Difference between revisions of "Species Products Discovery Objects"

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Revision as of 15:07, 21 January 2013

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: author, 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 by Darwin Core Terms.

author
Description 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 false
id
Description The unique identifier used for a name or taxon reference in the core data file.
Example
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
Darwin Core Term taxonomicStatus
Data Type TaxonomyStatus
Mandatory true

CommonName Fields

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

TaxonomyStatus Fields

Compilation

List of Species of the Brazilian Flora

Occurrence

The following schema describes the fields in an occurrence object.


Field Description Mapping
basisOfRecord The specific nature of the data record. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).

Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation".


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/basisOfRecord

gbif-spd-plugin: basisOfRecordString

obis-spd-plugin: table obis.drs -> basisofrecord

species-link-spd-plugin: <dwcore:BasisOfRecord>

catalogNumber An identifier (preferably unique) for the record within the data set or collection.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/catalogNumber

gbif-spd-plugin: catalogNumber

obis-spd-plugin: table obis.dxs -> catalognumber

species-link-spd-plugin: <dwcore:CatalogNumber>

citation Citation information specified by the data publisher.

Example: Accessed through: speciesLink at http://splink.cria.org.br


Data Type: string

Required: false

DwC term: ?

gbif-spd-plugin: citation

obis-spd-plugin: table obis.dxs -> citation

species-link-spd-plugin:

country The name of the country or major administrative unit in which the Location occurs.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/country

gbif-spd-plugin: country

obis-spd-plugin: table obis.dxs -> country

species-link-spd-plugin: <dwcore:Country>

collectionCode The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/collectionCode

gbif-spd-plugin: collectionCode

obis-spd-plugin: table obis.dxs -> collectioncode

species-link-spd-plugin: <dwcore:CollectionCode>

dateLastModified The most recent date-time on which the resource was changed.

Examples: "1963-03-08T14:07-0600"


Data Type: date

Required: false

DwC term: http://purl.org/dc/terms/modified

gbif-spd-plugin:

obis-spd-plugin: table obis.dxs -> datelastmodified

species-link-spd-plugin: <dwcore:DateLastModified>

decimalLatitude The geographic latitude.


Data Type: float

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/decimalLatitude

gbif-spd-plugin: decimalLatitude

obis-spd-plugin: table obis.drs -> latitude

species-link-spd-plugin: <dwgeo:DecimalLatitude>

decimalLongitude The geographic longitude.


Data Type: float

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/decimalLongitude

gbif-spd-plugin: decimalLongitude

obis-spd-plugin: table obis.drs -> longitude

species-link-spd-plugin: <dwgeo:DecimalLongitude>

eventDate The date-time when the event was recorded.

Examples: "1963-03-08T14:07-0600"


Data Type: date

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/eventDate

gbif-spd-plugin: earliestDateCollected

obis-spd-plugin: table obis.drs -> datecollected

species-link-spd-plugin:

kingdom The full scientific name of the kingdom in which the taxon is classified.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/kingdom

gbif-spd-plugin:

obis-spd-plugin: table obis.dxs -> concatenated

species-link-spd-plugin: <dwcore:Kingdom>

family The full scientific name of the family in which the taxon is classified.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/family

gbif-spd-plugin:

obis-spd-plugin: table obis.dxs -> concatenated

species-link-spd-plugin: <dwcore:Family>

id The unique identifier used for a name or taxon reference in the core data file.


Data Type: string

Required: true

DwC term: http://rs.tdwg.org/dwc/terms/taxonID

gbif-spd-plugin: gbifKey (attribute of TaxonOccurrence)

obis-spd-plugin: table obis.drs -> id

species-link-spd-plugin: <dwcore:GlobalUniqueIdentifier>


identifiedBy A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.

Example: "James L. Patton"


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/identifiedBy

gbif-spd-plugin: citation

obis-spd-plugin:

species-link-spd-plugin: <dwcur:IdentifiedBy xsi:nil="true"/>

institutionCode The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.


Data Type: string

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/institutionCode

gbif-spd-plugin: institutionCode

obis-spd-plugin: table obis.dxs -> institutioncode

species-link-spd-plugin: <dwcore:InstitutionCode>

maximumDepthInMeters The greater depth of a range of depth below the local surface, in meters.


Data Type: float

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/maximumDepthInMeters

gbif-spd-plugin: maximumDepthInMeters

obis-spd-plugin: table obis.dxs -> maximumdepth

species-link-spd-plugin: <dwcore:MaximumDepthInMeters xsi:nil="true"/>

minimumDepthInMeters The lesser depth of a range of depth below the local surface, in meters.


Data Type: float

Required: false

DwC term: http://rs.tdwg.org/dwc/terms/minimumDepthInMeters

gbif-spd-plugin: maximumDepthInMeters

obis-spd-plugin: table obis.dxs -> minimumdepth

species-link-spd-plugin: <dwcore:MinimumDepthInMeters xsi:nil="true"/>

scientificName The scientific name of taxon with or without authorship information depending on the format of the source database.


Data Type: string

Required: true

DwC term: http://rs.tdwg.org/dwc/terms/scientificName

gbif-spd-plugin: nameComplete

obis-spd-plugin: table obis.dxs -> concatenated

species-link-spd-plugin: <dwcore:ScientificName>

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