Difference between revisions of "Species Products Discovery Objects"

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=='''TaxonomyItem'''==
+
<!-- CATEGORIES -->
 +
[[Category:Developer's Guide]]
 +
<!-- END CATEGORIES -->
 +
{| align="right"
 +
||__TOC__
 +
|}
  
 +
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 | TaxonomyItem]], i.e. a characterisation of species taxa;
 +
* [[#Occurrence | 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 | scientificNameAuthorship]]''',
 +
'''[[#citation | citation]]''',
 +
'''[[#commonNames | commonNames]]''',
 +
'''[[#credits | credits]]''',
 +
'''[[#id | id]]''',
 +
'''[[#lsid | lsid]]''',
 +
'''[[#modified | modified]]''',
 +
'''[[#parent | parent]]''',
 +
'''[[#properties | properties]]''',
 +
'''[[#rank | rank]]''',
 +
'''[[#scientificName | scientificName]]''',
 +
and
 +
'''[[#status | status]]'''.
 +
 +
commonNames, properties and status are compound objects and the fields characterising them are described in dedicated sections respectively, i.e.   
 +
'''[[#CommonName_Fields | commonNames Fields]]''',
 +
'''[[#ElementProperty_Fields | ElementProperty Fields]]''',
 +
and
 +
'''[[#TaxonomyStatus_Fields | TaxonomyStatus Fields]]'''.
 +
 +
The semantic of these fields is inherited from [http://rs.tdwg.org/dwc/terms Darwin Core Terms]. A quick guide [https://gcube.wiki.gcube-system.org/gcube/index.php/Darwin_Core_Terms here].
  
 
{|border="1" cellpadding="5" cellspacing="0"
 
{|border="1" cellpadding="5" cellspacing="0"
 +
 +
<!-- %%% scientificNameAuthorship %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="scientificNameAuthorship">scientificNameAuthorship</div>
 
|-
 
|-
−
! scope="col" width= "10%" style="background:#efefef;" | '''Field'''
+
|| Description
−
! scope="col" style="background:#efefef;" | '''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.
−
! scope="col" style="background:#efefef;" | '''Mapping'''
+
|-
 +
|| Example
 +
|| (Schltdl.) Crins
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/scientificNameAuthorship scientificNameAuthorship]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 
|-
 
|-
−
| '''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
+
<!-- %%% CITATION %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="citation">citation</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/nameAccordingTo nameAccordingTo]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
 +
<!-- %%% COMMONNAMES %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="commonNames">commonNames</div>
 +
|-
 +
|| Description
 +
|| A common or vernacular name.
 +
|-
 +
|| Example
 +
|| see [[#CommonName Fields | commonName fields]].
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/vernacularName vernacularName]
 +
|-
 +
|| Data Type
 +
|| <nowiki>List <CommonName></nowiki>
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
''Data Type: string''
+
<!-- %%% CREDITS %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="credits">credits</div>
 +
|-
 +
|| 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
 +
|| [http://purl.org/dc/terms/bibliographicCitation bibliographicCitation]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
''Required: false''
+
<!-- %%% ID %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="id">id</div>
 +
|-
 +
|| Description
 +
|| The unique identifier used for a name or taxon reference in the core data file.
 +
|-
 +
|| Example
 +
|| "37829"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/taxonID taxonID]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/scientificNameAuthorship''
+
<!-- %%% LSID %%% -->
−
| brazilian-flora-spd-plugin: au
+
! colspan=2 bgcolor=lightgrey | <div id="lsid">lsid</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/scientificNameID scientificNameID]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-  
 +
|| Mandatory
 +
|| false
 +
|-
  
−
catalogue-of-life-spd-plugin: author
+
<!-- %%% MODIFIED %%% -->
 +
! 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
 +
|-
  
−
irmng-spd-plugin: scientificnameauthorship
+
<!-- %%% PARENT %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="parent">parent</div>
 +
|-
 +
|| Description
 +
|| The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| n/a
 +
|-
 +
|| Data Type
 +
|| TaxonomyItem
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
itis-spd-plugin: table taxon_authors_lkp → taxon_author
+
<!-- %%% PROPERTIES %%% -->
 +
! 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
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> tauthor
+
<!-- %%% RANK %%% -->
 +
! 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
 +
|| "subspecies", "varietas", "forma", "species", "genus"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/taxonRank taxonRank]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- %%% SCIENTIFICNAME %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="scientificName">scientificName</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/scientificName scientificName]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getAuthority()
+
<!-- %%% STATUS %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="status">status</div>
 +
|-
 +
|| Description
 +
|| The status of the taxon represented by the TaxonomiItem.
 +
|-
 +
|| Example
 +
|| "invalid", "misapplied", "homotypic synonym", "accepted"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/taxonomicStatus taxonomicStatus]
 +
|-
 +
|| Data Type
 +
|| TaxonomyStatus
 +
|-
 +
|| Mandatory
 +
|| true
 +
 
 +
|}
 +
 
 +
==== CommonName Fields ====
 +
 
 +
A CommonName is characterised by the following fields: 
 +
'''[[#cn.language | language]]'''
 +
and
 +
'''[[#cn.name | name]]'''.
 +
 +
{|border="1" cellpadding="5" cellspacing="0"
  
 +
<!-- %%% LANGUAGE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="cn.language">language</div>
 +
|-
 +
|| Description
 +
|| The language of the resource.
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| [http://purl.org/dc/terms/language language]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 
|-
 
|-
−
| '''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
+
<!-- %%% NAME %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="cn.name">name</div>
 +
|-
 +
|| Description
 +
|| A common or vernacular name.
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/vernacularName vernacularName]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-  
 +
|| Mandatory
 +
|| false
  
 +
|}
  
−
''Data Type: string''
+
==== ElementProperty Fields ====
  
−
''Required: false''
+
An ElementProperty is characterised by the following fields: 
 +
'''[[#ep.name | name]]'''
 +
and
 +
'''[[#ep.value | value]]'''.
 +
 +
{|border="1" cellpadding="5" cellspacing="0"
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/nameAccordingTo''
+
<!-- %%% NAME %%% -->
−
| brazilian-flora-spd-plugin:
+
! colspan=2 bgcolor=lightgrey | <div id="ep.name">name</div>
 +
|-
 +
|| Description
 +
|| Key used to identify comments or notes.
 +
|-
 +
|| Example
 +
|| “Reference”, “Source”
 +
|-
 +
|| Darwin Core Term
 +
|| n/a
 +
|-
 +
|| Data Type
 +
|| string
 +
|-  
 +
|| Mandatory
 +
|| false
 +
|-
  
−
catalogue-of-life-spd-plugin:  
+
<!-- %%% VALUE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="ep.value">value</div>
 +
|-
 +
|| 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
 +
|}
  
−
irmng-spd-plugin: nameaccordingto
+
==== TaxonomyStatus Fields ====
  
−
itis-spd-plugin:
+
A TaxonomyStatus is characterised by the following fields:
 +
'''[[#ts.status | status]]''',
 +
'''[[#ts.refId | refId]]''',
 +
and
 +
'''[[#ts.statusAsString | statusAsString]]'''.
  
