[Ontology-editors] [OBO-Edit Working Group] Ontology development mailing list
Jennifer Deegan (nee Clark)
jdeegan at ebi.ac.uk
Thu Jul 3 08:30:40 PDT 2008
Hi,
I'll write to Amelia and ask her to put it on the website. Midori would
you like to announce it on the list or shall I?
Jen
Chris Mungall wrote:
>
> 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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>>>> _______________________________________________
>>>> 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
>>
--
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium
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