Difference between revisions of "Species Products Discovery Objects"
(→TaxonomyItem) |
(→TaxonomyItem) |
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itis-spd-plugin: | itis-spd-plugin: | ||
| − | obis-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: | ncbi-spd-plugin: | ||
| Line 129: | Line 129: | ||
itis-spd-plugin: Table longnames → tsn | itis-spd-plugin: Table longnames → tsn | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.tnames -> id |
ncbi-spd-plugin: Table nodes → tax_id | ncbi-spd-plugin: Table nodes → tax_id | ||
| Line 205: | Line 205: | ||
itis-spd-plugin: table taxonomic_units → parent_tsn | itis-spd-plugin: table taxonomic_units → parent_tsn | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.tnames -> parent_id |
ncbi-spd-plugin: table nodes → parent_tax_id | ncbi-spd-plugin: table nodes → parent_tax_id | ||
| Line 229: | Line 229: | ||
itis-spd-plugin: | itis-spd-plugin: | ||
| − | obis-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: | ncbi-spd-plugin: | ||
| Line 259: | Line 259: | ||
itis-spd-plugin: table taxon_unit_types → rank_name | itis-spd-plugin: table taxon_unit_types → rank_name | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.ranks -> rank_name |
ncbi-spd-plugin: Table nodes → rank | ncbi-spd-plugin: Table nodes → rank | ||
| Line 286: | Line 286: | ||
itis-spd-plugin: table longnames → completename | itis-spd-plugin: table longnames → completename | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.tnames -> tname |
ncbi-spd-plugin: Table names → name_txt | ncbi-spd-plugin: Table names → name_txt | ||
| Line 334: | Line 334: | ||
itis-spd-plugin: table taxonomic_units → name_usage | itis-spd-plugin: table taxonomic_units → name_usage | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: constant ACCEPTED |
ncbi-spd-plugin: Table names → name_class | ncbi-spd-plugin: Table names → name_class | ||
| Line 425: | Line 425: | ||
itis-spd-plugin: | itis-spd-plugin: | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.cnames -> lanname |
ncbi-spd-plugin: | ncbi-spd-plugin: | ||
| Line 449: | Line 449: | ||
itis-spd-plugin: | itis-spd-plugin: | ||
| − | obis-spd-plugin: | + | obis-spd-plugin: table obis.cnames -> cname |
ncbi-spd-plugin: | ncbi-spd-plugin: | ||
| Line 488: | Line 488: | ||
itis-spd-plugin: Source | itis-spd-plugin: Source | ||
| − | obis-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: | ncbi-spd-plugin: | ||
| Line 512: | Line 512: | ||
itis-spd-plugin: | itis-spd-plugin: | ||
| − | obis-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: | ncbi-spd-plugin: | ||
Revision as of 16:52, 7 January 2013
TaxonomyItem
| 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
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()
|
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:
obis-spd-plugin: 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:
obis-spd-plugin: 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:
obis-spd-plugin: 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:
obis-spd-plugin: 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:
obis-spd-plugin: species-link-spd-plugin: <dwcore:CollectionCode> |
| decimalLatitude | The geographic latitude.
Required: false |
gbif-spd-plugin:
obis-spd-plugin: species-link-spd-plugin: <dwgeo:DecimalLatitude> |
| decimalLongitude | The geographic longitude.
Required: false |
gbif-spd-plugin:
obis-spd-plugin: 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:
obis-spd-plugin: species-link-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 |
gbif-spd-plugin:
obis-spd-plugin: species-link-spd-plugin: <dwcore:GlobalUniqueIdentifier> |
| 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: 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: species-link-spd-plugin: <dwcore:Family> |
| 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:
obis-spd-plugin: species-link-spd-plugin: <dwcore:InstitutionCode> |
| 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:
obis-spd-plugin: species-link-spd-plugin: <dwcore:Country> |
| maximumDepthInMeters | The greater depth of a range of depth below the local surface, in meters.
Required: false |
gbif-spd-plugin:
obis-spd-plugin: 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:
obis-spd-plugin: 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"
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"
Required: false |
gbif-spd-plugin:
obis-spd-plugin: species-link-spd-plugin: <dwcur:IdentifiedBy 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:
obis-spd-plugin: species-link-spd-plugin: <dwcore:ScientificName> |