−
obis-spd-plugin: generated string
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
ncbi-spd-plugin:
+
<!-- %%% STATUS %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="ts.status">status</div>
 +
|-
 +
|| Description
 +
|| The status of the use of the scientificName as a label for a taxon.<br/>Controlled vocabulary: "accepted", "invalid", "misapplied", "provisional", “synonym”, “unknown”, “valid”.
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/taxonomicStatus taxonomicStatus]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getCitation()
+
<!-- %%% REFID %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="ts.refId">refId</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/acceptedNameUsageID acceptedNameUsageID]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
 +
<!-- %%% STATUSASSTRING %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="ts.statusAsString">statusAsString</div>
 
|-
 
|-
−
| '''commonNames'''
+
|| Description
−
| A common or vernacular name.
+
|| Comments or notes about the taxon or name.
 +
|-
 +
|| Example
 +
|| “Type consists of a skull and skeletal fragments”.
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/taxonRemarks taxonRemarks]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|}
  
−
Example: “Andean Condor", "Condor Andino", "American Eagle", "Gönsegeier"
+
=== 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_Compilation:_List_of_Species_of_the_Brazilian_Flora | TaxonomyItem Compilation: List of Species of the Brazilian Flora]],
 +
* [[#TaxonomyItem Compilation: Catalogue of Life | TaxonomyItem Compilation: Catalogue of Life]],
 +
* [[#TaxonomyItem Compilation: IRMNG | TaxonomyItem Compilation: IRMNG]],
 +
* [[#TaxonomyItem Compilation: ITIS | TaxonomyItem Compilation: ITIS]],
 +
* [[#TaxonomyItem Compilation: NCBI | TaxonomyItem Compilation: NCBI]],
 +
* [[#TaxonomyItem Compilation: WoRMS | TaxonomyItem Compilation: WoRMS]].
  
−
''<nowiki>Data Type: List <CommonName> </nowiki>''
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
''Required: false''
+
! TaxonomyItem Field
 +
! FloraDoBrasil
 +
! CoL
 +
! IRMNG
 +
! ITIS
 +
! OBIS
 +
! NCBI
 +
! WoRMS
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/vernacularName''
+
<!-- AUTHOR -->
−
| brazilian-flora-spd-plugin:
+
| '''[[#author | author]]'''
 +
| align=center| <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
| align=center| <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
| align=center| <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
| align=center| <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
| align=center| <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- NCBI -->
 +
|align=center| <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
catalogue-of-life-spd-plugin: common_names
+
<!-- CITATION -->
 +
| '''[[#citation | citation]]'''
 +
|align=center| <!-- FloraBR -->
 +
|align=center| <!-- CoL -->
 +
|align=center| <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center| <!-- ITIS -->
 +
|align=center| <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center| <!-- NCBI -->
 +
|align=center| <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
irmng-spd-plugin:
+
<!-- COMMONNAMES -->
 +
| '''[[#commonNames | commonNames]]'''
 +
|align=center|  <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS -->
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI -->
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
itis-spd-plugin: Table vernaculars →
+
<!-- CREDITS -->
 +
| '''[[#credits | credits]]'''
 +
|align=center|  <!-- FloraBR -->
 +
|align=center|  <!-- CoL -->
 +
|align=center|  <!-- IRMNG -->
 +
|align=center|  <!-- ITIS -->
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI -->
 +
|align=center|  <!-- WoRMS -->
 +
|-
  
−
obis-spd-plugin: table obis.cnames
+
<!-- ID -->
 +
| '''[[#id | id]]'''
 +
|align=center|  <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI --> [[#TaxonomyItem_Compilation:_NCBI | Compiled]]
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- LSID -->
 +
| '''[[#lsid | lsid]]'''
 +
|align=center|  <!-- FloraBR -->
 +
|align=center|  <!-- CoL -->
 +
|align=center|  <!-- IRMNG -->
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS -->
 +
|align=center|  <!-- NCBI -->
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
worms-spd-plugin: WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID())
+
<!-- MODIFIED -->
 +
| '''[[#modified | modified]]'''
 +
|align=center|  <!-- FloraBR -->
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS -->
 +
|align=center|  <!-- NCBI -->
 +
|align=center|  <!-- WoRMS -->
 +
|-
  
 +
<!-- PARENT -->
 +
| '''[[#parent | parent]]'''
 +
|align=center|  <!-- FloraBR -->
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI --> [[#TaxonomyItem_Compilation:_NCBI | Compiled]]
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 
|-
 
|-
−
| '''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/)
+
<!-- PROPERTIES -->
 +
| '''[[#properties | properties]]'''
 +
|align=center|  <!-- FloraBR -->
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG -->
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI -->
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
 +
<!-- RANK -->
 +
| '''[[#rank | rank]]'''
 +
|align=center|  <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI --> [[#TaxonomyItem_Compilation:_NCBI | Compiled]]
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
''Data Type: string''
+
<!-- SCIENTIFICNAME -->
 +
| '''[[#scientificName | scientificName]]'''
 +
|align=center|  <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI --> [[#TaxonomyItem_Compilation:_NCBI | Compiled]]
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|-
  
−
''Required: false''
+
<!-- STATUS -->
 +
| '''[[#status | status]]'''
 +
|align=center|  <!-- FloraBR --> [[#TaxonomyItem_Compilation:_List_of_Species_of_the_Brazilian_Flora | Compiled]]
 +
|align=center|  <!-- CoL --> [[#TaxonomyItem_Compilation:_Catalogue_of_Life | Compiled]]
 +
|align=center|  <!-- IRMNG --> [[#TaxonomyItem_Compilation:_IRMNG | Compiled]]
 +
|align=center|  <!-- ITIS --> [[#TaxonomyItem_Compilation:_ITIS | Compiled]]
 +
|align=center|  <!-- OBIS --> [[#TaxonomyItem_Compilation:_OBIS | Compiled]]
 +
|align=center|  <!-- NCBI --> [[#TaxonomyItem_Compilation:_NCBI | Compiled]]
 +
|align=center|  <!-- WoRMS --> [[#TaxonomyItem_Compilation:_WoRMS | Compiled]]
 +
|}
  
−
''DwC term: http://purl.org/dc/terms/bibliographicCitation''
+
==== TaxonomyItem Compilation: List of Species of the Brazilian Flora ====
−
| brazilian-flora-spd-plugin:
+
  
−
catalogue-of-life-spd-plugin:  
+
In the case of [http://floradobrasil.jbrj.gov.br/ List of Species of the Brazilian Flora] TaxonomyItem objects are compiled by relying on the [http://checklist.florabrasil.net/service Brazilian Flora Web Service].
  
−
irmng-spd-plugin:
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
itis-spd-plugin:
+
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 +
|-
 +
|colspan=2| '''[[#author | author]]'''
 +
|| au
 +
||
 +
|-
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| status
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#id | id]]'''
 +
|| id
 +
||
 +
|-
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#modified | modified]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
obis-spd-plugin: "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)"
+
<!-- PROPERTIES -->
 +
|rowspan=2| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- RANK -->
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| rank
 +
||
 +
|-
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| html_full_name
 +
||
 +
|-
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| status
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| qualifier
 +
||
 +
|}
  
−
worms-spd-plugin:  
+
==== TaxonomyItem Compilation: Catalogue of Life ====
  
 +
In the case of [http://www.catalogueoflife.org/ Catalogue of Life] TaxonomyItem objects are compiled by relying on the [http://www.catalogueoflife.org/col/webservice Web service].
 +
 +
{|border="1" cellpadding="5" cellspacing="0"
 +
 +
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 
|-
 
|-
−
| '''id'''
+
|colspan=2| '''[[#author | author]]'''
−
| The unique identifier used for a name or taxon reference in the core data file.
+
|| author
 +
||
 +
|-
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| name_status
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#id | id]]'''
 +
|| id
 +
||
 +
|-
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#modified | modified]]'''
 +
|| record_scrutiny_date
 +
||
 +
|-
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| classification
 +
||
 +
|-
 +
|rowspan=4| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| Source Database
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| <font color=red>'''???'''</font>
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| Reference
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| <font color=red>'''???'''</font>
 +
||
 +
|-
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| rank
 +
||
 +
|-
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| name
 +
||
 +
|-
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| name_status
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| '''n/a'''
 +
||
 +
|}
  
 +
==== TaxonomyItem Compilation: IRMNG ====
  
−
''Data Type: string''
+
In the case of [http://www.cmar.csiro.au/datacentre/irmng/ IRMNG] TaxonomyItem objects are compiled by relying on the database dump in DarwinCore (DwC) Archive.
  
