GtoImmuPdb: technical update December 2016

Our final technical update for 2016 covers our v2.0 alpha-release, presentation at Pharmacology 2016 and future plans.

An early synopsis of the project can be found in this blog post. Previous technical blogs are available for February, MayAugustSeptember & November 2016.

Development Progress

Alpha-Release v2.0

Menu-bars

The menu-bars have been further development to include Processes and Cell Types. This basically extends the menu bar to have direct links to the new data types in GtoImmuPdb. The About and Resources menu items have been modified to make them specific to GtoImmuPdb. The ultimate aim of these developments is to make navigation through GtoImmuPdb user-friendly and logical. This will continue to be developed as we gather feedback. 

Documentation and Tutorial

The documentation and user-guide tutorial were both updated upon v2.0 release.

Ligand List pages

We have developed the ligand list pages (which are linked to from the portal ‘ligand’ panel) to include an immuno tab that when selected lists all ligands tagged in the database as being included in GtoImmuPdb. The page now has a toggle button to switch between the GtoImmuPdb and GtoPdb views. We have also put in place a new ‘immuno ligand’ icon, to be displayed in the table with the other icons when the ligand has been tagged in GtoImmuPdb.

Ligand pages

We have extended the ligand pages to contain a new ‘Immunopharmacology’ section (with in the Summary tab). This contains any specific immunopharmacology comments specific to the ligand.

Pharmacology 2016

During December it was an privlege to be able to attend the BPS Pharmacology 2016. We not only presented a poster describing the Guide to IMMUNOPHARMACOLOGY, but were also given the opportunity to present this as a 2-miunute, one slide, flash poster presentation.  The session was well attended and both the poster and presentation well received.

View poster on slideshare 

View presentation on slideshare

Other Development and Next Steps

The submission tool has been extended to incorporate ligand to disease associations. This is one of the first steps to fully incorporating disease association into GtoImmuPdb. These developments accompany additions to the database schema which now contains new tables to store these associations. Our expectation is to extend the schema and submission tool to also capture target-disease associations.

There are some disease terms in the database already, mostly linked to OMIM, the Disease Ontology or Orphanet. While these data resource may be adequate for annotating and describing immunological diseases and related diseases, we are exploring whether to include ICD disease classifications. Our aim is to have some GtoImmuPdb disease association in place prior to the beta-release in Spring 2017, but we are keeping this under-review.

In the next couple of months we will also be improving the current display of comments and references linked to new data types (processes and cell-types).  We will also be incorporating references to the ligands tagged in GtoImmuPdb, and surfacing their display.

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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