Development of the Guide to Immunopharmacology (GtoImmuPdb) continues and this is an update of progress since our last update in February 2016. Since then, the GtoImmuPdb April Meeting was held in Edinburgh, where a detailed update on the status of GtoImmuPdb was delivered and discussions held about key points to focus over the next phase of development.
As a reminder, a early synopsis of the project can be found in this blog post.
Refinements have been added to the way GO biological process, of relevance to immunology, are identified and extracted from OBO files. The OBO-Edit export omitted some terms where ancestral relationship involved combinations of being ‘part-of’ something that in-turn ‘regulates’ a parent term that falls under either immune system process (GO:0002376) or inflammatory response (GO:0006954). As of 19 May 2016 the database holds 1,957 GO process terms. There are 393 targets (with cross-references to UniProt) annotated to these terms, with the total number of annotations being 1,379.
Extensions have been made to the web-application search mechanism to incorporate the high-level GtoImmuPdb process categories. These categories are: Immune system development and differentiation; Proliferation and cell death; Production of signals and mediators; Regulation and responses to signals, Cell-mediated immunity; Inflammation. The search links the GtoImmuPdb process categories to targets and is currently functional on our test site (restricted access). This needs to be extended to include GO process term, GO IDs and GtoImmuPdb process definitions.
Parsers have been developed to capture and populate cell type data from the Cell Ontology. The database now holds the cell types from the ontology, plus relationships and associations to GO processes (which will be helpful in cross-referencing). Our next steps are to determine high-level, immuno-relevant cell type classes for use on the site. A potential source are categories similar to the Immunological Genome Project; B-cells, γδT-cells, αβT-cells, T-cell activation, NK cells, myeloid cells, stromal cells, dendritic cells & stem cells. The database also needs extended further to capture target to cell-type relationships and develop associated submission tool (for editing/curation) and web-application (to surface the data to users) extensions.
An alpha-version of the GtoImmuPdb portal has been developed (restricted access). The layout aims to compliment the GtoPdb site, whilst ensuring it is distinct through styles, logos and branding.
The targets box has been developed to link to lists of targets and automatically highlight target families where there is relevance to GtoImmuPdb (this is defined by the curators by flagging targets as relevant). A toggle-button enables users to switch on/off the immuno-view. The ability to toggle the view is likely be extend to other pages. The next step will be to extend the detailed target view to display GtoImmuPdb relevant data, in the first instance general comments and process associations.
Extensions have been made to enable curators to view, edit and manage associations between the high-level GtoImmuPdb Process categories and GO process terms. It also allows annotation of targets to the high-level process terms. This includes adaptations to the main webapp code that will be essential in ‘surfacing’ the process data on target detail pages. Future work will include extending to edit/manage cell type data and to enable interactions to be curated as relevant 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).