[Ontology-editors] [OBO-Edit Working Group] non-critical warnings on GO file

[Jane Lomax]

I'd love to turn my verification checker back on but it hasn't been 
working properly for a while now. I guess others might be having the 
same problem which is why the file is accumulating errors.

The problem is that it doesn't see all those words that Jen added to the 
dictionary so I get zillions of warnings when I run it. I have submitted 
a SF item: 
https://sourceforge.net/tracker/?func=detail&aid=2784937&group_id=36855&atid=418257

Jane

Karen Christie wrote:
> Hi GO ontology editors,
>
> I did an edit today and noticed that there were 26 non-critical warnings. 
> I went through all of them to see what they were. There are a couple types 
> of warnings where we should probably change what the verification check 
> looks for (which is why I cc'd the OEWG on this), but there were a bunch 
> of user errors which people should have fixed before they committed.
>
> In the process of releasing OE2, Jen did a lot of work to clean up the 
> hundreds of these that we used to have, so that people could actually use 
> the verification checks to catch problems they introduced. But if we start 
> collecting a whole bunch of these again, then everyone will ignore the 
> verification checks again and we'll be back to where we were, and 
> eventually someone will have to go through and clean them up again.
>
> I think it would be best if we can keep GO "clean" of these types of 
> problems so that the verification checks are useful to each person as they 
> save, so they can use it to fix their own problems BEFORE they commit 
> them.
>
> Below is what I found in going through the warnings. Maybe we can talk 
> about appropriate procedure to avoid accumulating these warnings, and 
> perhaps the OEWG can talk about whether two of the checks are picking up 
> things they shouldn't be.
>
> thanks,
>
> -Karen
>
>
> 1. User Errors: Almost half were simple typos, e.g. "anaphasep" instead of 
> "anaphase.", internal newlines within definitions, or missing final 
> periods from definitions, the latter often occurring in defs from EC or 
> MetaCyc.
>
> It seems that people should NOT be committing the ontology with these 
> types of errors, they should fix them before they commit so that we con't 
> accumulate scads of them.
>
> There was also one url in a definition. By comparison with the other urls 
> that the verificatino check flagged, it seems that perhaps this should be 
> in the comment, not the definition?
>
>
> 2. Verification Check issues:
>
> Then, there were two other types of warnings, where it looks like maybe 
> the checks are picking up things that should be allowed.
>
> Repeated word - There were four "repeated words" reported where it ignored 
> the fact that there was punctuation in between the two instances of the 
> repeated word. While two of these might be less than gramatically ideal to 
> use the same word twice in close succession, none of these are illegal, 
> and two of them there is probably no other way to phrase it. Perhaps it 
> should not report repeated words when there is punctuation in between.
>
> Issue with sentence boundaries - Most of the rest of the warnings were 
> about periods with no whitespace after them, resulting in two warnings:
> - sentences that do not start with a capital
> - sentences that are not separated by whitespace.
>
> However, none of the flagged issues were supposed to be sentences. Most 
> were urls in comment fields. A couple others were names or formulas that 
> contained periods where there was no whitespace after the period. Perhaps 
> we should not look for periods followed by a non-whitespace character.
>
>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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