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

[Jane Lomax]

I started using OBO-Edit 2.0 with clean preferences - I didn't copy my 
old preferences file across.

Jane

Alexander Diehl wrote:
> 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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>>
>>   
>
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468