−
''Required: true''
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/taxonID''
+
!colspan=2| TaxonomyItem Field
−
| brazilian-flora-spd-plugin: id
+
! Source
 +
! Note
 +
|-
 +
|colspan=2| '''[[#author | author]]'''
 +
|| scientificnameauthorship
 +
||
 +
|-
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| nameaccordingto
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin: id
+
<!-- COMMONNAMES -->
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| taxonomicstatus
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| acceptednameusageid
 +
||
 +
|-
  
−
irmng-spd-plugin: taxonid
+
<!-- CREDITS -->
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
itis-spd-plugin: Table longnames → tsn
+
<!-- ID -->
 +
|colspan=2| '''[[#id | id]]'''
 +
|| taxonid
 +
||
 +
|-
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#modified | modified]]'''
 +
|| modified
 +
||
 +
|-
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| parentnameusageid
 +
||
 +
|-
 +
|rowspan=2| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| taxonrank
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> id
+
<!-- SCIENTIFIC NAME -->
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| scientificname
 +
||
 +
|-
  
−
ncbi-spd-plugin: Table nodes → tax_id
+
<!-- STATUS -->
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| taxonomicstatus
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| acceptednameusageid
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| taxonremarks
 +
||
 +
|}
  
−
worms-spd-plugin: AphiaRecord record - record.getAphiaID()
+
==== TaxonomyItem Compilation: ITIS ====
  
 +
In the case of [http://www.itis.gov/ ITIS] TaxonomyItem objects are compiled by relying on the [http://www.itis.gov/downloads/ database dump files] (MySQL by table).
 +
 +
{|border="1" cellpadding="5" cellspacing="0"
 +
 +
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 
|-
 
|-
−
| '''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”
+
<!-- AUTHOR -->
 +
|colspan=2| '''[[#author | author]]'''
 +
|| table taxon_authors_lkp → taxon_author
 +
||
 +
|-
  
 +
<!-- CITATION -->
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''Data Type: string''
+
<!-- COMMONNAMES -->
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''Required: false''
+
<!-- CREDITS -->
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/scientificNameID''
+
<!-- ID -->
−
| brazilian-flora-spd-plugin:
+
|colspan=2| '''[[#id | id]]'''
 +
|| Table longnames → tsn
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin:  
+
<!-- LSID -->
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| urn:lsid:itis.gov:itis_tsn:TSN
 +
||
 +
|-
  
−
irmng-spd-plugin:
+
<!-- MODIFIED -->
 +
|colspan=2| '''[[#modified | modified]]'''
 +
|| table taxonomic_units → update_date
 +
||
 +
|-
  
−
itis-spd-plugin: urn:lsid:itis.gov:itis_tsn:TSN
+
<!-- PARENT -->
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| table taxonomic_units → parent_tsn
 +
||
 +
|-
  
−
obis-spd-plugin:
+
<!-- PROPERTIES -->
 +
|rowspan=2| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| Source
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| <font color=red>'''???'''</font>
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- RANK -->
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| table taxon_unit_types → rank_name
 +
||
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getLsid()
+
<!-- SCIENTIFICNAME -->
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| table longnames → completename
 +
||
 +
|-
  
 +
<!-- STATUS -->
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| table taxonomic_units → name_usage
 +
||
 
|-
 
|-
−
| '''modified'''
+
|| '''[[#ts.refId | refId]]'''
−
| Date when the record was last updated
+
|| '''n/a'''
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| table taxonomic_units → unaccept_reason
 +
||
 +
|}
  
−
Example: “2009-08-21”
+
==== TaxonomyItem Compilation: OBIS ====
  
 +
In the case of [http://www.iobis.org/ OBIS] TaxonomyItem objects are compiled by relying on ...
  
−
''Data Type: calendar''
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
''Required: false''
+
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 +
|-
  
−
''DwC term: http://purl.org/dc/terms/modified''
+
<!-- AUTHOR -->
−
| brazilian-flora-spd-plugin:
+
|colspan=2| '''[[#author | author]]'''
 +
|| table obis.tnames -> tauthor
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin: record_scrutiny_date
+
<!-- CITATION -->
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)";
 +
||
 +
|-
  
−
irmng-spd-plugin: modified
+
<!-- COMMONNAMES -->
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| lanname
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| table obis.cnames -> cname
 +
||
 +
|-
  
−
itis-spd-plugin: table taxonomic_units → update_date
+
<!-- CREDITS -->
 +
|colspan=2| '''[[#credits | 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."
 +
||
 +
|-
  
−
obis-spd-plugin:
+
<!-- ID -->
 +
|colspan=2| '''[[#id | id]]'''
 +
|| table obis.tnames -> id
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- LSID -->
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
worms-spd-plugin:
+
<!-- MODIFIED -->
 +
|colspan=2| '''[[#modified | modified]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
 +
<!-- PARENT -->
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| table obis.tnames -> parent_id
 +
||
 
|-
 
|-
−
| '''parent'''
 
−
| The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).
 
  
 +
<!-- PROPERTIES -->
 +
|rowspan=8| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| worms_id
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| table obis.tnames -> worms_id
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| col_id
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| table obis.tnames -> col_id
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| irmng_id
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| table obis.tnames -> irmng_id
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| itis_id
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| table obis.tnames -> itis_id
 +
||
 +
|-
  
−
''Data Type: TaxonomyItem''
+
<!-- RANK -->
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| table obis.ranks -> rank_name
 +
||
 +
|-
  
−
''Required: false''
+
<!-- SCIENTIFICNAME -->
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| table obis.tnames -> tname
 +
||
 +
|-
  
−
''DwC term: none''
+
<!-- STATUS -->
−
| brazilian-flora-spd-plugin:
+
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| ACCEPTED
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| '''n/a'''
 +
||
 +
|}
  
−
catalogue-of-life-spd-plugin: classification
+
==== TaxonomyItem Compilation: NCBI ====
  
−
irmng-spd-plugin: parentnameusageid
+
In the case of [http://www.ncbi.nlm.nih.gov/ NCBI] TaxonomyItem objects are compiled by relying on [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ FTP: NCBI Taxonomy]. This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs.
  
−
itis-spd-plugin: table taxonomic_units → parent_tsn
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
obis-spd-plugin: table obis.tnames -> parent_id
+
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 +
|-
  
−
ncbi-spd-plugin: table nodes → parent_tax_id
+
<!-- AUTHOR -->
 +
|colspan=2| '''[[#author | author]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
worms-spd-plugin: WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID())
+
<!-- CITATION -->
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
 +
<!-- COMMONNAMES -->
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| '''n/a'''
 +
||
 
|-
 
|-
−
| '''properties'''
 
−
| Comments or notes about the taxon or name or data sources.
 
  
 +
<!-- CREDITS -->
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''<nowiki>Data Type: List<ElementProperty></nowiki>''
+
<!-- ID -->
 +
|colspan=2| '''[[#id | id]]'''
 +
|| Table nodes → tax_id
 +
||
 +
|-
  
−
''Required: false''
+
<!-- LSID -->
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''DwC term: none''
+
<!-- MODIFIED -->
−
| brazilian-flora-spd-plugin:
+
|colspan=2| '''[[#modified | modified]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin: references
+
<!-- PARENT -->
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| table nodes → parent_tax_id
 +
||
 +
|-
  
−
irmng-spd-plugin:
+
<!-- PROPERTIES -->
 +
|rowspan=2| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
itis-spd-plugin:
+
<!-- RANK -->
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| Table nodes → rank
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id
+
<!-- SCIENTIFICNAME -->
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| Table names → name_txt
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- STATUS -->
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| Table names → name_class
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| '''n/a'''
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| '''n/a'''
 +
||
 +
|}
  
−
worms-spd-plugin:  
+
==== TaxonomyItem Compilation: WoRMS ====
  
 +
In the case of [http://www.marinespecies.org/ WoRMS] TaxonomyItem objects are compiled by relying on the [http://http://www.marinespecies.org/aphia.php?p=webservice/ WoRMS webservice].
 +
 +
{|border="1" cellpadding="5" cellspacing="0"
 +
 +
!colspan=2| TaxonomyItem Field
 +
! Source
 +
! Note
 
|-
 
|-
−
| '''rank'''
 
−
| The taxonomic rank of the most specific name in the scientificName.
 
