsid Compiled Compiled
modified Compiled Compiled Compiled
parent Compiled Compiled Compiled Compiled Compiled Compiled
properties Compiled Compiled Compiled Compiled
rank Compiled Compiled Compiled Compiled Compiled Compiled Compiled
scientificName Compiled Compiled Compiled Compiled Compiled Compiled Compiled
status Compiled Compiled Compiled Compiled Compiled Compiled Compiled

TaxonomyItem Compilation: List of Species of the Brazilian Flora

In the case of List of Species of the Brazilian Flora TaxonomyItem objects are compiled by relying on the Brazilian Flora Web Service.

TaxonomyItem Field Source Note
author au
citation n/a
commonNames language status
name n/a
credits n/a
id id
lsid n/a
modified n/a
parent n/a
properties name n/a
value n/a
rank rank
scientificName html_full_name
status status status
refId n/a
statusAsString qualifier

TaxonomyItem Compilation: Catalogue of Life

In the case of Catalogue of Life TaxonomyItem objects are compiled by relying on the Web service.

TaxonomyItem Field Source Note
author author
citation n/a
commonNames language name_status
name n/a
credits n/a
id id
lsid n/a
modified record_scrutiny_date
parent classification
properties name Source Database
value ???
name Reference
value ???
rank rank
scientificName name
status status name_status
refId n/a
statusAsString n/a

TaxonomyItem Compilation: IRMNG

In the case of IRMNG TaxonomyItem objects are compiled by relying on the database dump in DarwinCore (DwC) Archive.

TaxonomyItem Field Source Note
author scientificnameauthorship
citation nameaccordingto
commonNames language taxonomicstatus
name acceptednameusageid
credits n/a
id taxonid
lsid n/a
modified modified
parent parentnameusageid
properties name n/a
value n/a
rank taxonrank
scientificName scientificname
status status taxonomicstatus
refId acceptednameusageid
statusAsString taxonremarks

TaxonomyItem Compilation: ITIS

In the case of ITIS TaxonomyItem objects are compiled by relying on the database dump files (MySQL by table).

TaxonomyItem Field Source Note
author table taxon_authors_lkp → taxon_author
citation n/a
commonNames language n/a
name n/a
credits n/a
id Table longnames → tsn
lsid urn:lsid:itis.gov:itis_tsn:TSN
modified table taxonomic_units → update_date
parent table taxonomic_units → parent_tsn
properties name Source
value ???
rank table taxon_unit_types → rank_name
scientificName table longnames → completename
status status table taxonomic_units → name_usage
refId n/a
statusAsString table taxonomic_units → unaccept_reason

TaxonomyItem Compilation: OBIS

In the case of OBIS TaxonomyItem objects are compiled by relying on ...

TaxonomyItem Field Source Note
author table obis.tnames -> tauthor
citation "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)";
commonNames language lanname
name table obis.cnames -> cname
credits "This information object has been generated via the Species Product Discovery service on DATE by interfacing with the Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org."
id table obis.tnames -> id
lsid n/a
modified n/a
parent table obis.tnames -> parent_id
properties name worms_id
value table obis.tnames -> worms_id
name col_id
value table obis.tnames -> col_id
name irmng_id
value table obis.tnames -> irmng_id
name itis_id
value table obis.tnames -> itis_id
rank table obis.ranks -> rank_name
scientificName table obis.tnames -> tname
status status ACCEPTED
refId n/a
statusAsString n/a

TaxonomyItem Compilation: NCBI

In the case of NCBI TaxonomyItem objects are compiled by relying on FTP: NCBI Taxonomy. This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs.

TaxonomyItem Field Source Note
author n/a
citation n/a
commonNames language n/a
name n/a
credits n/a
id Table nodes → tax_id
lsid n/a
modified n/a
parent table nodes → parent_tax_id
properties name n/a
value n/a
rank Table nodes → rank
scientificName Table names → name_txt
status status Table names → name_class
refId n/a
statusAsString n/a

TaxonomyItem Compilation: WoRMS

In the case of WoRMS TaxonomyItem objects are compiled by relying on the WoRMS webservice.

