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

[Alexander Diehl]

Have you tried running OE2 with a newly generated set of preference 
files, rather than copying over your preferences?

-- Alex


Jennifer Deegan (nee Clark) wrote:
> Hi,
>
> I'm seeing this bug too. Amina did you want to look at it since you 
> worked on this last, or shall I? It's strange that Karen isn't seeing 
> the bug when Jane is seeing it on the Mac and I have it on windows.
>
> Jen
>
> Jane Lomax wrote:
>   
>> 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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>>>       
>>     
>
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-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131