[Ontology-editors] [OBO-Edit Working Group] Ontology development mailing list
Chris Mungall
cjm at fruitfly.org
Thu Jul 3 08:24:56 PDT 2008
It should presumably go here:
http://www.geneontology.org/GO.mailing.lists.shtml
And get announced on the list
On Jul 3, 2008, at 2:06 AM, Jennifer Deegan (nee Clark) wrote:
> Hi again,
>
> I'm not 100% sure that I got everybody on the list that would have
> wanted to be on it. If anybody can think of anyone who is missing
> it would be great to pass the message on. Or a message could go to
> the GO list if that is better.
>
> Jen
>
> Jennifer Deegan (nee Clark) wrote:
>
>> Hi Chris,
>> Yes the list was created. We can start using it now.
>> Jen
>> Chris Mungall wrote:
>>> was the list created? I saw ontology-editors cc'd in an email
>>> from Jane (a *much* more sensible name than go-oe-users) but
>>> haven't seen an announcement.
>>>
>>> On Jun 25, 2008, at 7:53 AM, Jennifer Deegan (nee Clark) wrote:
>>>
>>>
>>>
>>>> Splendid. The scope of incorrect auto-completion would be great
>>>> too. I'll wait a bit to hear the Californian views then send
>>>> the conclusions.
>>>>
>>>> Jen
>>>>
>>>> Midori Harris wrote:
>>>>
>>>>
>>>>
>>>>> I think the potential for confusion is much, much less for 'go-
>>>>> oe- users' than for a new 'go-editors' that doesn't mean the
>>>>> same thing as the existing 'go-editors'! I therefore veto 'go-
>>>>> editors at geneontology.org'.
>>>>> I'd also not mind if some of the "anyone in GO that uses OBO-
>>>>> Edit" join the list; if it doesn't meet their expectations
>>>>> they can unsubscribe.
>>>>> That said, if anyone comes up with a better suggestion than 'go-
>>>>> oe- users', fine.
>>>>> m
>>>>> On Wed, 25 Jun 2008, Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Can people let me know if they are happy with this name 'go-
>>>>>> oe- users' before I write to request it? I want to be sure
>>>>>> that it won't confuse people into thinking that it is just a
>>>>>> list for anyone in GO that uses OBO-Edit (e.g. for browsing
>>>>>> or temporary content efforts).
>>>>>>
>>>>>> 'go-editors at ebi.ac.uk' is the list for the editorial office so
>>>>>> go- editors at geneontology.org for all the people who edit (and
>>>>>> commit) the GO regularly in the consortium might be good or
>>>>>> might be confusing. Any other thoughts? Like I say, I have no
>>>>>> preference as long as it seems sensible to people.
>>>>>>
>>>>>> Jen
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Thanks, and are you all happy with the name 'go-oe-users'?
>>>>>>>
>>>>>>> Jen
>>>>>>>
>>>>>>> Midori Harris wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> You seem to have it in hand, so go ahead.
>>>>>>>>
>>>>>>>> On Wed, 25 Jun 2008, Jennifer Deegan (nee Clark) wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Midori,
>>>>>>>>>
>>>>>>>>> Great. So will you write to Mike or shall I?
>>>>>>>>>
>>>>>>>>> Jen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Midori Harris wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Although, as I've said, I don't object to creating a list
>>>>>>>>>> for people who use OBO-Edit to edit GO, I'd like to
>>>>>>>>>> clarify a couple of things from this latest post:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> There is a really important discussion that we need to
>>>>>>>>>>> have about cross
>>>>>>>>>>> products that you are currently missing because you are
>>>>>>>>>>> not on the
>>>>>>>>>>> OBO-Edit working group list.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Note that there isn't a discussion of cross-products
>>>>>>>>>> taking place on the OEWG list at the moment, although the
>>>>>>>>>> subject has come up in a couple of recent
>>>>>>>>>> "meetings" (online chats).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> We need to have a list for people who edit
>>>>>>>>>>> and commit the GO files as a large part of their job, so
>>>>>>>>>>> that we can
>>>>>>>>>>> easily bring such important issues to their attention. It
>>>>>>>>>>> is not
>>>>>>>>>>> appropriate to write to the GO list when what we want to
>>>>>>>>>>> say is 'Can all
>>>>>>>>>>> GO OBO-Edit users run OBO-Edit 1.101 on their computers
>>>>>>>>>>> with the
>>>>>>>>>>> reasoner on?' This would spam too many other people.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I don't actually think it would be a bad thing to inform
>>>>>>>>>> the GO list of which version of OBO-Edit we're using for
>>>>>>>>>> files we commit; it changes infrequently enough that it
>>>>>>>>>> does not amount to an excessive quantity of list traffic.