  
−
Recommended vocabulary:
+
<!-- AUTHOR -->
 +
|colspan=2| '''[[#author | author]]'''
 +
|| AphiaRecord record - record.getAuthority()
 +
||
 +
|-
  
−
http://rs.gbif.org/vocabulary/gbif/rank.xml
+
<!-- CITATION -->
 +
|colspan=2| '''[[#citation | citation]]'''
 +
|| AphiaRecord record - record.getCitation()
 +
||
 +
|-
  
−
Example: "subspecies", "varietas", "forma", "species", "genus"
+
<!-- COMMONNAMES -->
 +
|rowspan=2| '''[[#commonNames | commonNames]]'''
 +
|| '''[[#cn.language | language]]'''
 +
|| Vernacular vernacular - vernacular.getLanguage()
 +
||
 +
|-
 +
|| '''[[#cn.name | name]]'''
 +
|| Vernacular vernacular - vernacular.getVernacular()
 +
||
 +
|-
  
 +
<!-- CREDITS -->
 +
|colspan=2| '''[[#credits | credits]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''Data Type: string''
+
<!-- ID -->
 +
|colspan=2| '''[[#id | id]]'''
 +
|| AphiaRecord record - record.getAphiaID()
 +
||
 +
|-
  
−
''Required: true''
+
<!-- LSID -->
 +
|colspan=2| '''[[#lsid | lsid]]'''
 +
|| AphiaRecord record - record.getLsid()
 +
||
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/taxonRank''
+
<!-- MODIFIED -->
−
| brazilian-flora-spd-plugin: rank
+
|colspan=2| '''[[#modified | modified]]'''
 +
|| '''n/a'''  
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin: rank
+
<!-- PARENT -->
 +
|colspan=2| '''[[#parent | parent]]'''
 +
|| WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID())
 +
||
 +
|-
  
−
irmng-spd-plugin: taxonrank
+
<!-- PROPERTIES -->
 +
|rowspan=6| '''[[#properties | properties]]'''
 +
|| '''[[#ep.name | name]]'''
 +
|| additional source
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| Source source – source.getReference()
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| basis of record
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| source.getLink()
 +
||
 +
|-
 +
|| '''[[#ep.name | name]]'''
 +
|| context source (Deepsea)
 +
||
 +
|-
 +
|| '''[[#ep.value | value]]'''
 +
|| source.getUrl()
 +
||
 +
|-
  
−
itis-spd-plugin: table taxon_unit_types → rank_name
+
<!-- RANK -->
 +
|colspan=2| '''[[#rank | rank]]'''
 +
|| AphiaRecord record - record.getRank()
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.ranks -> rank_name
+
<!-- SCIENTIFICNAME -->
 +
|colspan=2| '''[[#scientificName | scientificName]]'''
 +
|| AphiaRecord record - record.getScientificname()
 +
||
 +
|-
  
−
ncbi-spd-plugin: Table nodes → rank
+
<!-- STATUS -->
 +
|rowspan=3| '''[[#status | status]]'''
 +
|| '''[[#ts.status | status]]'''
 +
|| AphiaRecord record - record.getStatus()
 +
||
 +
|-
 +
|| '''[[#ts.refId | refId]]'''
 +
|| AphiaRecord record - record.getValid_AphiaID()
 +
||
 +
|-
 +
|| [[#ts.statusAsString | statusAsString]]
 +
|| AphiaRecord record - record.getStatus()
 +
||
 +
|}
  
−
worms-spd-plugin: AphiaRecord record - record.getRank()
+
== Occurrence ==
 +
 
 +
=== The Fields ===
 +
 
 +
A Occurrence object is characterised by the following fields:  
 +
'''[[#o.basisOfRecord | basisOfRecord]]''',
 +
'''[[#o.catalogNumber | catalogNumber]]''',
 +
'''[[#o.citation | citation]]''',
 +
'''[[#o.country | country]]''',
 +
'''[[#o.collectionCode | collectionCode]]''',
 +
'''[[#o.coordinateUncertaintyInMeters | coordinateUncertaintyInMeters]]''',
 +
'''[[#o.credits | credits]]''',
 +
'''[[#o.dateLastModified | dateLastModified]]''',
 +
'''[[#o.decimalLatitude | decimalLatitude]]''',
 +
'''[[#o.decimalLongitude | decimalLongitude]]''',
 +
'''[[#o.eventDate | eventDate]]''',
 +
'''[[#o.kingdom | kingdom]]''',
 +
'''[[#o.family | family]]''',
 +
'''[[#o.id | id]]''',
 +
'''[[#o.identifiedBy | identifiedBy]]''',
 +
'''[[#o.institutionCode | institutionCode]]''',
 +
'''[[#o.maximumDepthInMeters | maximumDepthInMeters]]''',
 +
'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]''',
 +
'''[[#o.recordedBy | recordedBy]]''',
 +
'''[[#o.scientificName | scientificName]]''',
 +
and
 +
'''[[#o.scientificNameAuthorship | scientificNameAuthorship]]'''.
 +
 
 +
The semantic of these fields is inherited from [http://rs.tdwg.org/dwc/terms Darwin Core Terms]. A quick guide [https://gcube.wiki.gcube-system.org/gcube/index.php/Darwin_Core_Terms here].
 +
 
 +
{|border="1" cellpadding="5" cellspacing="0"
  
 +
<!-- %%% BASISOFRECORD %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.basisOfRecord">basisOfRecord</div>
 +
|-
 +
|| 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 http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm].
 +
|-
 +
|| Example
 +
|| "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/basisOfRecord basisOfRecord]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 
|-
 
|-
−
| '''scientificName'''
 
−
| The scientific name of taxon with or without authorship information depending on the format of the source database.
 
  
 +
<!-- %%% CATALOGNUMBER %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.catalogNumber">catalogNumber</div>
 +
|-
 +
|| Description
 +
|| An identifier (preferably unique) for the record within the data set or collection.
 +
|-
 +
|| Example
 +
|| "9669"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/catalogNumber catalogNumber]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
Examples: "Coleoptera" , "Vespertilionidae”, "Manis" , "Ctenomys sociabilis", "Ambystoma tigrinum diaboli", "Quercus agrifolia var. oxyadenia (Torr.)"
+
<!-- %%% CITATION %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.citation">citation</div>
 +
|-
 +
|| Description
 +
|| Citation information specified by the data publisher.
 +
|-
 +
|| Example
 +
|| "Accessed through: speciesLink at http://splink.cria.org.br"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/nameAccordingTo nameAccordingTo]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
 +
<!-- %%% COUNTRY %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.country">country</div>
 +
|-
 +
|| Description
 +
|| The name of the country or major administrative unit in which the Location occurs.
 +
|-
 +
|| Example
 +
|| "Brasil"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/country country]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
''Data Type: string''
+
<!-- %%% COLLECTIONCODE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.collectionCode">collectionCode</div>
 +
|-
 +
|| Description
 +
|| The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
 +
|-
 +
|| Example
 +
|| "BAH"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/collectionCode collectionCode]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
''Required: true''
 
