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

Fri May 1 07:11:32 PDT 2009

Hi,

These files are also in place for me.

Jen

Midori Harris wrote:
> 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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