Difference between revisions of "Species Products Discovery Objects"

From Gcube Wiki
Jump to: navigation, search
(→‎Occurrence)
(→‎TaxonomyItem)
Line 27: Line 27:
 
itis-spd-plugin: table taxon_authors_lkp → taxon_author
 
itis-spd-plugin: table taxon_authors_lkp → taxon_author
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.tnames -> tauthor
  
 
ncbi-spd-plugin:
 
ncbi-spd-plugin:
Line 53: Line 53:
 
itis-spd-plugin:
 
itis-spd-plugin:
  
−
obis-spd-plugin:
+
obis-spd-plugin: generated string
  
 
ncbi-spd-plugin:
 
ncbi-spd-plugin:
Line 79: Line 79:
 
itis-spd-plugin: Table vernaculars →  
 
itis-spd-plugin: Table vernaculars →  
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.cnames
  
 
ncbi-spd-plugin:
 
ncbi-spd-plugin:

Revision as of 16:39, 7 January 2013

TaxonomyItem

Field Description Mapping
author 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


Data Type: string

Required: false

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

brazilian-flora-spd-plugin: au

catalogue-of-life-spd-plugin: author

irmng-spd-plugin: scientificnameauthorship

itis-spd-plugin: table taxon_authors_lkp → taxon_author

obis-spd-plugin: table obis.tnames -> tauthor

ncbi-spd-plugin:

worms-spd-plugin: AphiaRecord record - record.getAuthority()

citation 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


Data Type: string

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

irmng-spd-plugin: nameaccordingto

itis-spd-plugin:

obis-spd-plugin: generated string

ncbi-spd-plugin:

worms-spd-plugin: AphiaRecord record - record.getCitation()

commonNames A common or vernacular name.

Example: “Andean Condor", "Condor Andino", "American Eagle", "Gönsegeier"


Data Type: List <CommonName>

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin: common_names

irmng-spd-plugin:

itis-spd-plugin: Table vernaculars →

obis-spd-plugin: table obis.cnames

ncbi-spd-plugin:

worms-spd-plugin: WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID())

credits 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/)


Data Type: string

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

irmng-spd-plugin:

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin:

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

brazilian-flora-spd-plugin: id

catalogue-of-life-spd-plugin: id

irmng-spd-plugin: taxonid

itis-spd-plugin: Table longnames → tsn

obis-spd-plugin:

ncbi-spd-plugin: Table nodes → tax_id

worms-spd-plugin: AphiaRecord record - record.getAphiaID()

lsid 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”


Data Type: string

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

irmng-spd-plugin:

itis-spd-plugin: urn:lsid:itis.gov:itis_tsn:TSN

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: AphiaRecord record - record.getLsid()

modified Date when the record was last updated

Example: “2009-08-21”


Data Type: calendar

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin: record_scrutiny_date

irmng-spd-plugin: modified

itis-spd-plugin: table taxonomic_units → update_date

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin:

parent The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).


Data Type: TaxonomyItem

Required: false

DwC term: none

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin: classification

irmng-spd-plugin: parentnameusageid

itis-spd-plugin: table taxonomic_units → parent_tsn

obis-spd-plugin:

ncbi-spd-plugin: table nodes → parent_tax_id

worms-spd-plugin: WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID())

properties Comments or notes about the taxon or name or data sources.


Data Type: List<ElementProperty>

Required: false

DwC term: none

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin: references

irmng-spd-plugin:

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin:

rank 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"


Data Type: string

Required: true

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

brazilian-flora-spd-plugin: rank

catalogue-of-life-spd-plugin: rank

irmng-spd-plugin: taxonrank

itis-spd-plugin: table taxon_unit_types → rank_name

obis-spd-plugin:

ncbi-spd-plugin: Table nodes → rank

worms-spd-plugin: AphiaRecord record - record.getRank()

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


Examples: "Coleoptera" , "Vespertilionidae”, "Manis" , "Ctenomys sociabilis", "Ambystoma tigrinum diaboli", "Quercus agrifolia var. oxyadenia (Torr.)"