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/scientificName''
+
<!-- %%% CREDITS %%% -->
−
| brazilian-flora-spd-plugin: html_full_name
+
! colspan=2 bgcolor=lightgrey | <div id="o.credits">credits</div>
 +
|-
 +
|| 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
 +
|| [http://purl.org/dc/terms/rightsHolder rightsHolder]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-  
 +
|| Mandatory
 +
|| true
 +
|-
  
−
catalogue-of-life-spd-plugin: name
 
  
−
irmng-spd-plugin: scientificname
+
<!-- %%% DATELASTMODIFIED %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.dateLastModified">dateLastModified</div>
 +
|-
 +
|| Description
 +
|| The most recent date-time on which the resource was changed.
 +
|-
 +
|| Example
 +
|| "1963-03-08T14:07-0600"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://purl.org/dc/terms/modified modified]
 +
|-
 +
|| Data Type
 +
|| Date
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
itis-spd-plugin: table longnames → completename
+
<!-- %%% DECIMALLATITUDE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.decimalLatitude">decimalLatitude</div>
 +
|-
 +
|| Description
 +
|| The geographic latitude.
 +
|-
 +
|| Example
 +
|| "-11.451111"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/decimalLatitude decimalLatitude]
 +
|-
 +
|| Data Type
 +
|| float
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> tname
+
<!-- %%% DECIMALLONGITUDE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.decimalLongitude">decimalLongitude</div>
 +
|-
 +
|| Description
 +
|| The geographic longitude.
 +
|-
 +
|| Example
 +
|| "-46.161667"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/decimalLongitude decimalLongitude]
 +
|-
 +
|| Data Type
 +
|| float
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
ncbi-spd-plugin: Table names → name_txt
+
<!-- %%% EVENTDATE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.eventDate">eventDate</div>
 +
|-
 +
|| Description
 +
|| The date-time when the event was recorded.
 +
|-
 +
|| Example
 +
|| "1963-03-08T14:07-0600"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/eventDate eventDate]
 +
|-
 +
|| Data Type
 +
|| Date
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getScientificname()
+
<!-- %%% KINGDOM %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.kingdom">kingdom</div>
 +
|-
 +
|| Description
 +
|| The full scientific name of the kingdom in which the taxon is classified.
 +
|-
 +
|| Example
 +
|| "Plantae"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/kingdom kingdom]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
 +
<!-- %%% FAMILY %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.family">family</div>
 +
|-
 +
|| Description
 +
|| The full scientific name of the family in which the taxon is classified.
 +
|-
 +
|| Example
 +
|| "Bignoniaceae"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/family family]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 
|-
 
|-
−
| '''status'''
 
−
| The status of a taxon.
 
  
 +
<!-- %%% ID %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.id">id</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/dwcore/GlobalUniqueIdentifier GlobalUniqueIdentifier]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 +
|-
  
−
''Data Type: TaxonomyStatus''
+
<!-- %%% IDENTIFIEDBY %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.identifiedBy">identifiedBy</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/identifiedBy identifiedBy]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
''Required: true''
+
<!-- %%% INSTITUTIONCODE %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.institutionCode">institutionCode</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/institutionCode institutionCode]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/taxonomicStatus''
+
<!-- %%% MAXIMUMDEPTHINMETERS %%% -->
−
|  
+
! colspan=2 bgcolor=lightgrey | <div id="o.maximumDepthInMeters">maximumDepthInMeters</div>
 +
|-
 +
|| Description
 +
|| The greater depth of a range of depth below the local surface, in meters.
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/maximumDepthInMeters maximumDepthInMeters]
 +
|-
 +
|| Data Type
 +
|| float
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
|}
+
<!-- %%% MINIMUMDEPTHINMETERS %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.minimumDepthInMeters">minimumDepthInMeters</div>
 +
|-
 +
|| Description
 +
|| The lesser depth of a range of depth below the local surface, in meters.
 +
|-
 +
|| Example
 +
||
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/minimumDepthInMeters minimumDepthInMeters]
 +
|-
 +
|| Data Type
 +
|| float
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
  
−
==='''TaxonomyStatus'''===
+
<!-- %%% recordedBy %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.recordedBy">recordedBy</div>
 +
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/recordedBy recordedBy]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
 +
|-
  
−
{|border="1" cellpadding="5" cellspacing="0" width="100%"
+
<!-- %%% SCIENTIFICNAME %%% -->
 +
! colspan=2 bgcolor=lightgrey | <div id="o.scientificName">scientificName</div>
 
|-
 
|-
−
! scope="col" width="10%" style="background:#efefef;" | Field
+
|| Description
−
! scope="col" style="background:#efefef;" | Description
+
|| The scientific name of taxon with or without authorship information depending on the format of the source database.
−
! scope="col" style="background:#efefef;" | Mapping
+
|-
 +
|| Example
 +
|| "Jacaranda ulei"
 +
|-
 +
|| Darwin Core Term
 +
|| [http://rs.tdwg.org/dwc/terms/scientificName scientificName]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| true
 
|-
 
|-
  
−
| '''status'''
+
<!-- %%% scientificNameAuthorship %%% -->
−
| The status of the use of the scientificName as a label for a taxon.
+
! colspan=2 bgcolor=lightgrey | <div id="o.scientificNameAuthorship">scientificNameAuthorship</div>
−
Controlled vocabulary: "accepted", "invalid", "misapplied", "provisional", “synonym”, “unknown”, “valid”.
+
|-
 +
|| 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
 +
|| [http://rs.tdwg.org/dwc/terms/scientificNameAuthorship scientificNameAuthorship]
 +
|-
 +
|| Data Type
 +
|| string
 +
|-
 +
|| Mandatory
 +
|| false
  
−
''Data Type: string''
+
|}
  
−
''Required: true''
+
=== Occurrence Compilation ===
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/taxonomicStatus''
+
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 Compilation: GBIF | Occurrence Compilation: GBIF]],
 +
* [[#Occurrence Compilation: OBIS | Occurrence Compilation: OBIS]],
 +
* [[#Occurrence Compilation: speciesLink | Occurrence Compilation: speciesLink]].
  
−
| brazilian-flora-spd-plugin: status
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
catalogue-of-life-spd-plugin: name_status
+
! Occurrence Field
 +
! GBIF
 +
! OBIS
 +
! speciesLink
 +
|-
  
−
irmng-spd-plugin: taxonomicstatus
+
<!-- BASISOFRECORD -->
 +
|'''[[#o.basisOfRecord | basisOfRecord]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
itis-spd-plugin: table taxonomic_units → name_usage
+
<!-- CATALOGNUMBER -->
 +
|'''[[#o.catalogNumber | catalogNumber]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
obis-spd-plugin: constant ACCEPTED
+
<!-- CITATION -->
 +
|'''[[#o.citation | citation]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center|  <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
ncbi-spd-plugin: Table names → name_class
+
<!-- COUNTRY -->
 +
|'''[[#o.country | country]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getStatus()
+
<!-- COLLECTIONCODE -->
 +
|'''[[#o.collectionCode | collectionCode]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
 +
<!-- CREDITS -->
 +
|'''[[#o.credits | credits]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center|  <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 
|-
 
