References of "Birney, E"
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See detailFinding and sharing: new approaches to registries of databases and services for the biomedical sciences
Smedley, D.; Schofield, P.; Chen, C. K. et al

in Database: the Journal of Biological Databases and Curation (2010), Jul 6

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their ... [more ▼]

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf. [less ▲]

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See detailINTERPRO
Apweiler, R.; Attwood, T. K.; Bairoch, A. et al

in Bioinformatics (2000)

InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ... [more ▼]

InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc.. Merged and individual entries (i.e., those that have no counterpart in the companion resources) are assigned unique accession numbers. The first release of InterPro contains around 2,400 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 4,300 regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 370,000 hits in total). The database is accessible for text-based searches at http://www.ebi.ac.uk/ interpro/. [less ▲]

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