TaxonomyItem Field Source Note
author AphiaRecord record - record.getAuthority()
citation AphiaRecord record - record.getCitation()
commonNames language Vernacular vernacular - vernacular.getLanguage()
name Vernacular vernacular - vernacular.getVernacular()
credits n/a
id AphiaRecord record - record.getAphiaID()
lsid AphiaRecord record - record.getLsid()
modified n/a
parent WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID())
properties name additional source
value Source source – source.getReference()
name basis of record
value source.getLink()
name context source (Deepsea)
value source.getUrl()
rank AphiaRecord record - record.getRank()
scientificName AphiaRecord record - record.getScientificname()
status status AphiaRecord record - record.getStatus()
refId AphiaRecord record - record.getValid_AphiaID()
statusAsString AphiaRecord record - record.getStatus()

Occurrence

The Fields

A Occurrence object is characterised by the following fields: basisOfRecord, catalogNumber, citation, country, collectionCode, coordinateUncertaintyInMeters, credits, dateLastModified, decimalLatitude, decimalLongitude, eventDate, kingdom, family, id, identifiedBy, institutionCode, maximumDepthInMeters, minimumDepthInMeters, recordedBy, scientificName, and scientificNameAuthorship.

The semantic of these fields is inherited from Darwin Core Terms. A quick guide here.

basisOfRecord
Description The specific nature of the data record. Recommended best practice is to use a controlled vocabulary such as the http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm.
Example "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"
Darwin Core Term basisOfRecord
Data Type string
Mandatory false
catalogNumber
Description An identifier (preferably unique) for the record within the data set or collection.
Example "9669"
Darwin Core Term catalogNumber
Data Type string
Mandatory false
citation
Description Citation information specified by the data publisher.
Example "Accessed through: speciesLink at http://splink.cria.org.br"
Darwin Core Term nameAccordingTo
Data Type string
Mandatory false
country
Description The name of the country or major administrative unit in which the Location occurs.
Example "Brasil"
Darwin Core Term country
Data Type string
Mandatory false
collectionCode
Description The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
Example "BAH"
Darwin Core Term collectionCode
Data Type string
Mandatory false
credits
Description Citation information specified by the data publisher.
Example "This information object has been generated via the Species Product Discovery service on 2013-05-06 by interfacing with speciesLink (http://splink.cria.org.br/)"
Darwin Core Term rightsHolder
Data Type string
Mandatory true
dateLastModified
Description The most recent date-time on which the resource was changed.
Example "1963-03-08T14:07-0600"
Darwin Core Term modified
Data Type Date
Mandatory false
decimalLatitude
Description The geographic latitude.
Example "-11.451111"
Darwin Core Term decimalLatitude
Data Type float
Mandatory false
decimalLongitude
Description The geographic longitude.
Example "-46.161667"
Darwin Core Term decimalLongitude
Data Type float
Mandatory false
eventDate
Description The date-time when the event was recorded.
Example "1963-03-08T14:07-0600"
Darwin Core Term eventDate
Data Type Date
Mandatory false
kingdom
Description The full scientific name of the kingdom in which the taxon is classified.
Example "Plantae"
Darwin Core Term kingdom
Data Type string
Mandatory false
family
Description The full scientific name of the family in which the taxon is classified.
Example "Bignoniaceae"
Darwin Core Term family
Data Type string
Mandatory false
id
Description This is the Global Unique Identification (GUID) for the specimen. This identification code should be stable and uniquely identify the specimen relative to all other specimens within the world.
Example "8"
Darwin Core Term GlobalUniqueIdentifier
Data Type string
Mandatory true
identifiedBy
Description A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.
Example "James L. Patton"
Darwin Core Term identifiedBy
Data Type string
Mandatory false
institutionCode
Description The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
Example "EBDA"
Darwin Core Term institutionCode
Data Type string
Mandatory false
maximumDepthInMeters
Description The greater depth of a range of depth below the local surface, in meters.
Example
Darwin Core Term maximumDepthInMeters
Data Type float
Mandatory false
minimumDepthInMeters
Description The lesser depth of a range of depth below the local surface, in meters.
Example
Darwin Core Term minimumDepthInMeters
Data Type float
Mandatory false
recordedBy
Description A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.
Example
Darwin Core Term recordedBy
Data Type string
Mandatory false
scientificName
Description The scientific name of taxon with or without authorship information depending on the format of the source database.
Example "Jacaranda ulei"
Darwin Core Term scientificName
Data Type string
Mandatory true
scientificNameAuthorship
Description The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
Example "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)".
Darwin Core Term scientificNameAuthorship
Data Type string
Mandatory false

Occurrence Compilation

In the table below there is the list of compiled values by data source. A detailed description of the compilation policy is given in the related sections, i.e.

