Release notes

Updates of the GBIF.org software and infrastructure

Osmia-bicolor-iNat-gsanmartin-hero
Red-tailed mason bee (Osmia bicolor), Namur, Wallonia, Belgium. Photo 2019 Gilles San Martin via iNaturalist Research-grade Observations, licensed under CC BY-SA 4.0.

This pages details the main updates to the GBIF.org and related infrastructure. Further details are found in the GitHub repositories, including GBIF.org, occurrence web and download services, occurrence processing pipelines, checklistbank, registry, registry web portal and the Catalogue of Life checklistbank.

11 June 2021

GRSciColl

31 May 2021

Dataset filters
  • Dataset search API supports filters and facets by networkKey, hostingCountry and endorsingNodeKey
Dataset export services
Download statistics
Miscellanous

21 May 2021

Features
  • Search occurrences using modification date stated by publisher #219
  • Download filters support search “field has a value” using the isNull predicate #244
  • Registry console supports user filtering by roles and editor scopes #330
  • API response for dataset citation now includes authors as objects, if they are also contacts and indication if the citation was provided or generated #351
  • Dataset search API supports filters and facets by installationKey and endpointType #148
Bug fixes
  • Creating a network constituent for a non existing network no longer throws error #349
  • Network suggest no longer includes deleted entities #308
  • Consistent behaviour on GBIF.org and Registry management console for publisher search #198

17 May 2021

  • First GBIF Parquet export added to the Amazon Public Data Catalog, with data available on 5 continents

5 May 2021

API and processing
Derived datasets

20 April 2021

  • New Parquet download format added to the API
  • First GBIF Parquet export added to the Microsoft Planetary Computer data catalogue.

22 March 2021

Sequence ID tool
  • Classification of Bacteria and Archaea by 16S sequences matched against the Genome Taxonomy Database r95
  • ITS (Fungi) database updated to UNITE v8.2
  • COI (Animalia) database updated to International Barcode of Life v2021-02-08

11 March 2021

New backbone live
  • Data source replacements, primarily for Fabaceae family and the prokaryotic kingdoms Bacteria and Archaea
  • Improvement for stable identifiers, esp relating to OTUs
  • Algorithm improvements (misplaced taxa)
  • Removal of names / terms on a denylist
  • Please refer to the backbone build log for additional details

23 February 2021

  • Support for registering dataset endpoints in Catalogue of Life Data Package format
  • Flagging of potential duplicates added to assist editors in deduplication entries in the GRSciColl catalogue. E.g. Reuse of the code PCU
  • Ability to restrict permissions for GRSciColl editors to institution or collection, allowing more people to participate
  • Schema.org metadata tags revised on the dataset and taxon pages to improve search engine discoverability

11 February 2021

26 January 2021

  • Improvements to the handling of networks (groupings of datasets) including
    • Listing in search e.g. searching for Arctos
    • Listing the publishers, and the datasets in the summary e.g. OBIS network
    • Ability to control if they are visible on a dataset page
    • Ability to assign editorial control to trusted users in the registry
  • Support for DOIs for adhoc data exports by GBIFS staff (example https://doi.org/10.15468/dd.jskxae)
  • Bug fix for BioCASe protocol metadata synchronisation
  • Added the literature vocabularies type, topic and relevance to the API to support analyses by external data scientists
  • Added an experimental API categorisation of the griddedness of datasets (e.g. this example)
  • Added capability to associate ROR and GRID ids to organisations in the GBIF registry

2020

17 December 2020

15 December 2020

14 December 2020

  • API deployed to support Literature search by DOI. This API is documented in GitHub but documentation will be moved to the GBIF API documentation shortly

8 December 2020

  • The new Catalogue of Life website is live. This is the first deployment that is powered by GBIF and hosted on GBIF infrastructure. In addition to the public website are the common repository known as the checklistbank, and a new API which is supported in the rOpenSci client.

2 December 2020

  • Extension data now shown on all occurrence pages e.g. measurements example
  • Specimen-related occurrence records now link to the collection catalogue entries in addition to the dataset they originate from e.g. this record from SAIAB. Matching uses a variety of fields including collectionCode, institutionCode, collectionID and institutionID. See the FAQ on how to improve matching
  • New API to improve searching against the Collection Catalogue, e.g searching for "K"
  • Elasticsearch updated to version 7.10.0

9 November 2020