Identifiers.org is a project providing stable and perennial identifiers for data records used in the Life Sciences. The identifiers are provided in the form of Uniform Resource Identifiers (URIs). It is also a resolving system that relies on collections listed in the MIRIAM Registry to provide direct access to different instances of the identified records.

URIs and resolving system

The Identifiers.org URIs are perennial identifiers, that specify at once the data collection, using the namespaces of the Registry, and the record identifier within the collection in the form of a unique resolvable

URI Uri may refer to: Places * Canton of Uri, a canton in Switzerland * Úri, a village and commune in Hungary * Uri, Iran, a village in East Azerbaijan Province * Uri, Jammu and Kashmir, a town in India * Uri (island), off Malakula Island in V ...

. The Identifiers.org resolving system is built upon the information stored in the MIRIAM Registry, which is a database that stores namespaces assigned to commonly used data collections (databases and

ontologies In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More ...

) for the Life Sciences. It transforms an Identifiers.org URI into the various URLs leading to the various instances of the record identified by the URI. Identifiers.org is part of the

ELIXIR An elixir is a sweet liquid used for medical purposes, to be taken orally and intended to cure one's illness. When used as a dosage form, pharmaceutical preparation, an elixir contains at least one active ingredient designed to be taken orall ...

br>Interoperability Platform

Identifier structure

An Identifiers.org URI is formed of several parts: * Protocol. Identifiers.org URIs are

HTTP HTTP (Hypertext Transfer Protocol) is an application layer protocol in the Internet protocol suite model for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web, wher ...

URIs and start with "http:/" * Data collection. These are namespaces listed in the MIRIAM Registry. For instance "pubmed" for the publication resource

PubMed PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institute ...

, "ec-code" for the

enzyme nomenclature An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as produc ...

and "go" for

gene ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ...

* Record in the collection. For instance "9606" is "3-fluorotoluene" in the collection PubChem, it is "Homo sapiens" in the collection "taxonomy" and it is a social science publication in the collection "pubmed". * Optional: Identifiers.org URIs can be suffixed with parameters, for instance imposing which resource to use for resolving, "profiles" that control the resolver's behaviour etc.

Usage

The system allows a consistent and uniform annotation of datasets. This in turn facilitates data alignment and integration. Identifiers.org URIs are used to encode the metadata in the standard formats of the COMBINE initiative, such as

SBML The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of us ...

. In particular, databases such as

BioModels Database BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scie ...

and Reactome export their data in SBML with cross-references encoded using Identifiers.org URIs. These URIs are also used in various semantic web projects such as Bio2RDF, Open PHACTS and the EBI RDF platformS Jupp, J Malone, J Bolleman, M Brandizi, M Davies, L Garcia, A Gaulton, S Gehant, C Laibe, N Redaschi, SM Wimalaratne, M Martin, N Le Novère, H Parkinson, E Birney, AM Jenkinson (2014) The EBI RDF Platform: Linked Open Data for the Life Sciences. ''Bioinformatics'' Identifiers.org is part of th
Interoperability platform
of the European life-sciences Infrastructure for biological Information.

Comparison with other URI systems

Identifiers.org URIs have been developed since 2011 as a resolvable version of the

MIRIAM Miriam (, lit. ‘rebellion’) is described in the Hebrew Bible as the daughter of Amram and Jochebed, and the older sister of Moses and Aaron. She was a prophetess and first appears in the Book of Exodus. The Torah refers to her as "Miria ...

identifiers, developed since 2005, which were of a URN form, and not directly resolvable. Identifiers.org URIs are similar to

PURL A persistent uniform resource locator (PURL) is a uniform resource locator (URL) (i.e., location-based uniform resource identifier or URI) that is used to URL redirection, redirect to the location of the requested web resource. PURLs redirect HTT ...

s, albeit providing alternative resolutions for collections with several instances. They are also similar to DOIs, but provide human readable collection names, and re-use the record identifier assigned by the data provider.

References

{{Reflist

External links