Contents

1. Identifier resolution services


Recipe Overview
Reading Time
15 minutes
Executable Code
No
Difficulty
Identifier resolution services
FAIRPlus logo
Recipe Type
Background information
Audience
Principal Investigator, Data Manager, Data Scientist, Funder
Maturity Level & Indicator
[F+MM-1.1C] [F+MM-1.2C]
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1.1. Main Objective

Linked Data require on URL and HTTP protocols to ensure linking.

1.2. Introduction

CoolURI don’t change

1.3. Identifier Resolution - Enabling persistence through indirection

This relates to the following FAIR principle mentioned in the introduction:

A1. (Meta)data are retrievable by their identifier using a standardised communications protocol.

Tip

URI resolution is fundamentally about directing requests to the relevant identified entity.

The standard approach would be resolving a HTTP GET request using content negotiation to choose between different representations of the resource.

A PURL is a persistent URL, meaning that it provides a permanent address to access a resource on the web.

To understand the notion of PURL, one needs to first get familiar with the notion of url indirection (also known as url redirect or url forwarding ), which refers to the practice of providing a stable, fixed web address/url, but setting it up so that it points to another content, which may be periodically modified.

When a user retrieves a PURL, they will be redirected to the current location of the resource. When an author needs to move a page, they can update the PURL to point to the new location.

Tip

The practice of indirection comes handy as it ensures invariant url address for resources which are known to change, owing to version changes for instance or owing to change in ownership.

We can see this practice in action with the reliance on purl.org url for identifying OBO Foundry resources. For instance, the following url http://purl.obolibrary.org/obo/stato.owl is a redirect to the latest release of the file, which is https://raw.githubusercontent.com/ISA-tools/stato/dev/releases/latest_release/stato.owl.

PURLs with a common prefix are grouped together into domains. Each domain has a single maintainer who can add new PURLs to the domain and make changes to existing PURLs within the domain.

FAIR Principle A1 states that:

(meta)data should be retrievable by its identifier.

When the identifier is not a resolvable URL, then Identifier Resolution Services are required that know how to map an IRI to a location for the data.

1.3.1. Introducing CURIES or Compact URIs

CURIEs (short for compact URIs) are defined by a World Wide Web Consortium Working Group Note CURIE Syntax 1.0, and provide a human readable shortening of IRIs.

The CURIE consists of a namespace prefix followed by the local identifier.

There are some widely used and defined CURIEs such as DOIs and ISBN numbers. For example the DOI [doi:10.1038/sdata.2016.18] refers to the FAIR Principles paper. The Digital Object Identifier System web site (https://www.doi.org/) provides a resolution service for DOIs. The service is available as a web form on the site or can be used by appending a DOI to the website.The client will be redirected to the URL where the resource about the concept is located, e.g. for the FAIR Data Principles paper we can use the URL https://www.doi.org/10.1038/sdata.2016.18 to resolve the paper’s DOI. This results in the client being taken to the page at https://www.nature.com/articles/sdata201618.

Namespaces can be defined by convention, such as the case with doi, and registered with services to allow for the resolution of CURIEs (see Identifier Resolution Services below). These are extensively used to map CURIEs to URLs that can be resolved.

Going back to our Life Science context, we can use the following CURIE [uniprot:P38398] to refer to the UniProt record for the protein.

This is very useful for including unambiguous, global identifiers in scientific articles.

1.3.2. Identifier Resolution services

  • w3ids

    Permanent Identifiers for the Web. Secure, permanent URLs for your Web application that will stand the test of time.

    • authority registration service

    • resolution service

    • redirection service:

    Send a request to add a redirect to the public-perma-id@w3.org mailing list. Make sure to include the URL that you want on w3id.org, the URL that you want to redirect to, and the HTTP code that you want to use when redirecting. An administrator will then create the redirect for you.

  • Identifiers.org

    Identifiers.org is a Resolution Service provides consistent access to life science data using Compact Uniform Resource Identifiers, hosted by the EBI provides a resolution service, both as a web form and through the URL pattern 1. Compact Identifiers consist of an assigned, unique prefix and a local provider designated accession number (prefix:accession). The resolving location of Compact Identifiers is determined using information that is stored in the Identifiers.org Registry. Datasets can register their namespace prefix together with their identifier pattern. The service can then be used in the same way as the DOI resolution service. So for the UniProt page about BRCA1, we can resolve the CURIE [uniprot:P38938] using Identifiers.org. This means that the URL https://identifiers.org/uniprot:P38938 resolves to the UniProt page https://www.uniprot.org/uniprot/P38938.

  • Name2Things

    Name2Things (N2T) is a Resolution Service, maintained at the California Digital Library (CDL) within the University of California (UC) Office of the President. CDL supports electronic library services for ten UC campuses and affiliated law schools, medical centers, and national laboratories, as well as hundreds of museums, herbaria, botanical gardens, etc. Similar to URL shorteners like bit.ly, N2T serves content indirectly. N2T can store more than one “target” (forwarding link) for an identifier, as well as any kind or amount of metadata (descriptive information) N2T.net is also a “meta-resolver”. In collaboration with identifiers.org, it recognizes over 600 well-known identifier types and knows where their respective servers are. Failing to find forwarding information for a specific individual identifier, it uses the identifier’s type to look for an overall target rule.

  • Bioregistry

    Bioregistry is a Resolution Service, developed in a GitHub repository. Like Identifiers.org it has a registry, but also a registry of registries, and it imports data from Identifiers.org and Name-to-Thing but extends beyond identifiers for things but also supports, for example, ontologies. As a community effort, new namespace prefixes and their identifier patterns can be registered via GitHub issues. Compact identifiers are supported and the URL https://bioregistry.io/chebi:138488 resolves to the ChEBI page https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:138488. Bioregistry provides an API to query the registry itself.

1.3.3. PURL stands for Persistent URL

As defined in https://archive.org/services/purl/help, PURL are persistent URL and they provide a permanent http address to access a resource on the web [https://archive.org/services/purl/help]. The PURL service is administered by the Internet Archive. Users can request domains from the service under which to administer and mint persistent url.

1.4. Conclusion

1.5. References

References

1

N. Juty, N. Le Novère, and C. Laibe. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res, 40(Database issue):D580–586, Jan 2012.

1.6. Authors

Authors

Name

ORCID

Affiliation

Type

ELIXIR Node

Contribution

Philippe Rocca-Serra

University of Oxford

Writing - Original Draft
Infrastructure 2. Building a catalogue of datasets