The MIRIAM Registry , a by-product of the MIRIAM Guidelines, is a database of namespaces and associated information that is used in the creation of uniform resource identifiers . 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 of SBML Level 2 Version 2 (and above).
15-482: 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
30-569: 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 . In particular, databases such as BioModels Database 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
45-491: Is a registered project of the MIBBI (minimum information for biological and biomedical investigations). The MIRIAM Guidelines are composed of three parts, reference correspondence , attribution annotation , and external resource annotation , each of which deals with a different aspect of information that should be included within a model. 'Reference correspondence' deals with the basic reference information needed to make use of
60-490: Is used by several worldwide projects such as BioModels Database , SABIO-RK, COPASI, A more thorough listing can be found on the website. 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). It is also a resolving system that relies on collections listed in
75-507: The MIRIAM Registry to provide direct access to different instances of the identified records. 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 . The Identifiers.org resolving system is built upon the information stored in
90-552: The MIRIAM Registry , which is a database that stores namespaces assigned to commonly used data collections (databases and ontologies ) 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 Interoperability Platform . An Identifiers.org URI is formed of several parts: The system allows
105-762: The EBI RDF platform Identifiers.org is part of the Interoperability platform of the European life-sciences Infrastructure for biological Information . Identifiers.org URIs have been developed since 2011 as a resolvable version of the MIRIAM identifiers, developed since 2005, which were of a URN form, and not directly resolvable. Identifiers.org URIs are similar to PURLs , albeit providing alternative resolutions for collections with several instances. They are also similar to DOIs , but provide human readable collection names, and re-use
120-656: 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 source code for the entire project, including supporting features, is available from SourceForge.net . The MIRIAM Registry
135-484: 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 . To enable efficient use of
150-415: The core information may be supplemented with other data. 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. 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. Using
165-427: The model, detailing on a gross level the format of the model file, and its instantiability for simulation purposes. 'Attribution annotation' deals with the attribution information that must be embedded within the model file. 'External resource annotation' defines the manner in which annotations should be constructed. Those annotations contain references to entities in databases, classifications, ontologies, etc. One of
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#1732886803127180-418: 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: In this example,
195-401: The purposes of annotation is to allow unambiguous identification of the various model components. More information about the existing qualifiers is available from BioModels.net. So far, annotation is mainly a manual work, so to ensure their longevity the usage of perennial URIs is necessary. It was recognised that the generation of valid and unique URIs for annotation required the creation of
210-464: The record identifier assigned by the data provider. MIRIAM MIRIAM (Minimum Information Required In The Annotation of Models ) is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates
225-611: The sharing of software and service infrastructures built upon modeling activities. The idea of "a set of good practices" including "some obligatory metadata" was first proposed by Nicolas Le Novère in October 2004 as part of a discussion to develop a common database of models in systems biology (which led to the creation of BioModels Database ). These initial ideas were further refined at a meeting in Heidelberg, during ICSB 2004, with representatives from many other interested groups. MIRIAM
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