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

Fri May 1 05:37:34 PDT 2009

Just as another data point:

With a newly downloaded gene_ontology_write.obo file, if I open the file 
and immediately save with no changes, I get 19 non-critical warnings, 
using a fairly fresh install of OBO-Edit 2.0 on Mac OS X 10.4.11 with 
whatever up-to-date Java that that OS supports.

--Alex

Jane Lomax wrote:
> 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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>>>>> _______________________________________________
>>>>> Geneontology-oboedit-working-group mailing list
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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