GtoImmuPdb: technical update Feb 2016

The Guide to Immunopharmacology (GtoImmuPdb) held it’s first grant-holders meeting in London on 7th January. The meeting discussed and set-out plans for the initial phase of the project. This included discussion on new data types to include, form and content of a new homepage, which ontologies to utilise and how new data content would be generated.

An earlier synopsis of the project can be found in our previous blog post.

Some key technical decisions have been made:

  • The shortened name for the database will be GtoImmuPdb.
  • The GtoImmPdb will have its own homepage. This portal will provide an immunological perspective onto the database.
  • GtoImmPdb will use same database as GtoPdb. It will be extended to integrate GtoImmPdb data.
  • Processes/pathways – to provide a way to search data via biological processes we will be utilising target annotations to terms in the Gene Ontology (GO). There will be mapped to a simplified, GtoImmPdb specific, process list.
  • Cell Types – to provide a way to search data via cell-types we will be using cell-type terminology from the Cell Ontology.

Development progress

Methods to include GO biological process terms in the database have been generated. These selected all terms under 2 parent terms, immune system process (GO:0002376) and inflammatory response (GO:0006954), resulting in a total of 1,953 terms. All these terms, plus their parent-child relationships will be included in the database and support curation and querying.

To capture an initial set of annotations of these terms against targets in GtoPdb the advanced search of UniProt was utilised. Through UniProt, targets were selected that were annotated to the subset of GO terms and also cross-referenced in GtoPdb. This gave a total of 1,364 annotation to 317 targets.

Our next steps will be to integrate this data with our front-end search mechanisms and provide access to this search via the a new GtoImmPdb portal.

Submission Tool

Minor addition to the submission tool have been made to allow curators to flag targets and ligands in GtoPdb as being relevant to GtoImmuPdb. General comments fields also add for GtoImmuPdb relevant targets.

Other planned tasks

  • Domain name for portal will be guidetoimmunopharmacology.org (not yet running)
  • Alpha-version of homepage to be in place by April meeting (with limited function)
  • Extend GO annotation to ligands (e.g. cytokines)

Links

CiteULike Group – Immunopharmacology related to GtoImmuPdb

This project is supported by a 3-year grant awarded to Professor Jamie Davies at the University of Edinburgh by the Wellcome Trust (WT).

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Posted in Guide to Immunopharmacology, Technical
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