>>>>>>>>>>
>>>>>>>>>> Where a go-oe-users list will be useful is for
>>>>>>>>>> discussions leading up to the decision to change the GO
>>>>>>>>>> editing SOPs.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Please can we have this list set up?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Neither David nor I has said no, now that the scope of
>>>>>>>>>> the proposed list has been clarified.
>>>>>>>>>>
>>>>>>>>>> m
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Jen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> David Hill wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> I'm not opposed to a list like this, but I think it
>>>>>>>>>>>> should certainly be
>>>>>>>>>>>> supplemented with an SOP portion of the wiki where the
>>>>>>>>>>>> 'gold standard'
>>>>>>>>>>>> is kept. My concerns with a mailing list is that many
>>>>>>>>>>>> timee people on
>>>>>>>>>>>> the list don't know where discussion begins and ends
>>>>>>>>>>>> and policy starts.
>>>>>>>>>>>>
>>>>>>>>>>>> David
>>>>>>>>>>>>
>>>>>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Midori puts the intended scope of the list very clearly.
>>>>>>>>>>>>> GO's OBO-Edit users is basically what we had in mind.
>>>>>>>>>>>>> Any name is fine
>>>>>>>>>>>>> by me.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Jen
>>>>>>>>>>>>>
>>>>>>>>>>>>> Midori Harris wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Alex neatly identifies the key issue. The main reason
>>>>>>>>>>>>>> David and I
>>>>>>>>>>>>>> have hesitated to create a new list for ontology
>>>>>>>>>>>>>> content development
>>>>>>>>>>>>>> is that managing the membership of such a list would
>>>>>>>>>>>>>> be unwieldy at
>>>>>>>>>>>>>> best (e.g. do we include or exclude people who are
>>>>>>>>>>>>>> working on a
>>>>>>>>>>>>>> specific content area, especially the outside experts?).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The proposed list of members below suggests that
>>>>>>>>>>>>>> you're now asking
>>>>>>>>>>>>>> for a list, not of all ontology developers, but of
>>>>>>>>>>>>>> GO's OBO-Edit
>>>>>>>>>>>>>> users. That is a rather more narrowly defined scope,
>>>>>>>>>>>>>> with a smaller
>>>>>>>>>>>>>> and more stable membership, and is an altogether more
>>>>>>>>>>>>>> manageable
>>>>>>>>>>>>>> prospect. I would not object to creating this list,
>>>>>>>>>>>>>> provided that
>>>>>>>>>>>>>> David also agrees.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For this list, however, "ontology development" would
>>>>>>>>>>>>>> be a misnomer,
>>>>>>>>>>>>>> because it would miss out a number of regular
>>>>>>>>>>>>>> contributors to the
>>>>>>>>>>>>>> ontology content, not to mention the experts who are
>>>>>>>>>>>>>> more transiently
>>>>>>>>>>>>>> associated with the GO effort. I therefore do not
>>>>>>>>>>>>>> agree to name the
>>>>>>>>>>>>>> list "ontology-development" or "go-development"; we
>>>>>>>>>>>>>> should pick a
>>>>>>>>>>>>>> more accurate name such as "go-oboedit-users" or "go-
>>>>>>>>>>>>>> oe- users"
>>>>>>>>>>>>>> (better ideas welcome!).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> As for membership, the "go-oe-users" list should
>>>>>>>>>>>>>> include Donghui, and
>>>>>>>>>>>>>> Alex if he wants to join. There are a few others who
>>>>>>>>>>>>>> could be
>>>>>>>>>>>>>> invited, although if they opt out the list would
>>>>>>>>>>>>>> still serve its
>>>>>>>>>>>>>> purpose: Susan, Val, Pascale, Doug, Rama, Eurie, and
>>>>>>>>>>>>>> maybe Kimberly
>>>>>>>>>>>>>> or Ranjana. (They use OE and commit GO edits rarely
>>>>>>>>>>>>>> or not at all,
>>>>>>>>>>>>>> but any of them may take an interest in the practices
>>>>>>>>>>>>>> of those who do.)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sorry to be so longswinded!
