MIRIAM Registry

MIRIAM Registry are a set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models.

The core of MIRIAM Registry is a catalogue of data collections (corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP).

MIRIAM Registry is developed and maintained under the BioModels.net initiative, and are free for use by all.

Quick links

Registry

MIRIAM Registry is composed of four components: a database, some Web Services, a Java library and this web application.

Database

The core of the system is a MySQL database. It allows us to store the data collections (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns.

Each entry contains a diverse set of details about the data collection: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data collection can be associated with several resources (or physical locations).

Web Services

Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve URIs, but also to generate appropriate ones, based upon the provision of a data collection name and an accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try.

Java Library

A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it.

Web Application

A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.

Exports of the whole content of the database and submission of new data collection are available. Documentation relating to either the Registry or the Guidelines are available in the Documents section.

The Web Services demo enables users to perform queries such as the retrieval of valid physical locations (URLs) corresponding to a given URI, or generating a valid MIRIAM URI given a data collection name and an accession identifier. These results are immediately displayed in the browser, in a dynamic way, using Asynchronous JavaScript and XML (AJAX).

Publications

• Juty N., Le Novère N., Laibe C. (2012)

  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.

  Nucleic Acids Research, 40 (D1): D580-D586

  [Medline] [Oxford Journals]

• Li C., Courtot M., Le Novère N., Laibe C. (2009)

  BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

  Brief. Bioinformatics

  [Medline]

• Laibe C., Le Novère N. (2007)

  MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.

  BMC Systems Biology, 1: 58

  [Medline] [OpenAccess]

• Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005)

  Minimum Information Required In the Annotation of Models (MIRIAM)

  Nature Biotechnology, 23: 1509-1515.

  [Medline] [DOI]