The 4th alpha-release (v4.0) of the Guide to IMMUNOPHARMACOLOGY was released on 23rd March 2017. This blog post summarises some of the main features of the release and other developments as we moved toward our first public, beta-release in Spring 2017
An early synopsis of the project can be found in this blog post. You can also review our previous technical blogs on GtoImmPdb.
Alpha-Release v4.0 Portal
The disease panel on the portal is now active (Fig. 1). This contains two links, which link to different views of the Immuno Disease List page.
The Immuno Disease List pages provide an overview of the disease-target and disease-ligand associations, curated in the database specifically for GtoImmuPdb
Alpha-Release v4.0 Navigation
In conjunction with adding the Immuno Disease List pages we have extended the menu-bar navigation to contain a Disease menu. This holds two sub-menu items, one points to the disease list associations to targets and one to the disease list associations to ligands.
Disease List Page
The disease list page is designed to display all disease associations curated as part of the GtoImmuPdb. One single page, it is divided into two views, one showing disease associations to targets in the database and the other showing disease associations to ligands (Fig. 2).
Users can switch between the two views (Targets or Ligands) using a tab at the top of the page.
The format of the list of disease associations is similar for both targets and ligands. Both show one section or row per disease. Along with the disease name any external references to other disease resources (OMIM, Disease Ontology and Orphanet) are shown.
Next to each disease name are the total number of either targets or ligands associated in GtoImmuPdb to that disease. By default, the full details of the target or ligand associations are hidden. These can be displayed by clicking the ‘display all ….’ link.
At the top of the page are two toggle buttons that can be used to show or hide all the associations for all disease, if users so wish.
For targets, when the associations are displayed they show the name of the target and curated comments about the association. It also lists any ligands for which that target is a primary target and highlights if the ligand is an approved drug.
For ligands, it shows the name of the ligand, comments and any literature references for the association.
The ranking of search results has been developed to apply a weighting to targets and ligands that are returned from a search that are consider of greater immunological relevance. The weighting is only applied when searching from a GtoImmuPdb page, not from the standard GtoPdb pages.
The criteria used to determine the immune-relevancy (and it’s weighting) of a given target or ligand is based on the amount of immunological data curated against it. For example, targets that have process, cell type and disease data annotated against them will rank higher than targets with only process data. The weighting is applied in addition to existing search weightings – so exact matches (to target or ligand name for example) will still score highest. We will be refining this relevancy scoring during testing, both in alpha and beta releases.
Cell Type Associations – Definitions
We have extended the submission tool and database to better capture and store definitions of cell type categories. This enable reference and ligands to be tagged in the definition text. We have also further developed the cell type list page to display these definitions at the top of the table (Fig. 3) – with the ability to toggle 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).