planetary-knowledge-base

Institutions Data

institutions.csv

8135 rows × 5 columns

Data sources

Sourced from Global Registry of Scientific Collections https://www.gbif.org/grscicoll

(GRSciColl is synced weekly with Index Herbarium https://sweetgum.nybg.org/science/ih/)

Column definition

Columns: 'uuid','code','name','country', 'altCodes'

• uuid: Primary identifer
• code: Official institution short form code - e.g. BMNH
• name: Institution name - e.g. Natural History Museum
• country: ISO-3166 2-letter country code
• altCodes: Alternative institution codes - e.g. BM(NH), NHM

Relationships

• institution.country -> country.iso

Country Data

countries.csv

252 rows × 8 columns

Columns: 'ISO', 'ISO3', 'ISOnumeric', 'FIPS', 'countryName', 'Continent', 'geonameid', 'dependsFrom'

alternateCountryNames.csv

44430 rows × 15 columns

Columns: 'ISO', 'ISO3', 'ISOnumeric', 'FIPS', 'countryName', 'Continent', 'geonameid', 'dependsFrom', 'alternateNameId', 'isolanguage', 'altName', 'isPreferredName', 'isShortName', 'isColloquial', 'isHistoric'

Data sources

Sourced from GeoNames geographical database: https://www.geonames.org/

Column definition

• ISO : ISO-3166 2-letter country code
• ISO3 : 3-letter ISO country code
• ISOnumeric : Numeric ISO country code
• FIPS : Most admin1 code are FIPS codes
• countryName : Name of the geographical country point
• Continent : Geographical continent code
• geonameid : Integer id of record in geonames database
• dependsFrom : Dependent countries or territories
• alternateNameId : Integer id of this alternate name
• isolanguage : ISO 639 language code 2- or 3-characters; 4-characters 'post' for postal codes and 'iata','icao' and faac for airport codes, fr_1793 for French Revolution names, abbr for abbreviation, link to a website (mostly to wikipedia), wkdt for the wikidataid altName : alternate name or name variant
• isPreferredName : '1', if this alternate name is an official/preferred name
• isShortName : '1', if this is a short name
• isColloquial : '1', if this alternate name is a colloquial or slang term
• isHistoric : '1', if this alternate name is historic and was used in the past

Continent codes :

• AF : Africa geonameId=6255146
• AS : Asia geonameId=6255147
• EU : Europe geonameId=6255148
• NA : North America geonameId=6255149
• OC : Oceania geonameId=6255151
• SA : South America geonameId=6255150
• AN : Antarctica geonameId=6255152

Taxa Data

taxa.parquet

1907100 rows × 7 columns

Data sources

Sourced from GBIF Backbone Taxonomy https://doi.org/10.15468/39omei

Filtered on family=Plantae

Column definition

Columns: taxonID, name, authorship, taxonRank, status, parent, synonymOf

• taxonID: Primary identifer
• name: Taxonomic name e.g. Veronicastrum lungtsuanense
• authorship: Taxonomic name authorship e.g. M.Cheng & Z.J.Feng
• taxonRank: Taxonomic rank e.g. species
• status: Taxonomic status e.g. accepted
• parent: Parent taxonID of this taxon
• synonymOf: If taxon is a synonym, the taxonID of the accepted taxon

Relationships

• taxa.parent -> taxa.taxonID
• taxa.synonymOf -> taxa.taxonID

Specimens Data

loadSpecimen.ipynb

A data loading and preprocessing script.

Data sources

GBIF Occurrence Download - 105,738,391 specimen records.

DOI: https://doi.org/10.15468/dl.5qqpak

Column definition

Columns: 'gbifID', 'occurrenceID', 'verbatimScientificName', 'verbatimScientificNameAuthorship', 'countryCode', 'locality', 'stateProvince', 'occurrenceStatus', 'decimalLatitude', 'decimalLongitude', 'day', 'month', 'year', 'basisOfRecord', 'institutionCode', 'collectionCode', 'catalogNumber', 'recordNumber', 'identifiedBy', 'dateIdentified', 'recordedBy', 'typeStatus', 'lastInterpreted', 'issue', 'bottomTaxaRank', 'bottomTaxaValue'

• gbifID: Primary identifer
• occurrenceID: A unique identifier for a particular record of an occurrence (refers to an observed evidence of an organism at a particular time and place)
• verbatimScientificName: Exact original scientific name
• verbatimScientificNameAuthorship: Exact original scientific name authorship
• countryCode: ISO-3166 2-letter country code
• locality: Specific place where an organism was observed
• stateProvince: Name of the region or state where the observation took place
• occurrenceStatus Whether the organism is actually present or not
• decimalLatitude: Geographical decimal latitude
• decimalLongitude: Geographical decimal longitude
• day: Event day
• month: Event month
• year: Event year
• basisOfRecord: Source of the original observation or collection data
• institutionCode: Official institution short form code
• collectionCode: Collection code
• catalogNumber: Catalog number
• recordNumber: Record number
• identifiedBy: determined by - verbatim
• dateIdentified: Date of indentified
• recordedBy: collected by - verbatim
• typeStatus: Status of a specimen in defining the name of a species
• lastInterpreted: Most recent date and time when the record was processed or updated.
• issue: Potential problems or flags associated with a record
• taxonKey: unique identifier for the taxonomic classification of the organism observed.

Relationships

• specimens.taxonKey -> taxa.taxonID [determination]
• specimens.recordedBy -> person. [collectedBy]
• specimens.identifiedBy -> person. [determinedBy]
• specimens.institutionCode -> institutions.code
• specimens.countryCode -> country.iso

Person (TBC)