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Robert Hoehndorf
Talk: MIREOT: Minimal information to reference external ontology terms: Melanie Courtot
background: the OBI project, for description of investigations - Robert Hoehndorf
Many material entities in OBI are already described in other ontologies - Robert Hoehndorf
OBI uses a long list of other ontologies - Robert Hoehndorf
Challenges for import: large overhear: using large ontologies is problematic; true alignment: ontologies constructed using a different design, or not using BFO prevents full integration; fluid development of ontologies hinders integration - Robert Hoehndorf
Possibl solutions: create own terms and reference others; generate and import modules; import whole resources - Robert Hoehndorf
Module is a subset of an external ontology, containing classes and axioms, allowing original reasoning; problem to get the modules - Robert Hoehndorf
observation: terms in obo foundry ontologies stand on their own, if their meaning changes they are deprecated - Robert Hoehndorf
proposal: only import classes that are needed - Robert Hoehndorf
Pro: solves problems, Con: lose complete inference - Robert Hoehndorf
implementation: figure out how to automate as much as possible - Robert Hoehndorf
need to define minimal information: URI of class, URI of source ontology, position in ontology to put the class in - Robert Hoehndorf
additional information: label, definition, other annotations, superclasses - Robert Hoehndorf
step 1: import the term: Minimal info: URI of term, URI of source, superclass in target ontology - Robert Hoehndorf
Summary: works well :) - Robert Hoehndorf
Slides from David's tutorial has info on extracting modules from obo format ontologies: - Chris Mungall
Slides from the MIREOT talk available at: - Melanie
I believe you are also supposed to upload them to the Nature Preceedings website. - Robert Hoehndorf
oh. I thought this was for the short papers themselves, and that the ICBO organizers would do it? - Melanie
love the OBI/FMA slide - Chris Mungall
credit where credit is due, this "OBI scared" slide was an idea from James (@ebi) - thanks Mister Maloneeee :) - Melanie