Species Products Discovery Objects
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
Fields
| Field | Description | Mapping |
|---|---|---|
| author | If the authority is known and can be separated from the rest of the scientific name, the authority string should also be placed in the ‘author’ field.
Example: (Schltdl.) Crins Data Type: string Required: false DwC term: http://rs.tdwg.org/dwc/terms/scientificNameAuthorship |
brazilian-flora-spd-plugin: au
catalogue-of-life-spd-plugin: author irmng-spd-plugin: scientificnameauthorship itis-spd-plugin: table taxon_authors_lkp → taxon_author obis-spd-plugin: table obis.tnames -> tauthor ncbi-spd-plugin: worms-spd-plugin: AphiaRecord record - record.getAuthority() |
| citation | Citation information specified by the data publisher.
Example: Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=105838 on 2012-11-27
Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: irmng-spd-plugin: nameaccordingto itis-spd-plugin: obis-spd-plugin: generated string ncbi-spd-plugin: worms-spd-plugin: AphiaRecord record - record.getCitation() |
| commonNames | A common or vernacular name.
Example: “Andean Condor", "Condor Andino", "American Eagle", "Gönsegeier"
Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: common_names irmng-spd-plugin: itis-spd-plugin: Table vernaculars → obis-spd-plugin: table obis.cnames ncbi-spd-plugin: worms-spd-plugin: WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID()) |
| credits | Citation information specified by the data publisher.
Example: This information object has been generated via the Species Product Discovery service on 2012-11-26 by interfacing with speciesLink (http://splink.cria.org.br/)
Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: irmng-spd-plugin: itis-spd-plugin: obis-spd-plugin: "Intergovernmental Oceanographic Commission (IOC) of UNESCO. The Ocean Biogeographic Information System. Web. http://www.iobis.org. (Consulted on DATE)" ncbi-spd-plugin: worms-spd-plugin: |
| id | The unique identifier used for a name or taxon reference in the core data file.
Required: true DwC term: http://rs.tdwg.org/dwc/terms/taxonID |
brazilian-flora-spd-plugin: id
catalogue-of-life-spd-plugin: id irmng-spd-plugin: taxonid itis-spd-plugin: Table longnames → tsn obis-spd-plugin: table obis.tnames -> id ncbi-spd-plugin: Table nodes → tax_id worms-spd-plugin: AphiaRecord record - record.getAphiaID() |
| lsid | Exclusively used to reference an external and resolvable identifier that returns nomenclatural (not taxonomic) details of a name. Use taxonID to refer to taxa. Use to explicitly refer to an external nomenclatural record.
Example: “urn:lsid:ipni.org:names:37829-1:1.3”
Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: irmng-spd-plugin: itis-spd-plugin: urn:lsid:itis.gov:itis_tsn:TSN obis-spd-plugin: ncbi-spd-plugin: worms-spd-plugin: AphiaRecord record - record.getLsid() |
| modified | Date when the record was last updated
Example: “2009-08-21”
Required: false DwC term: http://purl.org/dc/terms/modified |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: record_scrutiny_date irmng-spd-plugin: modified itis-spd-plugin: table taxonomic_units → update_date obis-spd-plugin: ncbi-spd-plugin: worms-spd-plugin: |
| parent | The TaxonomyItem of the immediate higher-rank parent taxon (in a classification).
Required: false DwC term: none |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: classification irmng-spd-plugin: parentnameusageid itis-spd-plugin: table taxonomic_units → parent_tsn obis-spd-plugin: table obis.tnames -> parent_id ncbi-spd-plugin: table nodes → parent_tax_id worms-spd-plugin: WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID()) |
| properties | Comments or notes about the taxon or name or data sources.
Required: false DwC term: none |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: references irmng-spd-plugin: itis-spd-plugin: obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id ncbi-spd-plugin: worms-spd-plugin: |
| rank | The taxonomic rank of the most specific name in the scientificName.
Recommended vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml Example: "subspecies", "varietas", "forma", "species", "genus"
Required: true DwC term: http://rs.tdwg.org/dwc/terms/taxonRank |
brazilian-flora-spd-plugin: rank
catalogue-of-life-spd-plugin: rank irmng-spd-plugin: taxonrank itis-spd-plugin: table taxon_unit_types → rank_name obis-spd-plugin: table obis.ranks -> rank_name ncbi-spd-plugin: Table nodes → rank worms-spd-plugin: AphiaRecord record - record.getRank() |
| scientificName | The scientific name of taxon with or without authorship information depending on the format of the source database.
