CETAF Stable Identifier Guide

CETAF Stable Identifier Guide

CETAF ISTC Stable Identifier Initiative

The Stable Identifiers of the Consortium of European Taxonomic Facilities (CETAF) are globally unique, consistent and reliable identifiers for specimens in natural history collections. These identifiers are used in the world wide web to redirect users and systems to images, websites and metadata of the physical objects and to integrate them with the semantic web.

To align with modern global data infrastructures (such as DiSSCo and the Digital Specimen Architecture), CETAF strongly recommends provisioning for Digital Specimen DOIs. While CETAF URIs serve as the foundational, actionable Linked Open Data network entry points, Digital Specimen DOIs offer a globally recognized, persistent, and cross-disciplinary citation standard.

How do CETAF Stable Identifiers look like?

Example for the syntax of a CETAF Stable Identifier.

The CETAF identifier system is based on HTTP-URIs and Linked Data principles. It is simple and future-proof. Each collection object as well as its associated information resources (e.g. multimedia, RDF, webpages) are identified by stable HTTP-URIs that will never change. The URI Syntax for the objects is chosen and maintained by the institution owning them. This flexibility is one of the main advantages of the CETAF Stable Identifier system as it allows e.g. to include branding and local scope identifiers into the CETAF Stable Identifier URI. There are however some best practices for stable URIs. Examples are:

http://herbarium.bgbm.org/object/B100277113

http://www.botanicalcollections.be/specimen/BR0000005516339

http://data.rbge.org.uk/herb/E00421509

How are CETAF Stable Identifiers resolved?

Resolving URI-based collection identifiers using standard HTTP-redirection mechanisms.

A CETAF Stable Identifier allows the access of information about the corresponding collection object in various ways. If a human user tries to access a collection object by typing it’s CETAF Stable Identifier into a web-browser, he will be redirected to a human-readable representation (e.g. html web-page) of it. If a software-system tries to access the collection object via the same identifier, it will be redirected to a machine-processable RDF-encoded metadata record. The identifier is therefore integrated with the semantic web and can also be used in other RDF representations to link to the belonging collection object.

What can CETAF Stable Identifiers be used for?

As described above, CETAF Identifiers can first of all be used to redirect users and systems to images, websites and metadata of the physical objects they belong to. They can also be used to precisely reference specimens needed in scientific studies and serve as basis for data retrieval, integration and reproducibility of data experiments.

When paired with Digital Specimen DOIs, they provide dual-layered tracking. The CETAF URI drives semantic web integrations and localized lookups, while the DOI ensures that when a specimen is cited in an academic journal, data citations are automatically tracked, aggregated, and credited back to the home institution via cross-repository indexing (e.g., DataCite, Crossref).

Additionally, the stable identifiers enable new applications in the semantic web domain. An example for this is the Biology Pilot. The Botanic Garden and Botanical Museum Berlin, Meise Botanic Garden and other collections annotated thousands of specimens with the HUH and WikiData IDs of their collectors. The CETAF Stable Identifiers of the annotated specimens are available on GBIF and a server is crawling the identifiers to organize the RDF information in a Blaze Graph triple store. This graph enables us to search for specimen by their collector ID of HUH or WikiData, which is invariant to the different spelling variants the individual institutions may be using. The query will return all relevant specimens available in the joined set of specimens regardless of their origin institution. If the number of institutions using stable identifiers grows and the amount of machine readable annotations increases, this technology could be used to basically create a “google for specimens”.

How can I implement CETAF Stable Identifiers for my collection?

The CETAF Stable Identifiers can be implemented in three levels. They are described in detail in herbal.rbge.info’s documentation.

Following conditions have to be met to reach the corresponding implementation levels

Level 1 …	→ Level 2	→ Level 3
✓ you assigned a stable URI to each object of your collection, which will be never changed and preferably follows the best practices for stable URIs ✓ there exists a human-readable representation (web-page) for each of your collection objects ✓ a user trying to access a collection object by typing the stable URI of it into a web-browser will be redirected to the human-readable representation (web-page) of the object (you can test this by using the CETAF URI Tester)	✓ you reached Level 1 ✓ there exists a machine-readable RDF metadata record for each of your collection objects ✓ a machine trying to access a collection object via its identifier with application/rdf+xml header will be redirected to the objects machine-readable RDF metadata record (you can test this by using the CETAF URI Tester)	✓ you reached Level 2 ✓ the machine-readable RDF metadata record of each of your collection objects encodes application specific data (e.g. is compliant to the CETAF Specimen Preview Profile—CSPP) ✓ (Recommended:) A Digital Specimen DOI is minted for the object by DiSSCo and bi-directionally linked within the RDF metadata once it exists.

HTTP vs. HTTPS versions of CETAF URIs

As far as the Semantic web is concerned http://xyz and https://xyz are different things because they are different URIs. The recommendation for new implementations should be just to use HTTPS. If you have only HTTP or HTTPS versions, or want to change it you should take notice of the following:

HTTP	HTTPS
You have issued only HTTP versions of CETAF URIs and want to keep it that way have nothing to add technically, just have the usual 303 HTTP redirect to RDF or HTML resources in place	You have issued only HTTPS versions of CETAF URIs don’t need to resolve then HTTP if you have never issued any, because they aren’t out there to be resolved.
Want to change HTTP to HTTPS
You have issued HTTP versions of CETAF URIs but want to change to HTTPS have to keep resolving with a 303 redirect to HTTPS of the RDF or HTML resources. The RDF should contain an owl:sameAs assertion linking the HTTP and HTTPS versions of the URI, therefore only minor configure stuff for providers and transparent for users. could change to telling people to cite HTTPS rather than HTTP for your specimens but it shouldn’t matter too much as these things are linked together. The recommendation would be to cite as HTTPS if you have it implemented as at some point in the future a client may refuse to trust even a redirect from an HTTP URI (which is a bit paranoid but may happen).

