Difference between revisions of "Species Products Discovery Objects"
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{|border="1" cellpadding="5" cellspacing="0" | {|border="1" cellpadding="5" cellspacing="0" | ||
| − | ! TaxonomyItem Field | + | !colspan=2| TaxonomyItem Field |
! Source | ! Source | ||
! Note | ! Note | ||
|- | |- | ||
| − | | '''[[#author | author]]''' | + | |
| − | || <font color=red>'''n/a'''</font> | + | <!-- AUTHOR --> |
| + | |colspan=2| '''[[#author | author]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[#citation | citation]]''' | + | |
| − | || <font color=red>'''n/a'''</font> | + | <!-- CITATION --> |
| + | |colspan=2| '''[[#citation | citation]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[#commonNames | commonNames]]''' | + | |
| − | || <font color=red>'''n/a'''</font> | + | <!-- COMMONNAMES --> |
| + | |rowspan=2| '''[[#commonNames | commonNames]]''' | ||
| + | || '''[[#cn.language | language]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | || '''[[#cn.name | name]]''' |
| − | || <font color=red>'''n/a'''</font> | + | || <font color=red>'''n/a'''</font> |
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || | + | <!-- CREDITS --> |
| + | |colspan=2| '''[[#credits | credits]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || | + | <!-- ID --> |
| + | |colspan=2| '''[[#id | id]]''' | ||
| + | || Table nodes → tax_id | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || <font color=red>'''n/a'''</font> | + | <!-- LSID --> |
| + | |colspan=2| '''[[#lsid | lsid]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || | + | <!-- MODIFIED --> |
| + | |colspan=2| '''[[#modified | modified]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || | + | <!-- PARENT --> |
| + | |colspan=2| '''[[#parent | parent]]''' | ||
| + | || table nodes → parent_tax_id | ||
|| | || | ||
|- | |- | ||
| − | | '''[[# | + | |
| − | || | + | <!-- PROPERTIES --> |
| + | |rowspan=2| '''[[#properties | properties]]''' | ||
| + | || '''[[#ep.name | name]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | '''[[#scientificName | scientificName]]''' | + | || '''[[#ep.value | value]]''' |
| − | || Table names → name_txt | + | || <font color=red>'''n/a'''</font> |
| + | || | ||
| + | |- | ||
| + | |||
| + | <!-- RANK --> | ||
| + | |colspan=2| '''[[#rank | rank]]''' | ||
| + | || Table nodes → rank | ||
| + | || | ||
| + | |- | ||
| + | |||
| + | <!-- SCIENTIFICNAME --> | ||
| + | |colspan=2| '''[[#scientificName | scientificName]]''' | ||
| + | || Table names → name_txt | ||
| + | || | ||
| + | |- | ||
| + | |||
| + | <!-- STATUS --> | ||
| + | |rowspan=3| '''[[#status | status]]''' | ||
| + | || '''[[#ts.status | status]]''' | ||
| + | || Table names → name_class | ||
| + | || | ||
| + | |- | ||
| + | || '''[[#ts.refId | refId]]''' | ||
| + | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
|- | |- | ||
| − | | | + | || [[#ts.statusAsString | statusAsString]] |
|| <font color=red>'''n/a'''</font> | || <font color=red>'''n/a'''</font> | ||
|| | || | ||
Revision as of 18:04, 21 January 2013
The Species Product Discovery Service is the main service realising the Biodiversity Access facilities in gCube. This service aims at offering an unifying view over the data offered by diverse data sources. In order to do that, the service makes available two typologies of objects:
- TaxonomyItem, i.e. a characterisation of species taxa;
- Occurrence, i.e. a characterisation of a dataset of species occurrence records;
by interacting with the diverse data sources.
This page describes the fields characterising every typology of object produced by the Species Product Discovery Service and how these fields are populated by using the information produced by every data source.
TaxonomyItem
The Fields
A TaxonomyItem object is characterised by the following fields: author, citation, commonNames, credits, id, lsid, modified, parent, properties, rank, scientificName, and status.
commonNames, properties and status are compound objects and the fields characterising them are described in dedicated sections respectively, i.e. commonNames Fields, ElementProperty Fields, and TaxonomyStatus Fields.
