[Ontology-editors] freeze for regulates links

[Karen Christie]

My comment was only made in the context of Chris's argument that we -need- 
to change the rule to allow use of OE2 for committing. If it can all be 
done in OE1, then perhaps we don't NEED to change the rule.

-Karen

On Wed, 18 Feb 2009, Tanya Berardini wrote:

> Only commenting on this part:
>
>> If these relationships can only be done in OE2, which is not yet fully
> tested to demonstrate stability, >reliability, etc., then perhaps we weren't
> really ready to proceed.
>
> The 'regulates' relationships, both inter- and intra-ontology, can be and
> have been added, displayed and edited in OE1.
>
> Tanya
>
> On Wed, Feb 18, 2009 at 2:48 PM, Karen Christie
> <kchris at genome.stanford.edu>wrote:
>
>> Hi Chris,
>>
>> If rules need to be changed, and sometimes they do, it seems that this
>> should have been brought up before you chose to disregard the rule without
>> bringing it up for discussion.
>>
>> If these relationships can only be done in OE2, which is not yet fully
>> tested to demonstrate stability, reliability, etc., then perhaps we weren't
>> really ready to proceed.
>>
>> -Karen
>>
>>
>>
>> On Wed, 18 Feb 2009, Chris Mungall wrote:
>>
>>
>>> Thanks Midori!
>>>
>>> Sorry about ignoring the rule. It seemed arbitrary in this case as the
>>> diff was identical apart from the saved-by tag.
>>>
>>> We need to change this rule anyway:
>>>
>>> - OBO-Edit is constructed from two software components: OBO-Core and the
>>> UI
>>> - OBO-Core in OE2 is production, not beta
>>> - There are precisely zero people in the GO Consortium who are familiar
>>> with OBO-Core in OE1
>>> - We have been having mysterious problems with obo2obo in OE1 on the
>>> production side
>>> - OBO-Core in OE1 had no automated test suite
>>> - OBO-Core in OE2 has a comprehensive automated test suite
>>>
>>> Unfortunately we can't switch to the more stable OBO-Core2 until the OE2
>>> UI is acceptable for editors. However, in the interim I propose that we
>>> remove the ban on OE2 committing. Doing a roundtrip will serve no useful
>>> purpose anyway, as even if problems were to be introduced in OE1, the
>>> chances of them being propagated in a roundtrip are extremely high. I am in
>>> fact extremely paranoid and vigilant about errors in either format syntax or
>>> content leaking into the public version of GO, but I think this rule
>>> provides only a false sense of security.
>>>
>>> I do thing we should be far more rigorous in automated checking of
>>> gene_ontology_write.obo. We are now in a position to do this as we have a
>>> separate filtering step prior to propagation to the public. I seem to recall
>>> we started collecting possible checks on the wiki, but I can't find that
>>> right now.
>>>
>>> If the editors are in agreement I will propose to Mike that the rule be
>>> modified such that it applies to the core rather than the UI.
>>>
>>>
>>> On Feb 18, 2009, at 9:47 AM, Midori Harris wrote:
>>>
>>>  I have just issued a command to commit my changes from today, saved in
>>>> 1.101. So this time there's no need for Chris to do a separate commit.
>>>>
>>>> m
>>>>
>>>> On Wed, 18 Feb 2009, Karen Christie wrote:
>>>>
>>>>  It looks like you committed the file using beta55. Since Mike Cherry has
>>>>> explicitly stated that the GO file should always be produced using the
>>>>> official release version of the software, and NEVER with a beta version,
>>>>> could you please resave with OE-1.101
>>>>>
>>>>> format-version: 1.2
>>>>> date: 17:02:2009 18:07
>>>>> auto-generated-by: OBO-Edit 2.000-beta55
>>>>>
>>>>> -Karen
>>>>>
>>>>>
>>>>> On Tue, 17 Feb 2009, Chris Mungall wrote:
>>>>>
>>>>>  unfreeze.
>>>>>> as if by magic... we have inter-ontology and intra-MF regulates links!
>>>>>> Enjoy.
>>>>>> Remember, these will be invisible to most users for now, unless they
>>>>>> explicitly choose to load from gene_ontology_ext.obo. See ontology/README
>>>>>> for details
>>>>>> We should post announcements once everyone has had a chance to look
>>>>>> On Feb 17, 2009, at 4:19 PM, Chris Mungall wrote:
>>>>>>
>>>>>>> I'm freezing the ontology whilst I add the BP->MF and MF->MF regulates
>>>>>>> links. Should be done in a couple of hours, I'll announce the thaw then.
>>>>>>> _______________________________________________
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>>>>>>> Ontology-editors at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>
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>>>>>>
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>>>>>
>>>>>
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>
>
>
> -- 
> Tanya Berardini
> TAIR Curator
> www.arabidopsis.org
>