GtoImmuPdb: technical update March 2018 – beta-release v3

We are pleased to announce the third, beta-release of the Wellcome Trust-funded IUPHAR Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb). Since our last release in August 2017 we have implemented developments that include disease summary pages, graphical browsing features and extensions and improvements to the advanced search. This blog-post details the major developments in the v3.0 release. This release coincides with the latest 2018.1 GtoPdb release.

Portal layout (www.guidetoimmunopharmacology.org)

Some minor adjustments have been made to the portal with the social media feed panel switching to the right-hand column, updated news items included and changes to support navigation to the new disease page from the disease panel and from a new ‘Diseases’ menu bar item.

GtoImmuPdb beta v3.0 portal.

Disease associations and display

A major new development has been changes to the way disease associations are presented. Previously, we had listed diseases associated to targets and diseases associated to ligands separately. It made sense to consolidate these into a single list of diseases and then to provide specific disease summary pages where all curated information about a disease could be presented. This work was done in conjunction with the Guide to PHARMACOLOGY (GtoPdb) development, as GtoPdb already contains information on target pathophysiology and mutations relating to specific diseases.

New disease list page. Show alphabetical list of disease, with synonyms and count of associate targets and ligands.

The new disease list page, accessed from the new menu-bar item, lists all diseases with curated data in GtoPdb/GtoImmuPdb. A convenient alphabetical list of diseases, with links to the disease summary pages, synonyms and counts of associated targets and ligands.  Our longer-term aim is to provide several disease categories, but currently only two (selected from a tab at the top) can be viewed; all diseases and immuno disease. The immuno diseases category are diseases that have data curated specifically as part of GtoImmuPdb. These are diseases that are relevant to immunology, and/or are associated to targets and ligands of immunological-relevance.

The disease summery pages have been designed to display all pathophysiology, mutation and immunopharmacology data curated in GtoPdb and GtoImmuPdb in one place. See the disease summary for Psoriasis.

General information about the disease is shown, including synonyms, descriptions, links to external disease resources (OMIM, Orphanet, Disease Ontology) and counts of the total associated targets and ligands, alongside whether there is data of immuno-relevance.

Disease summary page for Psoriasis. Top section give overview of disease, including description, synonyms and links. Counts of associated targets and ligands are shown, along with whether the disease is immune relevant.

The detailed information on each target gives a summary of any curated pathophysiology data, including the role of the target along with information on drugs and their therapeutic use and side effects. If any mutation data is available this is indicated, with links back to the relevant section of the targets detail view page. The target information also shows any specific immunopharmacology comments and ligands for which their is interaction data where the ligand is also associated with the disease.

Detailed target and ligand sections of the disease summary pages (here showing for Psoriasis).

The ligand section is currently populated with data only curated through he GtoImmuPdb project. Included is information on whether the ligand is an approved drug, immunopharmacology comments and clinical use information.

Graphical browsing (Cell types)

GtoImmuPdb has been exploring different ways for users to explore and browse data, one of which is via the use of graphics and images. We took an tree diagram of immune system cell types from Wikimedia Commons and adapted it to show the cell types for which we have data. The image was re-labelled and an image map produced to make it interactive and a way to browse to different data types.

New graphical browsing of cell types implemented in GtoImmuPdb (http://www.guidetoimmunopharmacology.org/GRAC/CelltypesForward)

Advanced Search

The search facility has been extended to cover disease, processes and cell types. This has included ensuring that search on Cell and Gene Ontology terms work by inference. For example a search on ‘cytokine’ will match a GO parent term that contains the word ‘cytokine’ and bring back targets annotated to that term, or any of it’s children.

All immunopharmacology fields (comments, top-level categories, ontology terms, ontology IDs) have now been added to the advanced search for both targets and ligands – so searches can be restricted to these fields.

New immuno feature incorporated into the advanced search

Process Associations – GO evidence display

We have adjusted the display of GO terms in both Process Association to Target pages and the target detailed view pages. On the target detailed view page, the section on process associations only show GO term associated to the target if the have GO evidence other than ‘IEA’  (inferred by electronic annotation).  The IEA evidence is the only evidence used by GO that “is assigned by automated methods, without curatorial judgement”. As such we hide these by default (but users can expand the section to see them). On the process association page, the IEA terms are show, but italicised, to emphasise this difference.

Modifications to show/hide GO associations with IEA evidence.

Help

To reflect the changes made in this release our help pages have been updated (http://www.guidetoimmunopharmacology.org/immuno/immunoHelpPage.jsp), and we intended to follow this up by putting in place in-line pop-up help, help videos and a revised tutorial.

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