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

Fri May 1 05:42:49 PDT 2009

Hi,

If I delete my config files I get a number of errors too large to be 
counted. WinXP, OE2.

Jen

Alexander Diehl wrote:
> 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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>>>>>>         
>>>>>     
>>>>
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>>>
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>>
>>
> 
> 