Occurrence Field GBIF OBIS speciesLink
basisOfRecord Compiled Compiled Compiled
catalogNumber Compiled Compiled Compiled
citation Compiled Compiled Compiled
country Compiled Compiled Compiled
collectionCode Compiled Compiled Compiled
credits Compiled Compiled Compiled
dateLastModified Compiled Compiled
decimalLatitude Compiled Compiled Compiled
decimalLongitude Compiled Compiled Compiled
eventDate Compiled Compiled Compiled
kingdom Compiled Compiled
family Compiled Compiled
id Compiled Compiled Compiled
identifiedBy Compiled Compiled
institutionCode Compiled Compiled Compiled
maximumDepthInMeters Compiled Compiled Compiled
minimumDepthInMeters Compiled Compiled Compiled
recordedBy Compiled Compiled Compiled
scientificName Compiled Compiled Compiled
scientificNameAuthorship Compiled Compiled Compiled

Occurrence Compilation: GBIF

In the case of GBIF, Occurrence objects are compiled by relying on ...

Occurrence Field Source Note
basisOfRecord basisOfRecordString
catalogNumber catalogNumber
citation citation
country country
collectionCode collectionCode
credits Biodiversity occurrence data published by: DATA PROVIDER (Accessed through GBIF Data Portal, data.gbif.org, DATE)
dateLastModified n/a
decimalLatitude decimalLatitude
decimalLongitude decimalLongitude
eventDate earliestDateCollected
kingdom n/a
family n/a
id gbifKey (attribute of TaxonOccurrence)
identifiedBy citation
institutionCode institutionCode
maximumDepthInMeters maximumDepthInMeters
minimumDepthInMeters minimumDepthInMeters
recordedBy  ??
scientificName nameComplete
scientificNameAuthorship  ??

Occurrence Compilation: OBIS

In the case of OBIS, Occurrence objects are compiled by relying on ...

Occurrence Field Source Note
basisOfRecord table obis.drs -> basisofrecord
catalogNumber table obis.dxs -> catalognumber
citation table obis.dxs -> citation
country table obis.dxs -> country
collectionCode table obis.dxs -> collectioncode
credits Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)
dateLastModified table obis.dxs -> datelastmodified
decimalLatitude table obis.drs -> latitude
decimalLongitude table obis.drs -> longitude
eventDate table obis.drs -> datecollected
alternatively dxs.yearcollected, dxs.monthcollected, dxs.daycollected
kingdom table obis.dxs -> concatenated
family table obis.dxs -> concatenated
id table obis.drs -> id
identifiedBy table obis.dxs -> identifiedBy
institutionCode institutioncode
maximumDepthInMeters table obis.dxs -> maximumdepth
minimumDepthInMeters table obis.dxs -> minimumdepth
recordedBy table obis.dxs -> ???
scientificName table obis.dxs -> concatenated
scientificNameAuthorship table obis.tnames -> tauthor

Occurrence Compilation: speciesLink

In the case of speciesLink, Occurrence objects are compiled by relying on the Web Service based on the TAPIR protocol and on the DarwinCore data standard.

Occurrence Field Source Note
basisOfRecord <dwcore:BasisOfRecord>
catalogNumber <dwcore:CatalogNumber>
citation Accessed through: speciesLink at http://splink.cria.org.br on DATE
coordinateUncertaintyInMeters <dwcore:CoordinateUncertaintyInMeters>
country <dwcore:Country>
collectionCode <dwcore:CollectionCode>
credits This information object has been generated via the Species Product Discovery service on 2013-05-06 by interfacing with speciesLink (http://splink.cria.org.br/)
dateLastModified <dwcore:DateLastModified>
decimalLatitude <dwgeo:DecimalLatitude>
decimalLongitude <dwgeo:DecimalLongitude>
kingdom <dwcore:Kingdom>
family <dwcore:Family>
id <dwcore:GlobalUniqueIdentifier>
identifiedBy <dwcore:identifiedBy>
institutionCode <dwcore:InstitutionCode>
maximumDepthInMeters <dwcore:MaximumDepthInMeters>
minimumDepthInMeters <dwcore:MinimumDepthInMeters>
minimumDepthInMeters <dwcore:MinimumDepthInMeters>
scientificName <dwcore:scientificName>
scientificNameAuthorship <dwcore:AuthorYearOfScientificName>




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