The MIRIAM Registry, a by-product of the
MIRIAM
Miriam ( he, מִרְיָם ''Mīryām'', 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 Tor ...
Guidelines, is a database of namespaces and associated information that is used in the creation of
uniform resource identifiers
A Uniform Resource Identifier (URI) is a unique sequence of characters that identifies a logical or physical resource used by web technologies. URIs may be used to identify anything, including real-world objects, such as people and places, conc ...
. It contains the set of community-approved namespaces for databases and resources serving, primarily, the biological sciences domain. These shared namespaces, when combined with 'data collection' identifiers, can be used to create globally unique identifiers for knowledge held in data repositories. For more information on the use of URIs to annotate models, see the specification o
SBML Level 2 Version 2(and above).
A 'data collection' is defined as a set of data which is generated by a provider. A 'resource' is defined as a distributor of that data. Such a description allows numerous resources to be associated with a single collection, allowing accurate representation of how biological information is available on the World Wide Web; often the same information, from a single data collection, may be mirrored by different resources, or the core information may be supplemented with other data.
* data collection name: Gene Ontology
* data collection identifier: MIR:00000022
* data collection synonyms: GO
* data collection identifier pattern: ^GO:\d$
* data collection namespace: urn:miriam:obo.go
* data collection 'Root URL': http://identifiers.org/obo.go/
* data collection 'Root URN': urn:miriam:obo.go:
* collection resources:
** resource #1
*** resource identifier: MIR:00100012
*** resource location website: http://www.ebi.ac.uk/ego/
*** resource access URL (tokenised): http://www.ebi.ac.uk/ego/DisplayGoTerm?selected=$1
*** resource Description: QuickGO (Gene Ontology browser)
*** resource institution: European Bioinformatics Institute, United Kingdom
** resource #2
***
..
The MIRIAM Registry is a curated resource, which is freely available and open to all. Submissions for new collections can be made through the website.
Identifiers using the MIRIAM system
The MIRIAM Guidelines require the use of uniform resource identifiers in the annotation of model components. These are created using the shared list of namespaces defined in the MIRIAM Registry.
MIRIAM URIs
Using the namespaces defined in the MIRIAM Registry, it is possible to create identifiers in both a URN and a URL forms. This requires a unique collection-specific identifier, as well as a namespace to globally constrain the information space. Both the namespace and the root of each URI form are given for each data collection in the Registry. Both forms are derived from the same namespace. For example:
* urn form:
urn:miriam:pubmed:16333295
* url form:
http://identifiers.org/pubmed/16333295
In this example, the collection-specific identifier is 16333295, and the namespace is pubmed.
The URN form of identifiers requires the use of Web Services or programmatic means to access the referenced record. This means that one cannot simply put the URN form into a browser window and arrive at the referenced information. The URL form is directly resolvable, and relies on a resolving layer provided by
Identifiers.org
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). Identifiers.org is also a resolving system, that re ...
.
Supporting features and availability
To enable efficient use of the MIRIAM Registry and the rapid adoption of the annotation scheme, a number of supporting features are provided.
These include
Web Services, a website interface to access the Registry itself, and a Java library
The MIRIAM Registry is developed by the Proteomics Services Team at the
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Well ...
. The source code for the entire project, including supporting features, is available from
SourceForge.net
SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirroring ...
.
The MIRIAM Registry is used by several worldwide projects 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 ...
,
SABIO-RK, COPASI, A more thorough listing can be found on the website.
See also
*
Minimum information standards
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the ...
*
MIRIAM
Miriam ( he, מִרְיָם ''Mīryām'', 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 Tor ...
*
Identifiers.org
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). Identifiers.org is also a resolving system, that re ...
*
Metadata standards
A metadata standard is a requirement which is intended to establish a common understanding of the meaning or semantics of the data, to ensure correct and proper use and interpretation of the data by its owners and users. To achieve this common unde ...
*
Computational systems biology
*
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 ...
*
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 use ...
*
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models re ...
References
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Bioinformatics
Science and technology in Cambridgeshire
South Cambridgeshire District
Systems biology