Data Type: string

Required: true

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

brazilian-flora-spd-plugin: html_full_name

catalogue-of-life-spd-plugin: name

irmng-spd-plugin: scientificname

itis-spd-plugin: table longnames → completename

obis-spd-plugin:

ncbi-spd-plugin: Table names → name_txt

worms-spd-plugin: AphiaRecord record - record.getScientificname()

status The status of a taxon.


Data Type: TaxonomyStatus

Required: true

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


TaxonomyStatus

Field Description Mapping
status The status of the use of the scientificName as a label for a taxon.

Controlled vocabulary: "accepted", "invalid", "misapplied", "provisional", “synonym”, “unknown”, “valid”.

Data Type: string

Required: true

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

brazilian-flora-spd-plugin: status

catalogue-of-life-spd-plugin: name_status

irmng-spd-plugin: taxonomicstatus

itis-spd-plugin: table taxonomic_units → name_usage

obis-spd-plugin:

ncbi-spd-plugin: Table names → name_class

worms-spd-plugin: AphiaRecord record - record.getStatus()

refId This value points to the record representing the valid (zoological) or accepted (botanical) name using the taxonID of that record as the “pointer.”

Data Type: string

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

gbif-spd-plugin:

irmng-spd-plugin: acceptednameusageid

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

species-link-spd-plugin:

worms-spd-plugin: AphiaRecord record - record.getValid_AphiaID()

statusAsString Comments or notes about the taxon or name.

Example: “Type consists of a skull and skeletal fragments”.

Data Type: string

Required: false

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

brazilian-flora-spd-plugin: qualifier

catalogue-of-life-spd-plugin:

irmng-spd-plugin: taxonremarks

itis-spd-plugin: table taxonomic_units → unaccept_reason

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: AphiaRecord record - record.getStatus()

CommonName

Field Description Mapping
language The language of the resource.

Data Type: string

Required: true

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


brazilian-flora-spd-plugin: status

catalogue-of-life-spd-plugin: name_status

irmng-spd-plugin: taxonomicstatus

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: Vernacular vernacular - vernacular.getLanguage()

name A common or vernacular name.

Data Type: string

Required: false

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

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

irmng-spd-plugin: acceptednameusageid

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: Vernacular vernacular - vernacular.getVernacular()

ElementProperty

Field Description Mapping
name Key used to identify comments or notes.

Example: “Reference”, “Source”


Data Type: string

Required: false

DwC term: none


brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin: Source Database, Reference

irmng-spd-plugin:

itis-spd-plugin: Source

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: additional source, basis of record, context source (Deepsea)

value 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”

Data Type: string

Required: false

DwC term: none

brazilian-flora-spd-plugin:

catalogue-of-life-spd-plugin:

irmng-spd-plugin:

itis-spd-plugin:

obis-spd-plugin:

ncbi-spd-plugin:

worms-spd-plugin: Source source – source.getReference(), source.getLink(), source.getUrl()


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:

obis-spd-plugin:

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:

obis-spd-plugin:

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:

obis-spd-plugin:

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:

obis-spd-plugin:

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:

obis-spd-plugin:

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

decimalLatitude The geographic latitude.


Data Type: float

Required: false

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

gbif-spd-plugin:

obis-spd-plugin:

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:

obis-spd-plugin:

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:

obis-spd-plugin:

species-link-spd-plugin:

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:

obis-spd-plugin:

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

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:

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:

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

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:

obis-spd-plugin:

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

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:

obis-spd-plugin:

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

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:

obis-spd-plugin:

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:

obis-spd-plugin:

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

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:

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

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:

obis-spd-plugin:

species-link-spd-plugin: <dwcur:IdentifiedBy 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:

obis-spd-plugin:

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

Retrieved from "https://wiki.gcube-system.org/index.php?title=Species_Products_Discovery_Objects&oldid=17344"