The focus of development in the last month has been on preparing the GtoImmuPdb portal for alpha-release and building landing-pages for process and cell type association lists.
An early synopsis of the project can be found in this blog post. Previous technical blogs are available for February, May & August 2016.
List pages for process and cell type associations
We have developed landing pages that are reached when clicking on any of the main process or cell type categories in either of the process or cell type panel on the GtoImmuPdb portal (see Figure 1).
Figure 1: Links to process and cell type association lists pages from GtoImmuPdb portal (www.guidetopharmacology.org/immuno)
These pages list the protein targets in the database that are associated with either immunological processes or immune system cell types. In each case, the pages are split, using tabs, to show targets associated with each of the main process or cell type categories. The targets in each list are then separated by their target-class (e.g. GPCRs, ion channel, enzymes etc.). An example of the immuno process association list page is shown in figure 2.
Figure 2: GtoImmuPdb process association list page. Showing targets associated with the ‘proliferation and cell death’ category.
The table for the process associations gives the target name and family, any process association comments and lists Gene Ontology (GO) terms annotated to the target (with ID and evidence code). Two further columns show if the target has been specifically tagged as being in the Guide to IMMUNOPHARMACOLOGY by our curators, with any associated comments.
It is worth a reminder here that we auto-populate the GO annotations from UniProt. Therefore, we will see targets appearing under the process associations that have not been directly curated into GtoImmuPdb by our curators. For the time-being we will continue with the distinction between targets associated to processes (via GO only) and those that our curatorial team have identified as being of immunological relevance, and therefore directly curated as being ‘in GtoImmuPdb’.
The table for the cell type associations (see figure 3) gives the same colums as for process associations. With the exception that it lists Cell Ontology terms with their IDs.
Figure 3: GtoImmuPdb cell type association list page
Work has continued on implementing the site search to incorporate all new columns for process and cell type associations. This includes top-level category names, GO and Cell Ontology terms & definitions and all association comments.
A few fixes have been made to out submission tool to better handle cell type association input.
A new logo has been added to the Guide to IMMUNOPHARMACOLOGY portal. A bespoke design by Dr. Adam Pawson. The menu bar has been adjusted to include a link to the GtoPdb home page. We have also modified some of the links within the menu-bar to keep the GtoImmuPdb focus (for target links).
Our plan is to release the first alpha-version of the Guide to IMMUNOPHARMACOLOGY at the beginning of October.
This will be an internal release on our development site and will be accompanied by detailed release notes and a user guide to navigating the new pages.
This project is supported by a 3-year grant awarded to Professor Jamie Davies at the University of Edinburgh by the Wellcome Trust (WT).