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28:. 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
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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
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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
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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
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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.
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Li, C; Donizelli, M; Rodriguez, N; Dharuri, H; Endler, L; Chelliah, V; Li, L; He, E; Henry, A; Stefan, Melanie I; Snoep, Jacky L; Hucka, Michael; Le Novère, Nicolas; Laibe, Camille (2010).
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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.
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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
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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.
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given for each data collection in the
Registry. Both forms are derived from the same namespace. For example:
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432:"BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models"
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Guidelines, is a database of namespaces and associated information that is used in the creation of
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357:"BioModels.net Web Services, a free and integrated toolkit for computational modelling software"
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In this example, the collection-specific identifier is 16333295, and the namespace is pubmed.
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285:"MIRIAM Resources: Tools to generate and resolve robust cross-references in Systems Biology"
183:. The source code for the entire project, including supporting features, is available from
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405:"MIRIAM | Free Science & Engineering software downloads at SourceForge.net"
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198:, SABIO-RK, COPASI, A more thorough listing can be found on the website.
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The MIRIAM Registry is developed by the
Proteomics Services Team at the
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resource institution: European
Bioinformatics Institute, United Kingdom
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Li, C.; Courtot, M.; Le Novere, N.; Laibe, C. (2009).
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http://www.ebi.ac.uk/ego/DisplayGoTerm?selected=$ 1
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43:Example of an entry stored in the MIRIAM Registry
504:"SABIO-Reaction Kinetics Database Virtual Cell"
57:data collection identifier pattern: ^GO:\d{7}$
194:is used by several worldwide projects such as
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283:Laibe, Camille; Le Novère, Nicolas (2007).
525:"Complex Pathway Simulator and SBMLeditor"
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578:Science and technology in Cambridgeshire
51:data collection identifier: MIR:00000022
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150:http://identifiers.org/pubmed/16333295
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168:Supporting features and availability
122:Identifiers using the MIRIAM system
48:data collection name: Gene Ontology
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420:MIRIAM project on SourceForge.net
181:European Bioinformatics Institute
94:resource access URL (tokenised):
85:resource identifier: MIR:00100012
263:"New Collection Submission page"
68:http://identifiers.org/obo.go/
1:
583:South Cambridgeshire District
228:Computational systems biology
208:Minimum information standards
482:"BioModels Database Website"
72:data collection 'Root URN':
66:data collection 'Root URL':
54:data collection synonyms: GO
26:uniform resource identifiers
361:Briefings in Bioinformatics
88:resource location website:
60:data collection namespace:
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335:"MIRIAM Resources Website"
142:urn:miriam:pubmed:16333295
90:http://www.ebi.ac.uk/ego/
506:. Sabio.villa-bosch.de
449:10.1186/1752-0509-4-92
302:10.1186/1752-0509-1-58
79:collection resources:
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30:SBML Level 2 Version 2
20:, a by-product of the
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436:BMC Systems Biology
289:BMC Systems Biology
373:10.1093/bib/bbp056
233:BioModels Database
223:Metadata standards
196:BioModels Database
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74:urn:miriam:obo.go
62:urn:miriam:obo.go
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18:MIRIAM Registry
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411:on 2012-05-10
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32:(and above).
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550:. Retrieved
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529:. Retrieved
527:. Copasi.org
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508:. Retrieved
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486:. Retrieved
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413:. Retrieved
409:the original
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367:(3): 270–7.
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267:. Retrieved
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174:Web Services
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160:provided by
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108:resource #2
82:resource #1
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548:. Ebi.ac.uk
484:. Ebi.ac.uk
337:. Ebi.ac.uk
265:. Ebi.ac.uk
130:MIRIAM URIs
567:Categories
552:2012-10-09
531:2012-10-09
510:2012-10-09
488:2012-10-09
415:2012-10-23
341:2012-10-09
269:2012-10-09
249:References
147:url form:
139:urn form:
468:20587024
391:19939940
321:18078503
202:See also
459:2909940
382:2913671
312:2259379
502:SDBV.
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442:: 92.
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295:: 58.
243:CellML
213:MIRIAM
22:MIRIAM
464:PMID
387:PMID
317:PMID
238:SBML
190:The
16:The
454:PMC
444:doi
377:PMC
369:doi
307:PMC
297:doi
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