|-
−
| '''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''
+
<!-- DATELASTMODIFIED -->
 +
|'''[[#o.dateLastModified | dateLastModified]]'''
 +
| align=center| <!-- GBIF -->
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
''Required: false''
+
<!-- DECIMALLATITUDE -->
 +
|'''[[#o.decimalLatitude | decimalLatitude]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/acceptedNameUsageID''
+
<!-- DECIMALLONGITUDE -->
 +
|'''[[#o.decimalLongitude | decimalLongitude]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
| brazilian-flora-spd-plugin:
+
<!-- EVENTDATE -->
 +
|'''[[#o.eventDate | eventDate]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
catalogue-of-life-spd-plugin:  
+
<!-- KINGDOM -->
 +
|'''[[#o.kingdom | kingdom]]'''
 +
| align=center| <!-- GBIF -->
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
gbif-spd-plugin:  
+
<!-- FAMILY -->
 +
|'''[[#o.family | family]]'''
 +
| align=center| <!-- GBIF -->
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
irmng-spd-plugin: acceptednameusageid
+
<!-- ID -->
 +
|'''[[#o.id | id]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
itis-spd-plugin:
+
<!-- IDENTIFIEDBY -->
 +
|'''[[#o.identifiedBy | identifiedBy]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | ]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled ]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
obis-spd-plugin:
+
<!-- INSTITUTIONCODE -->
 +
|'''[[#o.institutionCode | institutionCode]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- MAXIMUMDEPTHINMETERS -->
 +
|'''[[#o.maximumDepthInMeters | maximumDepthInMeters]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
species-link-spd-plugin:
+
<!-- MINIMUMDEPTHINMETERS -->
 +
|'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getValid_AphiaID()
+
<!-- RECORDEDBY -->
 +
|'''[[#o.recordedBy | recordedBy]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|-
  
 +
<!-- SCIENTIFICNAME -->
 +
|'''[[#o.scientificName | scientificName]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 
|-
 
|-
−
| '''statusAsString'''
 
−
| Comments or notes about the taxon or name.
 
  
−
Example: “Type consists of a skull and skeletal fragments”.
+
<!-- SCIENTIFICNAMEAUTHORSHIP -->
 +
|'''[[#o.scientificNameAuthorship | scientificNameAuthorship]]'''
 +
| align=center| <!-- GBIF --> [[#Occurrence_Compilation:_GBIF | Compiled]]
 +
| align=center| <!-- OBIS --> [[#Occurrence_Compilation:_OBIS | Compiled]]
 +
| align=center| <!-- speciesLink --> [[#Occurrence_Compilation:_speciesLink | Compiled]]
 +
|}
  
−
''Data Type: string''
+
==== Occurrence Compilation: GBIF ====
  
−
''Required: false''
+
In the case of [http://www.gbif.org/ GBIF], Occurrence objects are compiled by relying on ...
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/taxonRemarks''
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
| brazilian-flora-spd-plugin: qualifier
+
! Occurrence Field
 +
! Source
 +
! Note
 +
|-
  
−
catalogue-of-life-spd-plugin:
+
<!-- BASISOFRECORD -->
 +
|'''[[#o.basisOfRecord | basisOfRecord]]'''
 +
|| basisOfRecordString
 +
||
 +
|-
  
−
irmng-spd-plugin: taxonremarks
+
<!-- CATALOGNUMBER -->
 +
|'''[[#o.catalogNumber | catalogNumber]]'''
 +
|| catalogNumber
 +
||
 +
|-
  
−
itis-spd-plugin: table taxonomic_units → unaccept_reason
+
<!-- CITATION -->
 +
|'''[[#o.citation | citation]]'''
 +
|| citation
 +
||
 +
|-
  
−
obis-spd-plugin:
+
<!-- COUNTRY -->
 +
|'''[[#o.country | country]]'''
 +
|| country
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- COLLECTIONCODE -->
 +
|'''[[#o.collectionCode | collectionCode]]'''
 +
|| collectionCode
 +
||
 +
|-
  
−
worms-spd-plugin: AphiaRecord record - record.getStatus()
+
<!-- CREDITS -->
 +
|'''[[#o.credits | credits]]'''
 +
|| Biodiversity occurrence data published by: DATA PROVIDER (Accessed through GBIF Data Portal, data.gbif.org, DATE)
 +
||
 +
|-
  
 +
<!-- DATELASTMODIFIED -->
 +
|'''[[#o.dateLastModified | dateLastModified]]'''
 +
|| '''n/a'''
 +
||
 
|-
 
|-
−
|}
 
  
−
==='''CommonName'''===
+
<!-- DECIMALLATITUDE -->
 +
|'''[[#o.decimalLatitude | decimalLatitude]]'''
 +
|| decimalLatitude
 +
||
 +
|-
  
 +
<!-- DECIMALLONGITUDE -->
 +
|'''[[#o.decimalLongitude | decimalLongitude]]'''
 +
|| decimalLongitude
 +
||
 +
|-
  
−
{|border="1" cellpadding="5" cellspacing="0" width="100%"
+
<!-- EVENTDATE -->
 +
|'''[[#o.eventDate | eventDate]]'''
 +
|| earliestDateCollected
 +
||
 
|-
 
|-
−
! scope="col" width="10%" style="background:#efefef;" | Field
+
 
−
! scope="col" style="background:#efefef;" | Description
+
<!-- KINGDOM -->
−
! scope="col" style="background:#efefef;" | Mapping
+
|'''[[#o.kingdom | kingdom]]'''
 +
|| '''n/a'''
 +
||
 
|-
 
|-
  
−
| '''language'''
+
<!-- FAMILY -->
−
| The language of the resource.
+
|'''[[#o.family | family]]'''
 +
|| '''n/a'''
 +
||
 +
|-
  
−
''Data Type: string''
+
<!-- ID -->
 +
|'''[[#o.id | id]]'''
 +
|| gbifKey (attribute of TaxonOccurrence)
 +
||
 +
|-
  
−
''Required: true''
+
<!-- IDENTIFIEDBY -->
 +
|'''[[#o.identifiedBy | identifiedBy]]'''
 +
|| citation
 +
||
 +
|-
  
−
''DwC term: http://purl.org/dc/terms/language''
+
<!-- INSTITUTIONCODE -->
 +
|'''[[#o.institutionCode | institutionCode]]'''
 +
|| institutionCode
 +
||
 +
|-
  
 +
<!-- MAXIMUMDEPTHINMETERS -->
 +
|'''[[#o.maximumDepthInMeters | maximumDepthInMeters]]'''
 +
|| maximumDepthInMeters
 +
||
 +
|-
  
−
| brazilian-flora-spd-plugin: status
+
<!-- MINIMUMDEPTHINMETERS -->
 +
|'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]'''
 +
|| minimumDepthInMeters
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin: name_status
+
<!-- RECORDEDBY -->
 +
|'''[[#o.recordedBy | recordedBy]]'''
 +
|| ??
 +
||
 +
|-
  
−
irmng-spd-plugin: taxonomicstatus
+
<!-- SCIENTIFICNAME -->
 +
|'''[[#o.scientificName | scientificName]]'''
 +
|| nameComplete
 +
||
 +
|-
  
−
itis-spd-plugin:
+
<!-- SCIENTIFICNAMEAUTHORSHIP -->
 +
|'''[[#o.scientificNameAuthorship | scientificNameAuthorship]]'''
 +
|| ??
 +
||
 +
|}
  
−
obis-spd-plugin: table obis.cnames -> lanname
+
==== Occurrence Compilation: OBIS ====
  
−
ncbi-spd-plugin:
+
In the case of [http://www.iobis.org/ OBIS], Occurrence objects are compiled by relying on ...
  
−
worms-spd-plugin: Vernacular vernacular - vernacular.getLanguage()
+
{|border="1" cellpadding="5" cellspacing="0"
  
 +
! Occurrence Field
 +
! Source
 +
! Note
 
|-
 
|-
−
| '''name'''
 
−
| A common or vernacular name.
 
