Latest revision as of 10:12, 29 June 2020

Introduction

The goal of this webpage is to provide an overview of the use of different (biodiversity) standards within the European museums and herbaria. The dashboard is created in the framework of work package 4 of Synthesys+.

The table contains a list of standards (columns) and institutes (rows). Whenever an institute is using one of the standards, the corresponding cell is colored yellow. For some of the standards, extra information is given in the cell (level of adopting the standard or version of the standard used).

List of standards

The different standards considered in this dashboard are listed here. Links to a more detailed description on the standard are given.

• CETAF persistent identifier
• International Image Interoperability Framework (IIIF)
• Darwin Core (DwC)
• Access to Biological Collection Data v2.06 (ABCD2)
• Access to Biological Collection Data v3.0 (ABCD3)
• Audubon Core (AC)
• Biological Collections Ontology (BCO)
• DEscription Language for TAxonomy (DELTA)
• ABCDEFG (Access to Biological Collection Databases Extended for Geosciences)
• Structured Descriptive Data (SDD)

This list of standards is not exhaustive and this is not a complete overview. In a first version of this dashboard, we focus on some of the more widely used/known standards in biodiversity informatics. A larger overview of the different standards can be found at FAIRsharing.org. In case another (important) standards are supported and missing from the list, don't hesitate to propose an addition.

Dashboard

Adoption of the CETAF stable identifier

A full overview on the adoption of the CETAF stable identifier can be found here. This document contains the syntax that is used by the different institutes.

In the table above, the level of adoption of the CETAF stable identifier is indicated. The levels are defined as follows:

• Level 0: Identifier syntax chosen
• Level 1: Web page for each specimen, identifier redirects to it^[1]
• Level 2: Machine readable representation for each specimen, accept-type^[2] aware redirection or aware content output
• Level 3: Machine readable representation is CSPP conform

Extra information

This section will provide the possibility to detail more on the adoption of the different standards.

NHM

• Example of CETAF ID: http://data.nhm.ac.uk/object/<id>
• DwC is used when data is published to the data portal

• Collections and bio/geodiversity data:
  • Darwin Core: A set of Darwin Core fields have been implemented in the Collections Management System (EMu). These are not part of the core schema, but are mapped to from EMu's native fields and updated daily via a script. The NHM Data Portal publishes collection data in Darwin Core format to the extent of the standard.
  • LOD-related: The NHM Data Portal has implemented N3, Turtle, XML and JSON-LD formats for LOD, with vocabularies used listed at view-source:https://data.nhm.ac.uk/catalog.ttl. It uses the DCAT standard (https://www.w3.org/TR/vocab-dcat-2/) for describing data catalogues.
  • Gradstein and Ogg (2012) timescale for Chronostratigraphy: Used for chronostratigraphy module in the CMS and Data Portal. Likely to be updated to the International Chronostratigraphic Chart (http://www.stratigraphy.org/index.php/ics-chart-timescale) at some point in the future.

• Molecular:
  • GGBN data standards (https://wiki.ggbn.org/ggbn/GGBN_Data_Standard): Not yet incorporated into the NHM's freezer management software (FreezerPro), but mapped to when publishing data to GGBN. Included in the NHM's collection data standards, and also used for a number of molecular datasets e.g. ABYSSLINE deep-sea benthic macroinvert dataset.
  • OBIS-ENV-DATA: DwC extension used for marine environmental datasets

• Digital media:
  • IIIF: Not yet implemented in the Data Portal, as the DAMS which serves images to the Portal doesn't support it (and won't in the forseeable future). There is also an ongoing project to transfer collection images from tape to faster disk storage, once complete the Data Portal team will build a IIIF service to sit on top of the Portal architecture. This will piloted beforehand on a beetle drawer annotation system.

• Geospatial:
  • GADM (https://gadm.org/index.html): Used in the CMS and Data Portal for site data
  • INSPIRE (https://defradigital.blog.gov.uk/2015/02/25/inspired/): A long-standing aspiration to use these for geo standards in the Data Portal, but not implemented yet. ISO international country and admin standards are a must, and are embedded in the INSPIRE standards to a degree.

• Library materials:
  • Resource Description and Access (RDA)
  • Descriptive Cataloguing of Rare Materials (DCRM)
  • MARC 21
  • Library of Congress Name Authority File (LCNAF)
  • Library of Congress Subject Headings (LCSH)
  • Library of Congress Genre/Form Terms (LCGFT)

• Archives:
  • ISAD(G) (General International Standard Archival Description): Used for archive cataloguing
  • ISAAR(CPF) (International Standard Archival Authority Record for Corporate Bodies, Persons and Families) and NCA Rules (NCA Rules for the Construction of Personal, Place and Corporate Names): Used for authority records

NHMW

• IIIF: implemented through the JACQ system

LUOMUS

• Example of CETAF ID http://id.luomus.fi/<id>
• DwC is used to publish

MNHM

Information for MNHN and the national french infrastructure recolnat (https://www.recolnat.org/) Both implement the Darwin core to publish specimens to GBIF .

