Biodiversity FDP — overarching index

Static FAIR Data Point index over biodiversity infrastructures. Each sub-catalog describes one resource and lists every way to obtain it: native portal and APIs, bulk files, cloud buckets and copies in aggregators (GBIF, QLever, Koetai). Provenance is preserved, not deduplicated: the iNaturalist subset in GBIF appears under both.

Machine-readable metadata: FAIR Data Point index (Turtle).

iNaturalist — citizen-science biodiversity observations

Community-sourced, photo-vouchered observations of organisms and the iNaturalist taxonomy. Native access on inaturalist.org, plus the research-grade subset republished through GBIF (portal, API, AWS Parquet snapshots and the QLever RDF graph).

• iNaturalist observations — All observations on iNaturalist (live database). Licence is chosen per observation and per photo by the observer (CC0, CC BY, CC BY-NC or all rights reserved); only CC0 / CC BY / CC BY-NC research-grade records flow on to GBIF.
  • REST / web API: iNaturalist API v1 — JSON
  • REST / web API: iNaturalist API v2 — JSON with field selection
  • Cloud object storage: iNaturalist Licensed Observation Images — AWS Open Data (metadata 2026-09-27)
  • Darwin Core Archive: iNaturalist research-grade observations — Darwin Core Archive
  • Bulk file download: iNaturalist observation export — CSV
  • Copy in an aggregator: Research-grade subset in GBIF — iNaturalist Research-grade Observations (doi:10.15468/ab3s5x)
  • Cloud object storage: Research-grade subset in the GBIF AWS Parquet snapshot (2026-10-01)
  • SPARQL endpoint: Research-grade subset in the GBIF RDF graph on QLever
  • Web portal: iNaturalist website — Explore
• iNaturalist taxonomy — The taxon tree used on iNaturalist (names, ranks, common names, external links), regenerated regularly.
  • REST / web API: iNaturalist API v1 — taxa
  • Darwin Core Archive: iNaturalist taxonomy — Darwin Core Archive

GBIF — Global Biodiversity Information Facility

Occurrence records aggregated from tens of thousands of publishers, and the GBIF Backbone Taxonomy. Native access on gbif.org and api.gbif.org, monthly Parquet snapshots on AWS Open Data, and an RDF copy queryable with SPARQL on QLever.

• GBIF Backbone Taxonomy 2023-08-28 — The taxonomic backbone every GBIF occurrence is matched to (doi:10.15468/39omei).
  • REST / web API: GBIF Species API
  • Darwin Core Archive: GBIF Backbone — Darwin Core Archive
  • SPARQL endpoint: GBIF Backbone as RDF on QLever
• GBIF occurrence data — live index — All occurrences currently indexed by GBIF (3 956 888 741 on 2026-10-06). Each record keeps its publisher licence: CC0, CC BY or CC BY-NC.
  • REST / web API: GBIF Occurrence API — JSON
  • Darwin Core Archive: GBIF occurrence download — DwC-A, simple CSV, species list or simple Parquet, with DOI
  • Web portal: GBIF.org occurrence search
  • SPARQL endpoint: GBIF as RDF on QLever — SPARQL
  • SQL query service: GBIF SQL download API
• GBIF monthly occurrence snapshot 2026-09-01 — Previous monthly snapshot (CC0 and CC BY records only). Older snapshots stay in the buckets for reproducibility.
  • Cloud object storage: GBIF snapshot 2026-09-01 — Parquet on AWS S3
• GBIF monthly occurrence snapshot 2026-10-01 — Monthly frozen export of all CC0 and CC BY occurrences (CC BY-NC records are excluded) as Parquet, mirrored in five AWS regions. Cite via the citation.txt in the snapshot folder.
  • Cloud object storage: GBIF snapshot 2026-10-01 — Parquet on AWS S3

BHL — Biodiversity Heritage Library

Open-access digitised biodiversity literature: titles, items, pages, parts, creators, subjects and page-level scientific-name mentions. Native access on biodiversitylibrary.org and its API and data export, plus RDF conversions on Koetai nodes of the Mangal network.

