GtoImmuPdb: technical update August 2016

Since our last update in May 2016 the major development extension to the Guide to Immunopharmacology (GtoImmuPdb) has been to incorporate cell type associations and develop the web-application code to display both process and cell type data.

As a reminder, a early synopsis of the project can be found in this blog post and earlier technical updates from February and May.

Development Progress

Cell Type Associations

Previously, we had written a parser to capture and populate cell type data from the Cell Ontology into the database. Since then we have determined a set of 7 high-level, immuno-relevant cell type classes (or categories), against which targets in GtoImmuPdb will be annotated. The 7 classes are as follows:

1: pro-B-lymphocytes, B lymphocytes & Plasma cells [B lymphcytes]
lymphocyte of B lineage CL:0000945
2: T lymphocytes (alpha-beta type) and their immediate progenitors [T lymphocytes (alpha-beta)]
alpha-beta T cell CL:0000789
3: T lymphocytes (gamma-delta type) and their immediate progenitors [T lymphocytes (gamma-delta)]
gamma-delta T cell CL:0000798
4: Natural Killer (NK) cells [NK cells]
natural killer cell CL:0000623
5: Polymorphonuclear leukocytes (neutrophils, eosinophils, basophils) [Polymorphonuclear leukocytes] [Granulocytes]
granulocyte CL:0000094
6: Mononuclear leukocytes (syn: monocytes) (macrophages, dendritic cells, Kupffer cells) [Mononuclear leukocytes]
monocyte CL:0000576
macrophage CL:0000235
dendritic cell CL:0000451
7: Mast cells
mast cell CL:0000097

We have assigned one or more Cell Ontology parent terms to each class. Curators will be able to annotate targets with any child terms of those parents when adding/editing cell type associations. There is also provision for free text comments about the association and the ability to include any references.

Submission Tool

The submission tool has been extended to enable the capture of cell type-target associations and related data. It has also been modified to better capture data relating to process associations (namely to include references).

GtoImmuPdb Portal

subtool_celltypes

Cell type associations form in submission tool

We have continued work on the alpha-version of the GtoImmuPdb portal, and extensions to the main GtoPdb web-application to incorporate and surface GtoImmuPdb data. Previously we had implemented a toggle on target family pages to highlight targets of relevance to GtoImmuPdb. The idea behind this is so that whichever route a user takes to get to a list of targets or target families – the immuno-view can be easily switch on or off.

We have also extended the detailed target pages to display immunopharmacology comments (specific to the target), cell type associations and process associations.

target_detail_2

Cell type and process association data being surface on the detailed target pages.

The layout of the cell type associations contains one section per each high-level cell type class. Within each section all Cell Ontology terms that have been annotated against the target are displayed, alongside comments and references.

close_up_cells

Close-up of Immuno Cell Type Associations section of detailed target page

Similarly, the layout of the process associations has one section per high-level process class, which includes comments and references. it also includes a list of Gene Ontology (GO) Processes that are annotated to the target. These GO annotations are not input by our curators, but picked up from GO and UniProt (auto-curated). We are including the GO evidence code for these annotations.

Please note, all web-app development is only available on our restricted access test site.

Our next steps will be to improve the layout of these sections – potentially collapsing the list of GO and Cell Ontology terms (in some cases the number of terms annotated to a target can be quite high).
We will also be working on extending the code that handles our site search to include all aspects of cell type associations.
We anticipate the full alpha-release to be made in late September/early October 2016.

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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