• MNHN CETAF-ID: http://coldb.mnhn.fr/catalognumber/{institutioncode}/{collectioncode}/{barcode}
• RECOLNAT CETAF-ID: https://explore.recolnat.org/occurrence/{UUID}
• IIIF: instance of mirador with annotation service. https://collections.recolnat.org/
• SSD: implemented into the annotate software (https://www.recolnat.org/annotate) which is linked with Xper3 application.

BGM

• CETAF-ID: http://www.botanicalcollections.be/specimen/<barcode>
• IIIF: an exemplar implementation is made. An instance of the Mirador viewer can be found here. A RESTful API is developed to generate the IIIF manifests on the fly: http://iiif-manifest.oxalis.br.fgov.be/specimen/<barcode>/manifest. At the moment, manifests are only generated based on the barcode. The IIIF 2.1 APIs (image and presentation) are implemented. The image API is provided by the Loris server and the source images are in JPG format.
• DwC: this standard is used to publish data to the Global Biodiversity Information Facility (GBIF)

BGBM

• CETAF-ID: herbarium.bgbm.org/object/<barcode>
• IIIF: https://herbarium.bgbm.org/data/iiif/<barcode>/manifest.json; upgrade to IIIF 3.0 is planned;
• ABCD: the standard is used for publishing specimen and observational data to GBIF, BioCASe, OpenUp (Euoropeana), GFBio (German Federation for Biological Data) as well as various Special Interest Networks.
• SDD: implemented into the EDIT Platform for Cybertaxonomy (http://www.cybertaxonomy.org) as an interface for descritptive data software systems.

RBGE

• DwC: We publish our herbarium and living collections data to GBIF (and anyone else who wants it) through daily updated DwC Archive files.
  • Herbarium Specimens The herbarium data includes links to scans of our specimens.
  • Living Collection DwCa The living collection data includes links to photographs of plants in cultivation and in the wild.
• CETAF IDs: All our herbarium specimens and living collection specimens are identified by CETAF ID. e.g.
  • http://data.rbge.org.uk/herb/E00421509
  • http://data.rbge.org.uk/living/19731361
• The RDF metadata returned by our CETAF URIs includes links to other resources that we intend to build on over the next year. Currently the data includes links to:
  • A limited number of collectors based on ORCID or Wikidata URIs
  • IIIF Manifest files for herbarium specimen images
  • JPEG images
• We have developed and maintain the CETAF Specimen URI Tester which is a resource to test/validate/develop CETAF Specimen URIs
• IIIF: We have a IIIF endpoint implementing the Presentation API (manifests) and Image API both version 3.0 for our herbarium specimen images and some experimental resources - details here.

ZFMK

• CETAF-ID: https://id.zfmk.de/collection_ZFMK/<barcode>
• ABCD2: publishing to GBIF, GGBN
• IIIF: under development...

SGN

• ABCD2: publishing to GBIF

SMNS

• CETAF-ID: http://id.smns-bw.org/smns/collection/<DWB-ID>
• ABCD2: publishing to GBIF, BOLD, Genbank, UNITE, MycoBank, TreeBASE, VertNet.

RMCA

• collection data (http://darwinweb.africamuseum.be/search_specimens) are not yet directly machine-readable but it could be accessible via the NaturalHeritage Search portal (http://www.naturalheritage.be/)
• some old data might be in DELTA, however SDD via Xper2/Xper3 will be used for taxonomic keys
• digitized biological specimens (http://digit03.africamuseum.be) are web searchable but not yet implemented in IIIF

SNSB

• CETAF-ID: Example: UNIT GUID http://id.snsb.info/snsb/collection/*
• DwC: the standard is used as Simple Darwin Core Text for publishing regional taxonomic lists with common names to GBIF.
• ABCD: the standard is used for publishing specimen and observational data to GBIF, BioCASe, GFBio (German Federation for Biological Data) as well as various Special Interest Networks.
• SDD: the standard is used for publishing trait and other kind of descriptive data via GFBio; data management done via DiversityDescriptions; SDD via NaviKey is used for taxonomic keys

Naturalis

Compliance to ABCD2: the Collection Registration System was based on ABCD (2.06 of 1.4)

Support of standards besides the ones listed in the table above:

• Library: MARC21, DublinCore
• Molecular/Genetic standards BOLD
• Digital media (through Audubon Core)
• Library: MARC21, DublinCore
• Archives - ISAD, SPECTRUM

Technical Notes

1. ↑ If a redirect is implemented it should be the HTTP response status code 303 “See Other” instead of the sometimes used 302 code “Found” or “Moved Temporarily” which is hard to tell how the client would interpret it
2. ↑ An identifier with HTTP Header Accept of 'application/rdf+xml' will be redirected to or will issue the objects of the machine-readable RDF metadata record (you can test this by using the CETAF URI Tester)