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Create an extendable set of lint-like checks #14

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ShahimEssaid opened this issue Feb 2, 2015 · 2 comments
Closed

Create an extendable set of lint-like checks #14

ShahimEssaid opened this issue Feb 2, 2015 · 2 comments
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@ShahimEssaid
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From HDie...@lbl.gov on September 19, 2011 16:45:05

Create code for the verification of ontologies.

In addition to being part of the release process, they can be called by GOLD to avoid opaque database errors

TODO

  1. Decide on how 'extendable' is implemented.
  2. What and when should be verified?
  3. How should be verified (on syntax level and/or with a reasoner)

Initial problem: Incomplete/self-references in definitions

[Term]
id: GO:0090388 ! phagosome-lysosome docking involved in apoptotic cell clearance
intersection_of: GO:0090384 ! phagosome-lysosome docking
intersection_of: part_of GO:0043277 ! apoptotic cell clearance

Original issue: http://code.google.com/p/owltools/issues/detail?id=14
@ShahimEssaid
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From HDie...@lbl.gov on September 22, 2011 13:16:50

added framework to oort to run checks on an ontology during release. Use class references, annotations and reflections to identify checks.

Checks are run at three stages in the release process (after loading, after mireot, and after reasoning).

TODO: add checks, currently there are only empty checks for demonstration purposes.

Status: Started

@ShahimEssaid
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From HDie...@lbl.gov on September 18, 2012 15:29:12

checks are now in use, e.g. cycle checks over is_a

Status: Fixed

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