Representing the Immune Epitope Database in OWL (ISMB Bio-Ont SIG 2009)

Jason Greenbaum et al. (Bjoern Peters presenting)

When a virus infects a mouse, the pieces of the virus end up on the cell surface where they are accessible to the immune cells.  Epitopes are the things that are recognized on the cell surface in this case. It is a role of a material entity that is realized when it binds to an adaptive immune receptor. Here, context is key: What immune receptor for the epitope? What host? What happened to the host previously? And remember, instances are not universals.

The goal of the IEDB is to catalogue and make accessible immune-epitope-related information. There are 10 full-time PhD-level curators, with 50,000 epitopes. They’ve completed about 99% of infectious disease and 90% allergies – next are autoimmune responses. This leads to large amounts of complex data which we have to deal with.

The IEDB development cycle is ontology development -> db (re)design -> content curation and back again. ONTIE = Ontology of Immune Epitopes at http://ontology.iedb.org. Ontie is intended to be superceded as other ontologies take up the terms present there. They’re database tables are aligned with the ontology, which relies very heavily on OBI. This is a method of “ontologic normalization” of the database. Data migration and consistency enforced by rule-based validation engine.

This alignment of ontology to db happened so we could have an easy db export to OWL.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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