[Ontology-editors] freeze for regulates links

[Karen Christie]

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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>