Meetings & Conferences Semantics and Ontologies Standards

Modelling biomedical experimental processes with OBI (ISMB Bio-Ont SIG 2009)

Larisa Soldatova et al.

OBI was created to meet the need for a standardised vocabulary for experiments that can be shared across many experiment types. OBI is community driven, with over 19 communities participating. It is a candidate OBO Foundry ontology, is complementary to existing bio-ontologies, and reuses existing ontologies where possible. It uses various ULOs for interoperability: BFO, RO, and IAO. material_entity class was introduced into BFO on request of the OBI developers, for instance.

OBI uses relations from BFO, RO, and IAO as well as creating relations specific to OBI. OBI relations could be merged with other relations ontologies in future. They try to have as few relations as possible. Two use cases were outlined in this paper. Firstly, analyte measuring assay, where you draw blood from a mouse and determine the concentration of glucose in it. Use case 2 was a vaccine protection study, where you measure how efficiently a vaccine induces protection against virulent pathogen infection in vivo.

Allyson’s thoughts: Disclosure: I am involved in the development of OBI.

FriendFeed Discussion:

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!

By Allyson Lister

Find me at and

Leave a Reply

Please log in using one of these methods to post your comment: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s