• BHL as RDF on Koetai — RDF conversion of the BHL data.zip export (items, titles, creators, parts, subjects, page-level scientific-name mentions), loaded in QLever on koetai.semscape.org.
  • Copy in an aggregator: BHL on Koetai @ bionames (Oxigraph, Mangal node)
  • Web portal: Koetai BHL — example SPARQL queries
  • Web portal: Koetai BHL — ShEx / SHACL shapes
  • SPARQL endpoint: Koetai BHL — SPARQL endpoint (QLever)
  • REST / web API: Koetai BHL — SPARQList REST API
  • REST / web API: Koetai BHL — VoID statistics
• BHL (sample) as RDF on Koetai — Small but structurally complete sample of the BHL RDF (whole titles with all their items, pages, parts and creators), same schema as the full graph. Meant for schema discovery and whole-graph tools.
  • SPARQL endpoint: Koetai BHL sample — SPARQL endpoint (Fuseki)
• Biodiversity Heritage Library — native collection — The BHL corpus and its bibliographic and name-index metadata as served by BHL itself.
  • REST / web API: BHL API v3 — JSON / XML
  • Bulk file download: BHL scans and OCR on the Internet Archive
  • Bulk file download: BHL data export — data.zip (tab-delimited)
  • Web portal: biodiversitylibrary.org — browse, read and search

Plazi — TreatmentBank and the Biodiversity Literature Repository

Taxonomic treatments, material citations, figures and bibliographic data liberated from published literature. Plazi publishes the same content through many channels: TreatmentBank, its APIs, XML and RDF in git, a SPARQL endpoint, Synospecies, GBIF and Zenodo.

• Biodiversity Literature Repository (BLR) on Zenodo — Plazi deposits treatments, figures and articles in the Zenodo community biosyslit, each with its own DOI.
  • REST / web API: Zenodo REST API — biosyslit records
  • OAI-PMH harvesting: Zenodo OAI-PMH — set user-biosyslit
  • Web portal: Zenodo community biosyslit
• Plazi TreatmentBank — Treatments extracted from taxonomic publications, each with a persistent identifier http://treatment.plazi.org/id/UUID, plus the material citations, figures and names they contain.
  • REST / web API: Plazi TreatmentBank API v1
  • Copy in an aggregator: Plazi in GBIF — one dataset per publication
  • Cloud object storage: Plazi material citations in GBIF AWS Parquet and QLever
  • RDF dump: treatments-rdf — all treatments as Turtle in git
  • SPARQL endpoint: Plazi treatment SPARQL endpoint
  • Bulk file download: TreatmentBank statistics / export (srsStats)
  • Web portal: Synospecies — synonymy and treatment browser
  • Web portal: TreatmentBank search (GgServer)
  • Version-controlled repository: treatments-xml — all treatments as XML in git

UniProt — Universal Protein Resource

Protein sequences and functional annotation (UniProtKB Swiss-Prot and TrEMBL, UniRef, UniParc, Proteomes) and the UniProt taxonomy. Links to biodiversity via NCBI taxon identifiers and up:scientificName.

• UniProt release 2026_03 — Current release, published 2 September 2026.
  • Bulk file download: UniProtKB bulk files — flat text, XML, FASTA
  • RDF dump: UniProt RDF dump — RDF/XML
  • REST / web API: EBI Proteins API
  • SPARQL endpoint: UniProt RDF on QLever
  • REST / web API: UniProt REST API
  • SPARQL endpoint: UniProt SPARQL endpoint (official)
  • Web portal: uniprot.org — search and entry pages
• UniProt previous releases — Archived releases (latest archived: 2026_02, 2026_01) for reproducing earlier analyses.
  • Bulk file download: UniProt previous_releases FTP

OpenStreetMap — collaborative map of the world

Nodes, ways and relations with free-form tags: protected areas, land cover, water bodies, trails and places that give spatial context to biodiversity records. Native APIs and planet files, plus the osm2rdf RDF conversion queryable on QLever.

