Standards compliance dashboard

Introduction

The goal of this webpage is to provide an overview of the use of different (biodiversity) standards within the institutes. 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
• 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 definitely not a complete overview. In a first version of this dashboard, we focus on some of the more widely used/known standards. A larger overview of the different standards can be found at FAIRsharing.org. In case another (important) standard is supported and missing from the list, don't hesitate to propose an addition.

Dashboard

Standards compliance dashboard

Institute	Acronym	CETAF ID	IIIF	DwC	ABCD2	ABCD3	AC	BCO	DELTA	ABCDEFG	SDD
NATURAL HISTORY MUSEUM (London)	NHM	L2
NATURHISTORISCHES MUSEUM WIEN (Vienna)	NHMW	L0
ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG (Bonn)	ZFMK	L3
HELSINGIN YLIOPISTO (Finland)	LUOMUS	L3
MUSEUM NATIONAL D'HISTOIRE NATURELLE (Paris)	MNHN	L3
THE HEBREW UNIVERSITY OF JERUSALEM (Israel)	HUJI
NATURHISTORISKA RIKSMUSEET (Stockholm)	NRM	L0
AGENTSCHAP PLANTENTUIN MEISE (Meise)	BGM	L3	v2.1
FREIE UNIVERSITÄT BERLIN	BGBM	L3	v2.1
AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS (Madrid)	CSIC
MUSEUM FUR NATURKUNDE (Berlin)	MfN	L3
ROYAL BOTANIC GARDEN EDINBURGH	RBGE	L3	v3.0	DwC Archive
ROYAL BOTANIC GARDENS KEW	RBGK	L3?
INSTITUT ROYAL DES SCIENCES NATURELLES DE BELGIQUE (Brussels)	RBINS	L0
MUSEE ROYAL DE L'AFRIQUE CENTRALE (Tervuren)	RMCA	L1
SENCKENBERG GESELLSCHAFT FUR NATURFORSCHUNG (Frankfurt)	SGN	L0
STAATLICHES MUSEUM FUER NATURKUNDE STUTTGART	SMNS	L1
STAATLICHE NATURWISSENSCHAFTLICHE SAMMLUNGEN BAYERNS	SNSB	L3

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
• Level 2: Machine readable representation for each specimen, accept-type aware redirection
• 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

NHMW

• IIIF: implemented through the JACQ system

LUOMUS

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

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 e.g. 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

• IIIF: Specific webpage provides a summary on the IIIF work

ZFMK

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

SGN

• ABCD2: publishing to GBIF

SMNS

• 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/97112/153455/93009 resolves to Unit ID: <Barcode> / 153455 / 93009, see SNSB RDF Service **http://services.snsb.info/***
• 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