Species Products Discovery Objects
From Gcube Wiki
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 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 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 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> |
|