  
−
''Data Type: string''
+
<!-- BASISOFRECORD -->
 +
|'''[[#o.basisOfRecord | basisOfRecord]]'''
 +
|| table obis.drs -> basisofrecord
 +
||
 +
|-
  
−
''Required: false''
+
<!-- CATALOGNUMBER -->
 +
|'''[[#o.catalogNumber | catalogNumber]]'''
 +
|| table obis.dxs -> catalognumber
 +
||
 +
|-
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/vernacularName''
+
<!-- CITATION -->
 +
|'''[[#o.citation | citation]]'''
 +
|| table obis.dxs -> citation
 +
||
 +
|-
  
−
| brazilian-flora-spd-plugin:
+
<!-- COUNTRY -->
 +
|'''[[#o.country | country]]'''
 +
|| table obis.dxs -> country
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin:
+
<!-- COLLECTIONCODE -->
 +
|'''[[#o.collectionCode | collectionCode]]'''
 +
|| table obis.dxs -> collectioncode
 +
||
 +
|-
  
−
irmng-spd-plugin: acceptednameusageid
 
  
−
itis-spd-plugin:
+
<!-- CREDITS -->
 +
|'''[[#o.credits | credits]]'''
 +
|| Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.cnames -> cname
+
<!-- DATELASTMODIFIED -->
 +
|'''[[#o.dateLastModified | dateLastModified]]'''
 +
|| table obis.dxs -> datelastmodified
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- DECIMALLATITUDE -->
 +
|'''[[#o.decimalLatitude | decimalLatitude]]'''
 +
|| table obis.drs -> latitude
 +
||
 +
|-
  
−
worms-spd-plugin: Vernacular vernacular - vernacular.getVernacular()
+
<!-- DECIMALLONGITUDE -->
 +
|'''[[#o.decimalLongitude | decimalLongitude]]'''
 +
|| table obis.drs -> longitude
 +
||
 +
|-
  
−
|}
+
<!-- EVENTDATE -->
 +
|'''[[#o.eventDate | eventDate]]'''
 +
|| table obis.drs -> datecollected <br/> alternatively dxs.yearcollected, dxs.monthcollected, dxs.daycollected
 +
||
 +
|-
  
−
==='''ElementProperty'''===
+
<!-- KINGDOM -->
 +
|'''[[#o.kingdom | kingdom]]'''
 +
|| table obis.dxs -> concatenated
 +
||
 +
|-
  
 +
<!-- FAMILY -->
 +
|'''[[#o.family | family]]'''
 +
|| table obis.dxs -> concatenated
 +
||
 +
|-
  
−
{|border="1" cellpadding="5" cellspacing="0" width="100%"
+
<!-- ID -->
 +
|'''[[#o.id | id]]'''
 +
|| table obis.drs -> id
 +
||
 
|-
 
|-
−
! scope="col" width="10%" style="background:#efefef;" | Field
+
 
−
! scope="col" style="background:#efefef;" | Description
+
<!-- IDENTIFIEDBY -->
−
! scope="col" style="background:#efefef;" | Mapping
+
|'''[[#o.identifiedBy | identifiedBy]]'''
 +
|| table obis.dxs -> identifiedBy
 +
||
 
|-
 
|-
  
−
|'''name'''
+
<!-- INSTITUTIONCODE -->
−
| Key used to identify comments or notes.
+
|'''[[#o.institutionCode | institutionCode]]'''
 +
|| institutioncode
 +
||
 +
|-
  
−
Example: “Reference”, “Source”
+
<!-- MAXIMUMDEPTHINMETERS -->
 +
|'''[[#o.maximumDepthInMeters | maximumDepthInMeters]]'''
 +
|| table obis.dxs -> maximumdepth
 +
||
 +
|-
  
 +
<!-- MINIMUMDEPTHINMETERS -->
 +
|'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]'''
 +
|| table obis.dxs -> minimumdepth
 +
||
 +
|-
  
−
''Data Type: string''
+
<!-- RECORDEDBY -->
 +
|'''[[#o.recordedBy | recordedBy]]'''
 +
|| table obis.dxs -> ???
 +
||
 +
|-
  
−
''Required: false''
+
<!-- SCIENTIFICNAME -->
 +
|'''[[#o.scientificName | scientificName]]'''
 +
|| table obis.dxs -> concatenated
 +
||
 +
|-
  
−
''DwC term: none''
+
<!-- SCIENTIFICNAMEAUTHORSCIP -->
 +
|'''[[#o.scientificNameAuthorship | scientificNameAuthorship]]'''
 +
|| table obis.tnames -> tauthor
 +
||
 +
|}
  
 +
==== Occurrence Compilation: speciesLink ====
  
−
| brazilian-flora-spd-plugin:
+
In the case of [http://splink.cria.org.br/ speciesLink], Occurrence objects are compiled by relying on the [http://tapir.cria.org.br/tapirlink/tapir.php/specieslink Web Service] based on the TAPIR protocol and on the DarwinCore data standard.
  
−
catalogue-of-life-spd-plugin: Source Database, Reference
+
{|border="1" cellpadding="5" cellspacing="0"
  
−
irmng-spd-plugin:
+
! Occurrence Field
 +
! Source
 +
! Note
 +
|-
  
−
itis-spd-plugin: Source
+
<!-- BASISOFRECORD -->
 +
|'''[[#o.basisOfRecord | basisOfRecord]]'''
 +
|| <dwcore:BasisOfRecord>
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id
+
<!-- CATALOGNUMBER -->
 +
|'''[[#o.catalogNumber | catalogNumber]]'''
 +
|| <dwcore:CatalogNumber>
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- CITATION -->
 +
|'''[[#o.citation | citation]]'''
 +
|| Accessed through: speciesLink at http://splink.cria.org.br on DATE
 +
||
 +
|-
  
−
worms-spd-plugin: additional source, basis of record, context source (Deepsea)
+
<!-- CoordinateUncertaintyInMeters -->
 +
|'''[[#o.coordinateUncertaintyInMeters | coordinateUncertaintyInMeters]]'''
 +
|| <dwcore:CoordinateUncertaintyInMeters>
 +
||
 +
|-
  
 +
<!-- COUNTRY -->
 +
|'''[[#o.country | country]]'''
 +
|| <dwcore:Country>
 +
||
 
|-
 
|-
−
| '''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''
+
<!-- COLLECTIONCODE -->
 +
|'''[[#o.collectionCode | collectionCode]]'''
 +
|| <dwcore:CollectionCode>
 +
||
 +
|-
  
−
''Required: false''
+
<!-- CREDITS -->
 +
|'''[[#o.credits | 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/)
 +
||
 +
|-
  
−
''DwC term: none''
+
<!-- DATELASTMODIFIED -->
 +
|'''[[#o.dateLastModified | dateLastModified]]'''
 +
|| <dwcore:DateLastModified>
 +
||
 +
|-
  
−
| brazilian-flora-spd-plugin:
+
<!-- DECIMALLATITUDE -->
 +
|'''[[#o.decimalLatitude | decimalLatitude]]'''
 +
|| <dwgeo:DecimalLatitude>
 +
||
 +
|-
  
−
catalogue-of-life-spd-plugin:  
+
<!-- DECIMALLONGITUDE -->
 +
|'''[[#o.decimalLongitude | decimalLongitude]]'''
 +
|| <dwgeo:DecimalLongitude>
 +
||
 +
|-
  
−
irmng-spd-plugin:
+
<!-- KINGDOM -->
 +
|'''[[#o.kingdom | kingdom]]'''
 +
|| <dwcore:Kingdom>
 +
||
 +
|-
  
−
itis-spd-plugin:
+
<!-- FAMILY -->
 +
|'''[[#o.family | family]]'''
 +
|| <dwcore:Family>
 +
||
 +
|-
  
−
obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id
+
<!-- ID -->
 +
|'''[[#o.id | id]]'''
 +
|| <dwcore:GlobalUniqueIdentifier>
 +
||
 +
|-
  
−
ncbi-spd-plugin:
+
<!-- IDENTIFIEDBY -->
 +
|'''[[#o.identifiedBy | identifiedBy]]'''
 +
|| <dwcore:identifiedBy>
 +
||
 +
|-
  