The semantic of these fields is inherited by Darwin Core Terms.
| 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 THIS IS NOT OK: we have a compound object |
| Data Type | List <CommonName> |
| Mandatory | false |
| credits
| |
| Description | Citation information specified by the data publisher. |
| Example | This information object has been generated via the Species Product Discovery service on 2012-11-26 by interfacing with speciesLink (http://splink.cria.org.br/) |
| Darwin Core Term | bibliographicCitation |
| Data Type | string |
| Mandatory | false |
| id
| |
| Description | The unique identifier used for a name or taxon reference in the core data file. |
| Example | |
| Darwin Core Term | taxonID |
| Data Type | string |
| Mandatory | true |
| lsid
| |
| Description | An identifier for the nomenclatural (not taxonomic) details of a TaxonomyItem. It is exclusively used to reference an external and resolvable identifier that returns nomenclatural (not taxonomic) details of a name. Use taxonID to refer to taxa. Use to explicitly refer to an external nomenclatural record. |
| Example | “urn:lsid:ipni.org:names:37829-1:1.3” |
| Darwin Core Term | scientificNameID |
| Data Type | string |
| Mandatory | false |
| modified
| |
| Description | Date when the record the TaxonomyItem is representing was last updated. |
| Example | “2009-08-21” |
| Darwin Core Term | modified |
| Data Type | calendar |
| Mandatory | false |
| parent
| |
| Description | The TaxonomyItem of the immediate higher-rank parent taxon (in a classification). |
| Example | |
| Darwin Core Term | n/a |
| Data Type | TaxonomyItem |
| Mandatory | false |
| properties
| |
| Description | Any property besides the others that is worth to associate with the TaxonomyItem. These properties might include comments or notes about the taxon or name or data sources. |
| Example | n/a |
| Darwin Core Term | n/a |
| Data Type | List <ElementProperty> |
| Mandatory | false |
| rank
| |
| Description | The taxonomic rank of the most specific name in the scientificName. Recommended vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml |
| Example | "subspecies", "varietas", "forma", "species", "genus" |
| Darwin Core Term | taxonRank |
| Data Type | string |
| Mandatory | true |
| scientificName
| |
| Description | The scientific name of taxon with or without authorship information depending on the format of the source database. |
| Example | "Coleoptera" , "Vespertilionidae”, "Manis" , "Ctenomys sociabilis", "Ambystoma tigrinum diaboli", "Quercus agrifolia var. oxyadenia (Torr.)" |
| Darwin Core Term | scientificName |
| Data Type | string |
| Mandatory | true |
| status
| |
| Description | The status of the taxon represented by the TaxonomiItem. |
| Example | |
| Darwin Core Term | taxonomicStatus THIS IS NOT OK: we have a compound object |
| 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 THIS IS NOT OK |
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 THIS IS NOT OK |
| 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 THIS IS NOT OK |
TaxonomyStatus Fields
An 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.”. THIS IS NOT CLEAR |
| 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
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 ...
| 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 ...
| 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 ...
| 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 | ||
| value | |||
| 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 ...
| 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 | Generated string | ||
| commonNames | language | lanname | |
| name | table obis.cnames -> cname | ||
| credits | "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)" | ||
| 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 ...
| 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 ...
| TaxonomyItem Field | Source | Note |
|---|---|---|
| author | AphiaRecord record - record.getAuthority() | |
| citation | AphiaRecord record - record.getCitation() | |
| commonNames | WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID()) | |
| credits | n/a | |
| id | AphiaRecord record - record.getAphiaID() | |
| lsid | AphiaRecord record - record.getLsid() | |
| modified | n/a | |
| parent | WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID()) | |
| properties | n/a | |
| rank | AphiaRecord record - record.getRank() | |
| scientificName | AphiaRecord record - record.getScientificname() | |
| status | n/a |
TaxonomyItem Compilation: Summary
| TaxonomyItem Field | FloraDoBrasil | CoL | IRMNG | ITIS | OBIS | NCBI | WoRMS |
|---|---|---|---|---|---|---|---|
| author | au | author | scientificnameauthorship | taxon_authors_lkp.taxon_author | obis.tnames.tauthor | AphiaRecord record - record.getAuthority() | |
| citation | nameaccordingto | generated string | AphiaRecord record - record.getCitation() | ||||
| commonNames | common_names | Table vernaculars | table obis.cnames | WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID()) | |||
| credits | string | ||||||
| id | id | id | taxonid | tsn | id | tax_id | AphiaRecord record - record.getAphiaID() |
| lsid | urn:lsid:itis.gov:itis_tsn:TSN | AphiaRecord record - record.getLsid() | |||||
| modified | record_scrutiny_date | table taxonomic_units → update_date | |||||
| parent | classification | parentnameusageid | table taxonomic_units → parent_tsn | table obis.tnames -> parent_id | table nodes → parent_tax_id | WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID()) | |
| properties | references | table obis.tnames -> worms_id table obis.tnames -> col_id table obis.tnames -> irmng_id table obis.tnames -> itis_id |
|||||
| rank | rank | rank | taxonrank | table taxon_unit_types → rank_name | table obis.ranks -> rank_name | Table nodes → rank | AphiaRecord record - record.getRank() |
| scientificName | html_full_name | name | scientificname | table longnames → completename | table obis.tnames -> tname | Table names → name_txt | AphiaRecord record - record.getScientificname() |
| status |
Occurrence
The following schema describes the fields in an occurrence object.
| Field | Description | Mapping |
|---|---|---|
| basisOfRecord | The specific nature of the data record. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).
Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation".
Required: false |
gbif-spd-plugin: basisOfRecordString
obis-spd-plugin: table obis.drs -> basisofrecord species-link-spd-plugin: <dwcore:BasisOfRecord> |
| catalogNumber | An identifier (preferably unique) for the record within the data set or collection.
Required: false |
gbif-spd-plugin: catalogNumber
obis-spd-plugin: table obis.dxs -> catalognumber species-link-spd-plugin: <dwcore:CatalogNumber> |
| citation | Citation information specified by the data publisher.
Example: Accessed through: speciesLink at http://splink.cria.org.br
Required: false DwC term: ? |
gbif-spd-plugin: citation
obis-spd-plugin: table obis.dxs -> citation species-link-spd-plugin: |
| country | The name of the country or major administrative unit in which the Location occurs.
Required: false DwC term: http://rs.tdwg.org/dwc/terms/country |
gbif-spd-plugin: country
obis-spd-plugin: table obis.dxs -> country species-link-spd-plugin: <dwcore:Country> |
| collectionCode | The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
Required: false |
gbif-spd-plugin: collectionCode
obis-spd-plugin: table obis.dxs -> collectioncode species-link-spd-plugin: <dwcore:CollectionCode> |
| dateLastModified | The most recent date-time on which the resource was changed.
Examples: "1963-03-08T14:07-0600"
Required: false DwC term: http://purl.org/dc/terms/modified |
gbif-spd-plugin:
obis-spd-plugin: table obis.dxs -> datelastmodified species-link-spd-plugin: <dwcore:DateLastModified> |
| decimalLatitude | The geographic latitude.
Required: false |
gbif-spd-plugin: decimalLatitude
obis-spd-plugin: table obis.drs -> latitude species-link-spd-plugin: <dwgeo:DecimalLatitude> |
| decimalLongitude | The geographic longitude.
Required: false |
gbif-spd-plugin: decimalLongitude
obis-spd-plugin: table obis.drs -> longitude species-link-spd-plugin: <dwgeo:DecimalLongitude> |
| eventDate | The date-time when the event was recorded.
Examples: "1963-03-08T14:07-0600"
Required: false DwC term: http://rs.tdwg.org/dwc/terms/eventDate |
gbif-spd-plugin: earliestDateCollected
obis-spd-plugin: table obis.drs -> datecollected species-link-spd-plugin: |
| kingdom | The full scientific name of the kingdom in which the taxon is classified.
Required: false DwC term: http://rs.tdwg.org/dwc/terms/kingdom |
gbif-spd-plugin:
obis-spd-plugin: table obis.dxs -> concatenated species-link-spd-plugin: <dwcore:Kingdom> |
| family | The full scientific name of the family in which the taxon is classified.
Required: false DwC term: http://rs.tdwg.org/dwc/terms/family |
gbif-spd-plugin:
obis-spd-plugin: table obis.dxs -> concatenated species-link-spd-plugin: <dwcore:Family> |
| id | The unique identifier used for a name or taxon reference in the core data file.
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"
Required: false |
gbif-spd-plugin: citation
obis-spd-plugin: species-link-spd-plugin: <dwcur:IdentifiedBy xsi:nil="true"/> |
| institutionCode | The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
Required: false |
gbif-spd-plugin: institutionCode
obis-spd-plugin: table obis.dxs -> institutioncode species-link-spd-plugin: <dwcore:InstitutionCode> |
| maximumDepthInMeters | The greater depth of a range of depth below the local surface, in meters.
Required: false |
gbif-spd-plugin: maximumDepthInMeters
obis-spd-plugin: table obis.dxs -> maximumdepth species-link-spd-plugin: <dwcore:MaximumDepthInMeters xsi:nil="true"/> |
| minimumDepthInMeters | The lesser depth of a range of depth below the local surface, in meters.
Required: false |
gbif-spd-plugin: maximumDepthInMeters
obis-spd-plugin: table obis.dxs -> minimumdepth species-link-spd-plugin: <dwcore:MinimumDepthInMeters xsi:nil="true"/> |
| scientificName | The scientific name of taxon with or without authorship information depending on the format of the source database.
Required: true |
gbif-spd-plugin: nameComplete
obis-spd-plugin: table obis.dxs -> concatenated species-link-spd-plugin: <dwcore:ScientificName> |