• OpenStreetMap — live database — The continuously edited OSM database, reachable through the editing API, read-only query services and minutely change feeds.
  • REST / web API: OSM editing API 0.6 — OSM XML / JSON
  • Change feed / replication diffs: Replication diffs — minutely, hourly, daily (osmChange)
  • REST / web API: Nominatim — geocoding and reverse geocoding
  • REST / web API: Overpass API — tag and area queries
  • Web portal: openstreetmap.org — map, search and object pages
• OpenStreetMap planet 2026-09-28 — Weekly full-planet export (planet-260928).
  • Cloud object storage: Planet on AWS Open Data — ORC (osm-pds)
  • Bulk file download: Geofabrik regional extracts
  • Bulk file download: Planet — OSM PBF
  • Bulk file download: Planet — OSM XML (bzip2)
• OpenStreetMap as RDF (osm2rdf) — The planet converted to RDF by osm2rdf (University of Freiburg): every node, way and relation with its tags, WKT geometries and precomputed GeoSPARQL relations (ogc:sfContains, ogc:sfIntersects).
  • RDF dump: osm2rdf Turtle extracts
  • SPARQL endpoint: OSM planet RDF on QLever — SPARQL
  • Version-controlled repository: osm2rdf — convert any PBF yourself

GeoNames — geographical names gazetteer

Over 12 million place names with coordinates, feature classes and administrative hierarchy; the usual way to resolve locality strings and country/admin codes in occurrence data.

• GeoNames gazetteer — Daily-updated gazetteer (allCountries dump refreshed 2026-10-06).
  • Bulk file download: GeoNames daily dump — tab-delimited
  • Web portal: GeoNames ontology (gn:)
  • RDF dump: GeoNames RDF dump — all-geonames-rdf.zip
  • Web portal: geonames.org — search and feature pages
  • REST / web API: GeoNames web services — JSON / XML

FLAIR-GG — FAIR network of Spanish plant germplasm banks

FLAIR-GG makes seed and germplasm banks FAIR without changing their databases: each bank exports CSV templates, YARRRML turns them into RDF following a shared semantic model (germplasm, location, administrative), and each bank runs its own FAIR Data Point and SPARQL endpoints. A Virtual Platform federates queries across all members. Six banks are live; this catalog lists every way to reach them.

