identifiers

Data interoperability and standards

ssuhr@ebi.ac.uk — Fri, 01 May 2015 15:25:51 +0000

Standards and identifiers

Manage cross-references between digital entities with different identifiers

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 09:37:55 +0000

myEquivalents is a system to manage cross-references between digital entities with different identifiers. It can help organisations maintaining data to manage their cross-references and aids finding multiple descriptions of the same biomedical entities.

Making sure standards are fit for purpose

ssuhr@ebi.ac.uk — Thu, 05 Feb 2015 09:33:06 +0000

The Metadata Model and Mapping Registry (MMMR) enables researchers to find a representative collection of meta-data artefacts (models, formats, minimal information guidelines, biobank data dictionaries, detailed clinical/research models) of use to the biomedical science community.

Life science data interoperability resources kick off collaboration

ssuhr@ebi.ac.uk — Fri, 03 Oct 2014 11:15:50 +0000

In the life sciences, users are faced with a choice of multiple resources to facilitate and promote the use of standards, policies, models, identifiers, databases, tools, services, and ontologies. Some of these resources are well established while others are less mature and, although the scope of each is quite specific, there is potential overlap.

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standards

identifiers

integration

collaboration

Standards and data harmonization: prerequisites to data integration

ssuhr@ebi.ac.uk — Fri, 04 Jul 2014 10:09:28 +0000

BioMedBridges workshop brings domain experts together

The workshop, hosted on 24-25 June by VUMC in Amsterdam, was attended by project partners and invited external experts from CDISC, BioSharing.org and identifiers.org. The aims of the workshop were to explore several aspects of standardisation, primarily:

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standards

identifiers

workshops

Online Dictionary of common molecular identifiers of the biomedical sciences research infrastructures

ssuhr@ebi.ac.uk — Fri, 13 Apr 2012 16:08:38 +0000

The provision and use of common and unambiguous identifiers for bio-molecules such as genes, proteins and bioactive compounds is key to supporting the information flow from basic science, model organism biology, bioinformatics and structural biology through to translational research and clinical care. The ESFRI BMS project partners have determined an interoperable ‘Dictionary’ of identifier types (Appendix 1) used in this project, and within clinical/translational research more broadly. At the request of the scientific advisory board, we have also expanded our WP3.1 activities to include the development of best practices documentation for identifiers (Appendix 2-1) which was based on our identifiers landscape analysis (Appendix 2-2). Part of the expanded work on identifiers includes a shortlist of the most relevant Identifier Resolution and Conversion Tools (Appendix 2-3); these have also been registered with the BioMedBridges Tools and Data Services Registry. Further documentation was developed to guide the selection of ontologies (Appendix 2-4) to support cross-domain data integration. Where no authoritative identifier standard exists, we have worked with the respective community to determine one that would support the activities of WP4 and BioMedBridges use cases. Relevant identifiers include those for samples (Task 2), small molecules, macromolecular assemblies, genes, proteins, drugs, diseases and phenotypes.