Difference between revisions of "Species Products Discovery Objects"

Revision as of 15:15, 6 May 2013 (view source) Valentina.marioli (Talk | contribs) (→‎Occurrence Compilation: speciesLink) ← Older edit		Revision as of 15:27, 6 May 2013 (view source) Valentina.marioli (Talk | contribs) (→‎The Fields) Newer edit →
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	'''[[#o.country | country]]''',		'''[[#o.country | country]]''',
	'''[[#o.collectionCode | collectionCode]]''',		'''[[#o.collectionCode | collectionCode]]''',
		+	'''[[#o.credits | credits]]''',
	'''[[#o.dateLastModified | dateLastModified]]''',		'''[[#o.dateLastModified | dateLastModified]]''',
	'''[[#o.decimalLatitude | decimalLatitude]]''',		'''[[#o.decimalLatitude | decimalLatitude]]''',
Line 1,404:		Line 1,405:
	|-		|-
	|| Darwin Core Term		|| Darwin Core Term
−	|| <font color=red>'''???'''</font>	+	|| [http://rs.tdwg.org/dwc/terms/nameAccordingTo nameAccordingTo]
	|-		|-
	|| Data Type		|| Data Type
Line 1,450:		Line 1,451:
	|| false		|| false
	|-		|-
		+
		+
		+	<!-- %%% CREDITS %%% -->
		+	! 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
		+	|| false
		+	|-
		+
	<!-- %%% DATELASTMODIFIED %%% -->		<!-- %%% DATELASTMODIFIED %%% -->

---

Revision as of 15:27, 6 May 2013

Contents 1 TaxonomyItem 1.1 The Fields 1.1.1 CommonName Fields 1.1.2 ElementProperty Fields 1.1.3 TaxonomyStatus Fields 1.2 TaxonomyItem Compilation 1.2.1 TaxonomyItem Compilation: List of Species of the Brazilian Flora 1.2.2 TaxonomyItem Compilation: Catalogue of Life 1.2.3 TaxonomyItem Compilation: IRMNG 1.2.4 TaxonomyItem Compilation: ITIS 1.2.5 TaxonomyItem Compilation: OBIS 1.2.6 TaxonomyItem Compilation: NCBI 1.2.7 TaxonomyItem Compilation: WoRMS 2 Occurrence 2.1 The Fields 2.2 Occurrence Compilation 2.2.1 Occurrence Compilation: GBIF 2.2.2 Occurrence Compilation: OBIS 2.2.3 Occurrence Compilation: speciesLink

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

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

by interacting with the diverse data sources.

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

TaxonomyItem

The Fields

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

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

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

author
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	false
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 Compilation: List of Species of the Brazilian Flora,
• TaxonomyItem Compilation: Catalogue of Life,
• TaxonomyItem Compilation: IRMNG,
• TaxonomyItem Compilation: ITIS,
• TaxonomyItem Compilation: NCBI,
• TaxonomyItem Compilation: WoRMS.

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: id, author, basisOfRecord, catalogNumber, citation, country, collectionCode, credits, dateLastModified, decimalLatitude, decimalLongitude, eventDate, kingdom, family, id, identifiedBy, institutionCode, maximumDepthInMeters, minimumDepthInMeters, and scientificName.

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

id
Description	The ID is supposed to (globally) uniquely identify an occurrence record, whether it is a specimen-based occurrence, a one-time observation of a species at a location, or one of many occurrences of an individual who is being tracked, monitored, or recaptured. Making it globally unique is quite a trick, one for which we don't really have good solutions in place yet, but one which ontologists insist is essential.
Example
Darwin Core Term	occurrenceID
Data Type	string
Mandatory	true
author
Description	The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
Example	Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)".
Darwin Core Term	scientificNameAuthorship
Data Type	string
Mandatory	false
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
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
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
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	false
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
Darwin Core Term	decimalLatitude
Data Type	float
Mandatory	false
decimalLongitude
Description	The geographic longitude.
Example
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
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
Darwin Core Term	family
Data Type	string
Mandatory	false
id
Description	The unique identifier used for a name or taxon reference in the core data file.
Example
Darwin Core Term	taxonID
Data Type	string
Mandatory	true
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
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
scientificName
Description	The scientific name of taxon with or without authorship information depending on the format of the source database.
Example
Darwin Core Term	scientificName
Data Type	string
Mandatory	true

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 Compilation: GBIF,
• Occurrence Compilation: OBIS,
• Occurrence Compilation: speciesLink.

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
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	Compiled
institutionCode	Compiled	Compiled	Compiled
maximumDepthInMeters	Compiled	Compiled	Compiled
minimumDepthInMeters	Compiled	Compiled	Compiled
scientificName	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
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
scientificName	nameComplete

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
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
scientificName	table obis.dxs -> concatenated

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	<dwc:BasisOfRecord>
catalogNumber	<dwc:CatalogNumber>
citation	Accessed through: speciesLink at http://splink.cria.org.br on DATE
country	<dwc:Country>
collectionCode	<dwc:CollectionCode>
dateLastModified	<dc:modified>
decimalLatitude	<dwc:decimalLatitude>
decimalLongitude	<dwc:decimalLongitude>
eventDate	<dwc:eventTime>
kingdom	<dwc:Kingdom>
family	<dwc:Family>
id	<dwc:occurrenceID>
identifiedBy	<dwc:identifiedBy>
institutionCode	<dwc:InstitutionCode>
maximumDepthInMeters	<dwc:MaximumDepthInMeters>
minimumDepthInMeters	<dwc:MinimumDepthInMeters>
scientificName	<dwc:ScientificName>