Difference between revisions of "Species Products Discovery Objects"

Revision as of 13:35, 21 January 2013

TaxonomyItem

The Fields

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

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	“Andean Condor", "Condor Andino", "American Eagle", "Gönsegeier"
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
Darwin Core Term
Data Type
Mandatory
xxx
Description
Example
Darwin Core Term
Data Type
Mandatory
xxx
Description
Example
Darwin Core Term
Data Type
Mandatory
xxx
Description
Example
Darwin Core Term
Data Type
Mandatory

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: constant ACCEPTED

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: table obis.cnames -> lanname

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: table obis.cnames -> cname

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: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id

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: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id

ncbi-spd-plugin:

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

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>

Difference between revisions of "Species Products Discovery Objects"

Revision as of 13:35, 21 January 2013

Contents

TaxonomyItem

The Fields

TaxonomyStatus

CommonName

ElementProperty

Compilation

List of Species of the Brazilian Flora

Occurrence

Navigation menu

Views

Personal tools

gCube Wiki

gCube features

gCube documentation

Integration and Distribution

Search

Tools

@@ Line 21: / Line 21: @@
 '''[[#id | id]]''',
 '''[[#lsid | lsid]]''',
+'''[[#modified | modified]]''',
+'''[[#parent | parent]]''',
+'''[[#properties | properties]]''',
+'''[[#rank | rank]]''',
 '''[[# | ]]''',
+'''[[# | ]]'''.
 The semantic of these fields is inherited by [http://rs.tdwg.org/dwc/terms Darwin Core Terms].
@@ Line 127: / Line 131: @@
 |-
 || Description
-|| 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.
+|| 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
@@ Line 142: / Line 146: @@
 |-
-<!-- %%% %%% -->
+<!-- %%% MODIFIED %%% -->
-! colspan=2 bgcolor=lightgrey | xxx
+! colspan=2 bgcolor=lightgrey | <div id="modified">modified</div>
 |-
 || Description
-||
+|| Date when the record the TaxonomyItem is representing was last updated.
 |-
 || Example
-||
+|| “2009-08-21”
 |-
 || Darwin Core Term
-||
+|| [http://purl.org/dc/terms/modified modified]
 |-
 || Data Type
-||
+|| calendar
 |-
 || Mandatory
-||
+|| false
 |-
-<!-- %%% %%% -->
+<!-- %%% PARENT %%% -->
-! colspan=2 bgcolor=lightgrey | xxx
+! colspan=2 bgcolor=lightgrey | <div id="parent">parent</div>
 |-
 || Description
-||
+|| The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).
 |-
 || Example
@@ Line 171: / Line 175: @@
 |-
 || Darwin Core Term
-||
+|| n/a
 |-
 || Data Type
-||
+|| TaxonomyItem
 |-
 || Mandatory
-||
+|| false
 |-
-<!-- %%% %%% -->
+<!-- %%% PROPERTIES %%% -->
-! colspan=2 bgcolor=lightgrey | xxx
+! colspan=2 bgcolor=lightgrey | <div id="properties">properties</div>
 |-
 || 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
-||
+|| <nowiki>List <ElementProperty></nowiki>
 |-
 || Mandatory
-||
+|| false
 |-
-<!-- %%% %%% -->
+<!-- %%% RANK %%% -->
-! colspan=2 bgcolor=lightgrey | xxx
+! colspan=2 bgcolor=lightgrey | <div id="rank">rank</div>
 |-
 || Description
-||
+|| The taxonomic rank of the most specific name in the scientificName. <br/> Recommended vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml
 |-
 || Example
@@ Line 273: / Line 277: @@
 || Mandatory
 ||
-|}
----
-{|border="1" cellpadding="5" cellspacing="0"
-|-
-! scope="col" width= "10%" style="background:#efefef;" | '''Field'''
-! scope="col" style="background:#efefef;" | '''Description'''
-! scope="col" style="background:#efefef;" | '''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"
-''<nowiki>Data Type: List <CommonName> </nowiki>''
-''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: "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)"
-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: table obis.tnames -> id
-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: table obis.tnames -> parent_id
-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.
-''<nowiki>Data Type: List<ElementProperty></nowiki>''
-''Required: false''
-''DwC term: none''
-| brazilian-flora-spd-plugin:
-catalogue-of-life-spd-plugin: references
-irmng-spd-plugin:
-itis-spd-plugin:
-obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id
-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: table obis.ranks -> rank_name
-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: table obis.tnames -> tname
-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''
-|
 |}