Required: true |
brazilian-flora-spd-plugin: html_full_name
catalogue-of-life-spd-plugin: name irmng-spd-plugin: scientificname itis-spd-plugin: table longnames → completename obis-spd-plugin: table obis.tnames -> tname ncbi-spd-plugin: Table names → name_txt worms-spd-plugin: AphiaRecord record - record.getScientificname() |
| status | The status of a taxon.
Required: true |
TaxonomyStatus
| Field | Description | Mapping |
|---|---|---|
| status | The status of the use of the scientificName as a label for a taxon.
Controlled vocabulary: "accepted", "invalid", "misapplied", "provisional", “synonym”, “unknown”, “valid”. Data Type: string Required: true |
brazilian-flora-spd-plugin: status
catalogue-of-life-spd-plugin: name_status irmng-spd-plugin: taxonomicstatus itis-spd-plugin: table taxonomic_units → name_usage obis-spd-plugin: constant ACCEPTED ncbi-spd-plugin: Table names → name_class worms-spd-plugin: AphiaRecord record - record.getStatus() |
| refId | This value points to the record representing the valid (zoological) or accepted (botanical) name using the taxonID of that record as the “pointer.”
Data Type: string Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: gbif-spd-plugin: irmng-spd-plugin: acceptednameusageid itis-spd-plugin: obis-spd-plugin: ncbi-spd-plugin: species-link-spd-plugin: worms-spd-plugin: AphiaRecord record - record.getValid_AphiaID() |
| statusAsString | Comments or notes about the taxon or name.
Example: “Type consists of a skull and skeletal fragments”. Data Type: string Required: false |
brazilian-flora-spd-plugin: qualifier
catalogue-of-life-spd-plugin: irmng-spd-plugin: taxonremarks itis-spd-plugin: table taxonomic_units → unaccept_reason obis-spd-plugin: ncbi-spd-plugin: worms-spd-plugin: AphiaRecord record - record.getStatus() |
CommonName
| Field | Description | Mapping |
|---|---|---|
| language | The language of the resource.
Data Type: string Required: true DwC term: http://purl.org/dc/terms/language
|
brazilian-flora-spd-plugin: status
catalogue-of-life-spd-plugin: name_status irmng-spd-plugin: taxonomicstatus itis-spd-plugin: obis-spd-plugin: table obis.cnames -> lanname ncbi-spd-plugin: worms-spd-plugin: Vernacular vernacular - vernacular.getLanguage() |
| name | A common or vernacular name.
Data Type: string Required: false |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: irmng-spd-plugin: acceptednameusageid itis-spd-plugin: obis-spd-plugin: table obis.cnames -> cname ncbi-spd-plugin: worms-spd-plugin: Vernacular vernacular - vernacular.getVernacular() |
ElementProperty
| Field | Description | Mapping |
|---|---|---|
| name | Key used to identify comments or notes.
Example: “Reference”, “Source”
Required: false DwC term: none
|
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: Source Database, Reference irmng-spd-plugin: itis-spd-plugin: Source obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id ncbi-spd-plugin: worms-spd-plugin: additional source, basis of record, context source (Deepsea) |
| value | Example: “Compagno, L.J.V.1999Checklist of living elasmobranchs.p. 471-498. In W.C. Hamlett (ed.) Sharks, skates, and rays: the biology of elasmobranch fishes. John Hopkins University Press, Maryland.”, “DatabaseFishBase”
Data Type: string Required: false DwC term: none |
brazilian-flora-spd-plugin:
catalogue-of-life-spd-plugin: irmng-spd-plugin: itis-spd-plugin: obis-spd-plugin: table obis.tnames -> worms_id, table obis.tnames -> col_id, table obis.tnames -> irmng_id, table obis.tnames -> itis_id ncbi-spd-plugin: worms-spd-plugin: Source source – source.getReference(), source.getLink(), source.getUrl() |
Compilation
List of Species of the Brazilian Flora
Occurrence
The following schema describes the fields in an occurrence object.
| Field | Description | Mapping |
|---|---|---|
| basisOfRecord | The specific nature of the data record. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).
Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation".
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> |
