[Ontology-editors] freeze for regulates links

[Tanya Berardini]

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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>>>>>>
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>>>>
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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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