MIRIAM Resources

MIRIAM Resources are a set of online services created to support MIRIAM Standard.

The core of MIRIAM Resources is a catalogue of data types (these can be 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).

Quick links

Resources

MIRIAM Resources are 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 types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources.

Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type 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). This API permits not only to resolve model annotations, but also to generate the correct URIs based on resource name and accession numbers. You have access to the list of services available, an online demonstration (in order to see with your browser what you can get via the Web Services), and of course, the WSDL.

Java Library

In order to easily communicate with the Web Services, we provide a Java library. The documentation explains where to download it, what are the depedencies 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 types are available. Moreover, access to several documents related to the resources or the standard is possible via the Documents section.

Moreover a demonstration of the Web Services able users to perform queries such as retrieving valid physical locations (URLs) corresponding to a given URI or generating a valid MIRIAM URIs and immediately get the results in a dynamic way, using Asynchronous JavaScript and XML (AJAX).

Publications

• 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]