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[bioontology-support] OBO Foundry group

Alan Ruttenberg alanruttenberg at gmail.com
Tue Nov 17 15:08:50 PST 2009


I notice that many of the ontologies that are listed in that list are
listed as OBO format. Yet all are available in OWL format as well. Can
the download links also include the OWL versions please?
Thanks,
Alan

On Tue, Nov 17, 2009 at 6:04 PM, Alan Ruttenberg
<alanruttenberg at gmail.com> wrote:
> My inclination would be to label this OBO Library, and then have an
> OBO Foundry category be added once we have gone through the process of
> formally admitting ontologies to the Foundry.
> -Alan
>
> On Tue, Nov 17, 2009 at 5:54 PM, Melanie Courtot <mcourtot at gmail.com> wrote:
>> To expand a bit more on my original question:
>> It is in reference to the page http://bioportal.bioontology.org/ontologies,
>> where one can browse the whole set of ontologies. One of my collaborators
>> just did a search on BioPortal, selecting the "OBO Foundry" subset, and
>> assumed that all these ontologies were Foundry ontologies.
>>
>> As far as I know there is no Foundry ontology as of today, there are only
>> candidates. All of those ontologies are however part of the OBO library.
>>
>> I was just wondering if others find that potentially confusing too, and if
>> yes if we shall we consider updating the label. I should have added these
>> details in my original enquiry, apologies for the imprecision.
>>
>> Thanks,
>> Melanie
>>
>>
>> On 17-Nov-09, at 2:48 PM, Alan Ruttenberg wrote:
>>
>>> On Tue, Nov 17, 2009 at 5:42 PM, Natasha Noy <noy at stanford.edu> wrote:
>>>>
>>>> Is there a description somewhere on what "OBO library" is?
>>>
>>>> Our agreement with OBO Foundry has always been that the OBO Foundry site
>>>> maintains the listing of OBO Foundry candidates -- the ones that agree to
>>>> try and conform to the principles and remove orthogonality, etc. That
>>>> site
>>>> will not be an alternative general library site for biomedical ontologies
>>>> --
>>>> lest the user community gets confused any more than it already is. Has
>>>> there
>>>> been a change in policy?
>>>
>>> I am unaware of such a policy.
>>>
>>>>
>>>> It seems quite confusing for users to understand the difference between
>>>> "NCBO library" and "OBO library". With the NCBO renewal due in less than
>>>> two
>>>> months, it would be helpful to understand the difference and the
>>>> position.
>>>
>>> The OBO library consists of ontologies that are, minimally, openly
>>> licensed and which have asked to be listed on the web site. The
>>> current obofoundry site has pointers to ontologies and is not a
>>> repository in the NCBO sense.
>>>
>>> There are many things that are confusing, even if NCBO stands alone. I
>>> have tried, in my email to you and the various lists, to point those
>>> out and will continue to do so, though I have no illusions that all
>>> confusions will be eliminated.
>>>
>>> -Alan
>>
>>
>



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