−
worms-spd-plugin: Source source – source.getReference(), source.getLink(), source.getUrl()
+
<!-- INSTITUTIONCODE -->
 +
|'''[[#o.institutionCode | institutionCode]]'''
 +
|| <dwcore:InstitutionCode>
 +
||
 +
|-
  
 +
<!-- MAXIMUMDEPTHINMETERS -->
 +
|'''[[#o.maximumDepthInMeters | maximumDepthInMeters]]'''
 +
|| <dwcore:MaximumDepthInMeters>
 +
||
 +
|-
  
−
|}
+
<!-- MINIMUMDEPTHINMETERS -->
 +
|'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]'''
 +
|| <dwcore:MinimumDepthInMeters>
 +
||
 +
|-
  
−
=='''Occurrence'''==
+
<!-- MINIMUMDEPTHINMETERS -->
 +
|'''[[#o.minimumDepthInMeters | minimumDepthInMeters]]'''
 +
|| <dwcore:MinimumDepthInMeters>
 +
||
 +
|-
  
 +
<!-- scientificName -->
 +
|'''[[#o.scientificName | scientificName]]'''
 +
|| <dwcore:scientificName>
 +
||
 +
|-
 +
 +
<!-- scientificNameAuthorship -->
 +
|'''[[#o.scientificNameAuthorship | scientificNameAuthorship]]'''
 +
|| <dwcore:AuthorYearOfScientificName>
 +
||
 +
 +
 +
|}
  
−
The following schema describes the fields in an occurrence object.
+
<!-- THE FOLLOWING TEXT SHOULD BE REMOVED -->
  
  
 +
<!-- OLD VERSION
 
{|border="1" cellpadding="5" cellspacing="0" width="100%"
 
{|border="1" cellpadding="5" cellspacing="0" width="100%"
 
|-
 
|-
Line 545: Line 2,280:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/basisOfRecord''
 
''DwC term: http://rs.tdwg.org/dwc/terms/basisOfRecord''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: basisOfRecordString
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.drs -> basisofrecord
  
 
species-link-spd-plugin: <dwcore:BasisOfRecord>
 
species-link-spd-plugin: <dwcore:BasisOfRecord>
Line 561: Line 2,296:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/catalogNumber''
 
''DwC term: http://rs.tdwg.org/dwc/terms/catalogNumber''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: catalogNumber
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> catalognumber
  
 
species-link-spd-plugin: <dwcore:CatalogNumber>
 
species-link-spd-plugin: <dwcore:CatalogNumber>
Line 579: Line 2,314:
  
 
''DwC term: ?''
 
''DwC term: ?''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: citation
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> citation
  
 
species-link-spd-plugin:
 
species-link-spd-plugin:
Line 595: Line 2,330:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/country''
 
''DwC term: http://rs.tdwg.org/dwc/terms/country''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: country
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> country
  
 
species-link-spd-plugin: <dwcore:Country>
 
species-link-spd-plugin: <dwcore:Country>
Line 611: Line 2,346:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/collectionCode''
 
''DwC term: http://rs.tdwg.org/dwc/terms/collectionCode''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: collectionCode
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> collectioncode
  
 
species-link-spd-plugin: <dwcore: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>
  
 
|-
 
|-
Line 627: Line 2,380:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/decimalLatitude''
 
''DwC term: http://rs.tdwg.org/dwc/terms/decimalLatitude''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: decimalLatitude
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.drs -> latitude
  
 
species-link-spd-plugin: <dwgeo:DecimalLatitude>
 
species-link-spd-plugin: <dwgeo:DecimalLatitude>
Line 643: Line 2,396:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/decimalLongitude''
 
''DwC term: http://rs.tdwg.org/dwc/terms/decimalLongitude''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: decimalLongitude
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.drs -> longitude
  
 
species-link-spd-plugin: <dwgeo:DecimalLongitude>
 
species-link-spd-plugin: <dwgeo:DecimalLongitude>
  
 
|-
 
|-
 +
 
| '''eventDate'''
 
| '''eventDate'''
 
| The date-time when the event was recorded.  
 
| The date-time when the event was recorded.  
Line 661: Line 2,415:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/eventDate''
 
''DwC term: http://rs.tdwg.org/dwc/terms/eventDate''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: earliestDateCollected
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.drs -> datecollected
  
 
species-link-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>
 
  
 
|-
 
|-
Line 696: Line 2,433:
 
| gbif-spd-plugin:  
 
| gbif-spd-plugin:  
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> concatenated
  
 
species-link-spd-plugin: <dwcore:Kingdom>
 
species-link-spd-plugin: <dwcore:Kingdom>
Line 712: Line 2,449:
 
| gbif-spd-plugin:  
 
| gbif-spd-plugin:  
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> concatenated
  
 
species-link-spd-plugin: <dwcore:Family>
 
species-link-spd-plugin: <dwcore:Family>
  
 
|-
 
|-
−
| '''institutionCode'''
+
| '''id'''
−
| The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
+
| 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"
  
  
Line 725: Line 2,482:
 
''Required: false''
 
''Required: false''
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/institutionCode''
+
''DwC term: http://rs.tdwg.org/dwc/terms/identifiedBy''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: citation
  
 
obis-spd-plugin:
 
obis-spd-plugin:
  
−
species-link-spd-plugin: <dwcore:InstitutionCode>
+
species-link-spd-plugin: <dwcur:IdentifiedBy xsi:nil="true"/>
  
 
|-
 
|-
−
| '''country'''
+
| '''institutionCode'''
−
| The name of the country or major administrative unit in which the Location occurs.
+
| The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
  
  
Line 741: Line 2,498:
 
''Required: false''
 
''Required: false''
  
−
''DwC term: http://rs.tdwg.org/dwc/terms/country''
+
''DwC term: http://rs.tdwg.org/dwc/terms/institutionCode''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: institutionCode
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> institutioncode
  
−
species-link-spd-plugin: <dwcore:Country>
+
species-link-spd-plugin: <dwcore:InstitutionCode>
  
 
|-
 
|-
 +
 
| '''maximumDepthInMeters'''
 
| '''maximumDepthInMeters'''
 
| The greater depth of a range of depth below the local surface, in meters.
 
| The greater depth of a range of depth below the local surface, in meters.
Line 758: Line 2,516:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/maximumDepthInMeters''
 
''DwC term: http://rs.tdwg.org/dwc/terms/maximumDepthInMeters''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: maximumDepthInMeters
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> maximumdepth
  
 
species-link-spd-plugin: <dwcore:MaximumDepthInMeters xsi:nil="true"/>
 
species-link-spd-plugin: <dwcore:MaximumDepthInMeters xsi:nil="true"/>
Line 774: Line 2,532:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/minimumDepthInMeters''
 
''DwC term: http://rs.tdwg.org/dwc/terms/minimumDepthInMeters''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: maximumDepthInMeters
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> minimumdepth
  
 
species-link-spd-plugin: <dwcore:MinimumDepthInMeters xsi:nil="true"/>
 
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"/>
 
  
 
|-
 
|-
Line 826: Line 2,548:
  
 
''DwC term: http://rs.tdwg.org/dwc/terms/scientificName''
 
''DwC term: http://rs.tdwg.org/dwc/terms/scientificName''
−
| gbif-spd-plugin:  
+
| gbif-spd-plugin: nameComplete
  
−
obis-spd-plugin:
+
obis-spd-plugin: table obis.dxs -> concatenated
  
 
species-link-spd-plugin: <dwcore:ScientificName>
 
species-link-spd-plugin: <dwcore:ScientificName>
  
 
|}
 
|}
 +
-->

Latest revision as of 12:18, 28 November 2014

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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