• BGUSAL germplasm collection — BGUSAL February 2025 — Banco de Germoplasma de la Universidad de Salamanca. Seeds of threatened flora of Castilla y León and spores and mycelium of fungi, hosted at CIALE since 2007. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • Web portal: BGUSAL FAIR Data Point (native metadata)
  • SPARQL endpoint: BGUSAL germplasm — SPARQL endpoint
  • REST / web API: BGUSAL IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: BGUSAL collecting sites — SPARQL endpoint
  • REST / web API: BGUSAL collecting-site coordinates by species — JSON
• BGV-UPM germplasm collection — BGV June 2023 — César Gómez Campo Banco de Germoplasma Vegetal de la UPM (Madrid). About 10 000 seed accessions of 3 500 wild plant species, the founding member of FLAIR-GG. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • SPARQL endpoint: BGV-UPM administrative data — SPARQL endpoint
  • Web portal: BGV-UPM FAIR Data Point (native metadata)
  • SPARQL endpoint: BGV-UPM FAIR Data Point metadata — SPARQL endpoint
  • SPARQL endpoint: BGV-UPM germplasm — SPARQL endpoint
  • REST / web API: BGV-UPM IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: BGV-UPM collecting sites — SPARQL endpoint
  • REST / web API: BGV-UPM collecting-site coordinates by species — JSON
• BG-JBCLM germplasm collection — JBCLM October 2025 — Banco de Germoplasma del Jardín Botánico de Castilla-La Mancha. Seed bank of wild and threatened flora of Castilla-La Mancha, started in 2007. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • Web portal: BG-JBCLM FAIR Data Point (native metadata)
  • SPARQL endpoint: BG-JBCLM germplasm — SPARQL endpoint
  • REST / web API: BG-JBCLM IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: BG-JBCLM collecting sites — SPARQL endpoint
  • REST / web API: BG-JBCLM collecting-site coordinates by species — JSON
• JBO germplasm collection — JBO August 2024 — Banco de Germoplasma del Jardín Botánico de Olarizu (Vitoria-Gasteiz). Threatened, endemic and rare wild flora and habitats of community interest of the Basque Country and surroundings. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • SPARQL endpoint: JBO administrative data — SPARQL endpoint
  • Web portal: JBO FAIR Data Point (native metadata)
  • SPARQL endpoint: JBO germplasm — SPARQL endpoint
  • REST / web API: JBO IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: JBO collecting sites — SPARQL endpoint
  • REST / web API: JBO collecting-site coordinates by species — JSON
• JBS germplasm collection — JBS February 2025 — Banco de Germoplasma del Jardí Botànic de Sóller (Mallorca). Mediterranean and especially Balearic flora; the garden was founded in 1985. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • Web portal: JBS FAIR Data Point (native metadata)
  • SPARQL endpoint: JBS germplasm — SPARQL endpoint
  • REST / web API: JBS IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: JBS collecting sites — SPARQL endpoint
  • REST / web API: JBS collecting-site coordinates by species — JSON
• FLAIR-GG semantic model, templates and FLAIR-in-a-Box — Everything a new bank needs to join: the FAO/IPGRI multi-crop passport descriptor ontology, CSV input templates with paired YARRRML mappings for the germplasm, location and administrative models, and FLAIR-in-a-Box, which installs a triplestore, FAIR Data Point and APIs in one go.
  • Version-controlled repository: CSV input templates (germplasm, location, administrative)
  • Version-controlled repository: FLAIR-in-a-Box — one-command deployment
  • RDF dump: Multi-crop passport descriptor ontology — OWL (RDF/XML)
  • RDF dump: Multi-crop passport descriptor ontology — Turtle
  • Web portal: Onboarding documentation
  • Version-controlled repository: YARRRML mapping templates
• BG URJC germplasm collection — BG URJC Nov 2024 — Banco de Germoplasma de la Universidad Rey Juan Carlos (Madrid). 512 accessions of 222 wild species in four collections: high mountain, semi-arid, Lupinus and Canary Islands; founded 2008. Data follow the FLAIR-GG semantic model (FAO/IPGRI multi-crop passport descriptors, SIO, Darwin Core, WFO taxonomy).
  • SPARQL endpoint: BG URJC administrative data — SPARQL endpoint
  • Web portal: BG URJC FAIR Data Point (native metadata)
  • SPARQL endpoint: BG URJC germplasm — SPARQL endpoint
  • REST / web API: BG URJC IUCN risk categorisation lookup — CSV / JSON
  • SPARQL endpoint: BG URJC collecting sites — SPARQL endpoint
  • REST / web API: BG URJC collecting-site coordinates by species — JSON
• FLAIR-GG Virtual Platform — federated access to all members — The Virtual Platform indexes the FAIR Data Points of all member banks plus third-party services and runs federated queries and analytics over them. It also federates UniProt SPARQL (described in the UniProt catalog of this FDP).
  • REST / web API: Dríada — legal protection status of Spanish flora
  • REST / web API: ENA sequence retrieval via TogoWS
  • REST / web API: Virtual Platform resource index — JSON
  • Copy in an aggregator: FLAIR-GG Virtual Platform portal
  • REST / web API: FDP Index Proxy — register a DCAT document
  • Web portal: Swagger UI for the FLAIR-GG service interfaces
• World Flora Online taxonomic backbone (as used by FLAIR-GG) — The WFO plant taxonomy that FLAIR-GG uses to reconcile species names across banks; every germplasm record points to a WFO identifier.
  • Darwin Core Archive: WFO taxonomic backbone — Darwin Core Archive (latest static version)
  • Web portal: WFO backbone record in the BGV-UPM FAIR Data Point