[Ontology-editors] freeze for regulates links

[Chris Mungall]

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.
>>>> _______________________________________________
>>>> Ontology-editors mailing list
>>>> Ontology-editors at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>
>