Difference between revisions of "Data Standards"
From mx Help Wiki
(New page: == Overview == This is a summary/reporduction of the db/standards_mapping.yaml file in the mx source. This will be periodically updated from that file. The mapping in the .yaml file take...) |
Revision as of 20:12, 18 July 2008
Overview
This is a summary/reporduction of the db/standards_mapping.yaml file in the mx source. This will be periodically updated from that file. The mapping in the .yaml file take precedence over those here (i.e. may be more recently updated.). Note that many other fields present in mx are not mapped here.
Legend
- single quote -> fixed strings
- ALL_CAPS -> an environment.rb constant
- nil -> not yet mapped
- Note that in most cases a lot object can be swapped for a specimen object
Mapping
(from source 0.2.1591)
Darwin_Core_1.4:
GlobalUniqueIdentifier: [InstitutionCode]:[CollectionCode]:specimen.id # or a URN environment.rb setting for LSIDs DateLastModified: specimens.updated_on # ACTION NEEDED: after update ces, dets, ids to touch specimen(s) BasisOfRecord: 'PreservedSpecimen' # at present this is fixed, easily extendable to variable InstitutionCode: repositories.coden # ACTION NEEDED: update db field name to 'coden' (silly) CollectionCode: COLLECTION_CODE CatalogNumber: specimen.id InformationWithheld: # free text, extend TagEngine with 'dc info witheld' keyword to fill this Remarks: # free text, extend TagEngine with 'dc remarks' keyword to fill this ScientificName: specimen.most_recent_determination.display_name HigherTaxon: specimen.most_recent_determination.all_names # ACTION NEEDED: write the method in TaxonNames Kingdom: nil Phylum: nil Class: nil Order: nil Family: specimen.most_recent_determination.name_at_rank('family') Genus: specimen.most_recent_determination.name_at_rank('genus') SpecificEpithet: specimen.most_recent_determination.name_at_rank('species') InfraspecificRank: specimen.most_recent_determination.name_at_rank('subspecies') InfraspecificEpithet: specimen.most_recent_determination.name AuthorYearOfScientificName: specimen.most_recent_determination.display_author_year NomenclaturalCode: 'ICZN' IdentificationQualifier: specimen.most_recent_determination.confidence.display_name HigherGeography: specimen.ce.geography # this is VERBATIM!, not the geog chain Continent: nil # pointless at the level of data we will serve WaterBody: # ? specimen.geog.water_body IslandGroup: # ? specimen.geog.water_body Island: # ? specimen.geog.water_body Country: specimen.ce.geog.country StateProvince: specimen.ce.geog.state County: specimen.ce.geog.county Locality: specimen.ce.geog.locality MinimumElevationInMeters: specimen.ce.elev_min MaximumElevationInMeters: specimen.ce.elev_max MinimumDepthInMeters: nil # not presently included, an easy addition MaximumDepthInMeters: nil # not presently included, an easy addition CollectingMethod: specimen.ce.mthd ValidDistributionFlag: nil # not presently recorded, add as a tag via TagEngine if needed EarliestDateCollected: specimen.ce.start_date LatestDateCollected: specimen.ce.end_date DayOfYear: nil # easily added function if necessary Collector: specimen.ce.collectors Sex: specimen.sex LifeStage: specimen.stage Attributes: # could concat measurements here, or tags or whatever, many possibilities ImageURL: # many possibilities here RelatedInformation: # could use tags etc., or extend to specimen.public_notes etc.
Darwin_Core_1.4_curatorial_extension:
CatalogNumberNumeric: specimen.id # unclear if this is really the id IdentifiedBy: specimen.most_recent_determination.determiner DateIdentified: specimen.most_recent_determination.det_year CollectorNumber: specimen.ce.trip_code FieldNumber: specimen.ce.trip_namespace FieldNotes: specimen.ce.verbatim_label VerbatimCollectingDate: nil # could provide verbatim label, otherwise it's extracted VerbatimElevation: nil # could provide verbatim label, otherwise it's extracted VerbatimDepth: nil # see core Preparations: nil # add TagEngine 'dc disposition' TypeStatus: specimen.type_specimens.type_type GenBankNumber: specimen.seq.genbank # OtherCatalogNumbers: specimen.display_identifiers RelatedCatalogedItems: # coming with the polymorphic relationship table Disposition: specimen.lost # add TagEngine 'dc disposition' to extend possibilities IndividualCount: lot.total_specimens
Darwin_Core_1.4_geospatial_extension:
DecimalLatitude: specimen.ce.lat DecimalLongitude: specimen.ce.long GeodeticDatum: CoordinateUncertaintyInMeters: specimen.ce.lat_lon_error_m PointRadiusSpatialFit: VerbatimCoordinates: VerbatimLatitude: specimen.ce.label_lat VerbatimLongitude: specimen.ce.label_long VerbatimCoordinateSystem: 'decimal degrees' GeoreferenceProtocol: GeoreferenceSources: GeoreferenceVerificationStatus: specimen.ce.err_checked GeoreferenceRemarks: FootprintWKT: FootprintSpatialFit:
Darwin_Core_1.4_interaction_extension:
RelationshipType: specimen_support.association.is_a GlobalUniqueIdentifier: specimen_support.specimen.id BasisOfRecord: PreservedSpecimen|HumanObservation # would have to tease this out Taxonomic Elements: # SEE CORE