>>>>>>>>>>>>>> midori
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, 25 Jun 2008, Alexander Diehl wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Jen,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Is this list intended for discussion of the mechanics
>>>>>>>>>>>>>>> of ontology file
>>>>>>>>>>>>>>> editing or discussions of ontology development and
>>>>>>>>>>>>>>> content?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> We would like to include anyone who regularly edits
>>>>>>>>>>>>>>>> GO ontology files,
>>>>>>>>>>>>>>>> and Chris since he is so heavily involved in
>>>>>>>>>>>>>>>> ontology file issues. I'm
>>>>>>>>>>>>>>>> not sure I know the complete list but I think it
>>>>>>>>>>>>>>>> would be something
>>>>>>>>>>>>>>>> like:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Midori
>>>>>>>>>>>>>>>> David
>>>>>>>>>>>>>>>> Chris
>>>>>>>>>>>>>>>> Tanya
>>>>>>>>>>>>>>>> Jane
>>>>>>>>>>>>>>>> Jen
>>>>>>>>>>>>>>>> Karen
>>>>>>>>>>>>>>>> Harold
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Did I forget anyone? We can always sign people up
>>>>>>>>>>>>>>>> after the list is
>>>>>>>>>>>>>>>> started if there are others.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Jen
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Midori Harris wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Who will be on the list?
>>>>>>>>>>>>>>>>> m
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Tue, 24 Jun 2008, Jennifer Deegan (nee Clark)
>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi David and Midori,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> This evening we were discussing on the OBO-Edit
>>>>>>>>>>>>>>>>>> Working Group
>>>>>>>>>>>>>>>>>> chat the need
>>>>>>>>>>>>>>>>>> for an ontology development mailing list for the
>>>>>>>>>>>>>>>>>> people who edit
>>>>>>>>>>>>>>>>>> the GO.
>>>>>>>>>>>>>>>>>> Chris and I would like to ask once again, rather
>>>>>>>>>>>>>>>>>> emphatically,
>>>>>>>>>>>>>>>>>> that such a
>>>>>>>>>>>>>>>>>> list should be made immediately. We have had
>>>>>>>>>>>>>>>>>> situations recently
>>>>>>>>>>>>>>>>>> where
>>>>>>>>>>>>>>>>>> information is not getting through to all the
>>>>>>>>>>>>>>>>>> people who need to
>>>>>>>>>>>>>>>>>> hear it, and
>>>>>>>>>>>>>>>>>> we would like to avoid having that happen again.
>>>>>>>>>>>>>>>>>> Also this
>>>>>>>>>>>>>>>>>> evening we were
>>>>>>>>>>>>>>>>>> discussing the current situation with cross
>>>>>>>>>>>>>>>>>> products and
>>>>>>>>>>>>>>>>>> OBO-Edit, and we
>>>>>>>>>>>>>>>>>> don't have a list to which we can send the
>>>>>>>>>>>>>>>>>> pertinent points to
>>>>>>>>>>>>>>>>>> keep everybody
>>>>>>>>>>>>>>>>>> in the loop. Please would it be possible for this
>>>>>>>>>>>>>>>>>> list to be set
>>>>>>>>>>>>>>>>>> up so we can
>>>>>>>>>>>>>>>>>> proceed?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Jen
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ------------------------------------------------------
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>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Geneontology-oboedit-working-group mailing list
>>>>>>>>>>>>>>>>> Geneontology-oboedit-working-
>>>>>>>>>>>>>>>>> group at lists.sourceforge.net
>>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/
>>>>>>>>>>>>>>>>> geneontology-oboedit-working-group
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>> --
>>>> Jennifer Deegan (nee Clark)
>>>> EMBL-European Bioinformatics Institute
>>>> Gene Ontology Consortium
>>>>
>>>
>>>
>>>
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>>> working-group
>
> --
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
>
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