Integrating Identifiers into Collection Management Systems

CRITICAL IMPLEMENTATION STEP: To ensure the integrity of both CETAF URIs and digital specimen DOIs, all identifiers must be stored directly within the primary Collection Management System (CMS) source systems (e.g., Specify, Axiell EMu, Brahms, Jacq, etc.).

• Source System as Single Source of Truth: Identifiers should never be generated ad-hoc during web publishing or aggregator exports. They must be generated or captured at the point of digitization or ingestion and written permanently into the local CMS database.
• Database Fields: Ensure your CMS schema contains dedicated, indexed fields for the CETAF URI and the Digital Specimen DOI. This guarantees absolute consistency across internal curation workflows, localized public portals, and external data pipelines. For the DOI there is a dedicated DarwinCore field dwc:digitalSpecimenID

Publishing CETAF IDs to GBIF

If your institution is using CETAF IDs and digital specimen DOIs, and you want them (and potential Specimen RDF) to be included into the CETAF Specimen Catalogue and global indexes, they need to be used as authoritativeGUIDs in the specimen data fed to GBIF. As described in CETAF Specimen Catalogue, the GBIF Index is used to discover CETAF IDs.

• If Darwin Core (DwC) is used:
  • Map the CETAF URI to occurrence ID.
  • Map the digital specimen DOI to digital specimen ID

As a TDWG-ratified term under the `MaterialEntity` class, `digitalSpecimenID` is explicitly reserved to hold the persistent, FAIR Digital Object identifier (a DataCite DOI) that references the internet-based digital surrogate of the physical specimen.

For ABCD:

• The concept UnitGUID should be used for the primary identifier (CETAF URI).
• Use UnitGUID variations or specialized metadata elements to explicitly supply the Digital Specimen DOI.

How can I discover specimens with CETAF IDs and corresponding Linked Open Data (LOD)?

You can discover specimens of institutions of the Stable Identifiers Implementers Group by using the CETAF Specimen Catalogue maintained at the BGBM, which offers a web service for getting a list of valid CETAF IDs. For implementers of level 2, who provide RDF representations of their specimens, a cache triple store with a SPARQL access point will be available soon.

What data fields or elements are recommended or standardized?

The CETAF Specimen Preview Profile (CSPP) is developed as a minimal set of agreed (RDF) collection metadata elements implemented consistently across CETAF organisations.

Under modern iterations of the profile, it is highly recommended to include standard properties to express alternate persistent identifiers. Specifically:

• prov:hadDerivation or dcterms:identifier should be utilized within the RDF metadata record to explicitly declare the digital specimen DOI associated with that specific URI, allowing semantic web harvesters to bridge the gap between the LOD web and DOI registries.

The CSPP is not meant to be comprehensive, which means that Linked Open (collection) Data implementations of CETAF institutions will usually provide much richer metadata with additional RDF-elements.

Further Questions

See on Questions, problem solutions and further discussions (Guide of best practices) and in general also in Category: Discussion.

Useful Links

• Best practices for stable URIs
• CETAF Specimen Preview Profile (CSPP)—A set of standard data components for data exchange
• Source code and example documents (git.bgbm.org)
• CETAF URI Tester (herbal.rbge.info)
• The Standards Compliance Dashboard of collaborating institutions
• Category: Guide for CETAF Stable Identifiers—Collection of pages related to this guide or handbook

Further reading

Kuzmova, I. ‘Pro-IBiosphere - Stable Identifiers for Specimens – A CETAF ISTC Initiative Supported by pro-IBiosphere’. EUBON. 1 July 2013. URL: https://www.pro-ibiosphere.eu/news/4296_stable_identifiers_for_specimens_-_a_cetaf_istc_initiative_supported_by_pro-ibiosphere/.

Güntsch, A. et al., ‘Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects’, Database (Oxford), vol. 2017; Jan. 2017. URL: https://doi.org/10.1093/database/bax003.

Groom, Q. et al., ‘Stable Identifiers for Collection Specimens’, Nature (Correspondence), 546.7656 (2017), 33; URL: https://doi.org/10.1038/546033d

Hardisty, A. ‘Natural Science Identifiers & CETAF Stable Identifiers’. DiSSCoTech (blog). 28 May 2020; URL:https://dissco.tech/2020/05/28/natural-science-identifiers-cetaf-stable-identifiers/.

Hyland, B. et al. ‘Best Practices for Publishing Linked Data.’ World Wide Web Consortium, 9 Jan. 2014; http://www.w3.org/TR/ld-bp/.

Wouter, A. ‘Identifiers for Our Institutes – GRID and ROR’, DiSSCoTech (blog), 11 April 2020; https://dissco.tech/2020/04/11/identifiers-for-our-institutes-grid-and-ror/.

McMurry, J. A. et al., ‘Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data’, PLOS Biology 15(6):e2001414 June 2017; URL:  https://doi.org/10.1371/journal.pbio.2001414.

Poster: CETAF stable identifiers for specimens (1.4MB, www.cetaf.org)

Meetings

• Edinburgh Meeting (June 2013)
• Joint ISTC/pro-iBiosphere workshop Berlin, October 2013 (archived version)
• Geneva Meeting (October 2015)
• Joint CETAF-ISTC / CETAF-DWG meeting (May 2016)
• Joint CETAF-ISTC / CETAF-DWG meeting (March 2017)
• (Virtual) LOD Hackathon (October 2017)
• Joint CETAF-ISTC / CETAF-DWG meeting (February 2018)
• ISTC QoS Workshop Copenhagen (June 2018)
• Joint CETAF-ISTC / CETAF-DWG meeting (February 2019)