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geneontology / termgenie

Web-application for pattern-based ontology class generation
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Sanity checks for Freeform TG requests #28

Open hdietze opened 9 years ago

hdietze commented 9 years ago

Original issue 28 created by hdietze on 2013-06-05T16:09:36.000Z:

Hi Heiko,

For freeform TG requests, could you add in a few checks, to ensure:

  1. The definitions end with a fullstop.
  2. Terms don't share exact synonyms (with another TG term or an existing term)
  3. Term definitions don't include extra white-spaces.
  4. Spell-check if possible (there's an OBO-Edit dictionary in the editors directory that could be referred to, if possible?)

Are any of these doable? The minor errors are flagged up in OBO-Edit checks, but would be good if they could be highlighted at the source.

Thank you. Becky

hdietze commented 9 years ago

Comment #1 originally posted by hdietze on 2013-06-06T18:35:33.000Z:

Hello Becky,

1) Added this check for all definition, including free form TermGenie. 2) There should be a check for synonyms, which detects similar ones. We actually had to make less restrictive. Do you have an example, where this did not work? 3) Added this check for all definitions, including free form TermGenie. 4) In theory yes, however there are many practical issues with that. Most of them have to do with configuration and the weird way, OBO-Edit does its spell-check.

hdietze commented 9 years ago

Comment #2 originally posted by hdietze on 2013-06-13T08:52:32.000Z:

Thanks Heiko.

For the shared synonyms (2), I think it was some virus terms where OE detected shared synonyms... I should have noted it down at the time, but I'll keep my eyes peeled for it happening again.

Also, I had a term yesterday (GO:1990121) that made it through the TG freeform checks, but broke the build because it had ocnflicting parents: is_a: GO:0044445 ! cytosolic part is_a: GO:0005667 ! transcription factor complex (has nuclear part parentage). Is this a check that could be added in?

Thank you Heiko! Becky

hdietze commented 9 years ago

Comment #3 originally posted by hdietze on 2013-06-17T17:24:37.000Z:

Hello Becky,

I have created a separate bug report (issue 29) for the disjoint checks in TermGenie. I'll leave this ticket open as a reminder about the exact shared synonym. If/when you find an example to test with, please add that here.

Thank you. Heiko

cmungall commented 8 years ago

coordinate with @balhoff to integrate https://github.com/balhoff/shacl-tests

OR abandon and do all tests downstream