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

Fri May 1 06:53:52 PDT 2009

in case it's any use ... I'm not getting the zillions of errors; I have 
Jen's *.dict files in this directory:

   ~/Library/Application\ Support/OBO-Edit2/dict/

I also have files called standard.dict and user.dict in the same 
directory, and I can add words to standard.dict and have them persist.

Unfortunately, I don't remember whether I copied the files from the OE2 
beta config directory or if they appeared by some sort of magic ...

m

On Fri, 1 May 2009, Jennifer Deegan (nee Clark) wrote:

> 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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