Re: [Obo-discuss] PURL request: MPIO

[Mathias B. <mbr...@gm...>]

Hi,

I think, I got a lot of good advice out of the conversation with Erick and
I will use ti to minimize the risks you both are concerned about to the
extend possible.

On Tue, Oct 31, 2017 at 11:11 AM, Chris Mungall <cjm...@lb...> wrote:

> I share some of Eric's concerns, but we can move ahead with the request
> since there is no formal objection and it meets minimal requirement for
> being registered. Follow-up here: https://github.com/
> OBOFoundry/OBOFoundry.github.io/issues/487
>
> On Fri, Oct 6, 2017 at 8:33 AM, Erick Antezana <eri...@gm...>
> wrote:
>
>> Hi Mathias,
>>
>> 1. Yes, that OBO file. It has some entries (e.g. physical interaction,
>> drug type) that might be of interest... It might have probably been already
>> under the radar of your community.
>>
>> 2. Ok, thanks.
>>
>> 3. From the experience I had with some overlapping ontologies and some
>> covering similar domains, I would strongly recommend avoiding having a
>> portfolio of multiple, similar ontologies for the sake of limiting the
>> confusion when users have to consume them as well as to minimize
>> maintenance (e.g. mappings, synonyms/aliases, inconsistent naming,
>> inconsistent IDs, ...). The example I typically struggle with goes around
>> crop traits... If you have the means to control those possible issues
>> (technical and social), then there is no reason to alarm. Moreover, if
>> DINTO and DIDEO are on their way to getting "married", then things are
>> fine. I was simply trying to avoid a multiplication of ontologies around
>> the same domain (even if they claim they are orthogonal).
>>
>> Have a nice weekend!
>> Erick
>>
>> On 5 October 2017 at 16:26, Mathias Brochhausen <mbr...@gm...>
>> wrote:
>>
>>> Hi,
>>>
>>> 1. This leads me to an obo file called "intact". Is that what you want
>>> me to look at?
>>>
>>> 2. As I said, I would create a new discussion thread on this discuss
>>> list.
>>>
>>> 3. The problem is that for the users in that group the two full fletched
>>> ontologies are confusing, since they are fairly big. I don't fully
>>> understand why you assume there is or will be a problem. This is a small,
>>> fairly flat resource that allows users that would probably normally not
>>> touch any ontology , which will help get annotation with OBO Foundry
>>> ontology "terms" out in the web. The group as a whole has carefully
>>> considered its options. It consistent of multiple members with tremendous
>>> experience in OWL ontologies and knowledge representation. This was the
>>> solution that was chosen, since it allows gently pulling users in a
>>> semantic web direction. Alignment of DINTO and DIDEO is on the way and was
>>> inspired and made possible by creating MPIO. Importing the 3 ontologies
>>> will also not create a problem since the ontologies are (or will be once a
>>> few more steps regarding the DINTO-DIDEO alignment are implemented. There
>>> will be documentation (and actually there partially already is)
>>> documentation explaining the relationship and the differences between DIDEO
>>> and DINTO. Again, I seem to miss the real problem here. I am sure you can
>>> clarify. Basically, we are seeking a namespace for a useful tool that will
>>> get OBO Foundry ontologies out there in the field and that will help
>>> tremendously.
>>>
>>> 4. See answer above. Also, keep in mind that as long as things have the
>>> same URI it doesn't really matter in which OWL file the are.
>>>
>>>
>>> Best,
>>> Mathias
>>>
>>> On Thu, Oct 5, 2017 at 9:09 AM, Erick Antezana <eri...@gm...
>>> > wrote:
>>>
>>>> Hello Mathias,
>>>>
>>>> 1. Could you try starting on this URL: https://www.ebi.ac.uk/intact/d
>>>> ownloads  then looking for "controlled vocabularies."?
>>>>
>>>> 2. I totally agree with you, this topic ("minimality") goes beyond the
>>>> interest of only this ontology. Any suggestions on following up?
>>>>
>>>> 3. Thanks for the background. I perfectly understand the motivation. If
>>>> MPIO is expected to fill the gap between DINTO and DIDEO, I guess there
>>>> are, on one hand, some missing terms that need to be created, and on the
>>>> other hand, there are some other terms already captured in DINTO&DIDEO.
>>>> Form that angle, have they (you) considered aligning and/or enlarging the
>>>> extant ontologies (DINTO & DIDEO) instead of generating a new resource that
>>>> could confuse users? at the end many people will end up importing the 3
>>>> ontologies to be sure they don't miss anything. If I were to use any of
>>>> those terms, I would be happy to import a single ontology... is that an
>>>> option? are those groups/communities collaborating somehow?
>>>>
>>>> 4. If the interest is really to identify/label a subset of the
>>>> terms/concepts/universals from DINTO&DIDEO, why not simply label them as
>>>> relevant for that IG? or application?  (e.g. OBO tag: subset)
>>>>
>>>> best regards,
>>>> Erick
>>>>
>>>> On 4 October 2017 at 22:18, Mathias Brochhausen <mbr...@gm...
>>>> > wrote:
>>>>
>>>>> Hi Erick,
>>>>>
>>>>> thanks for sharing your opinion.
>>>>>
>>>>> 1. I cannot open the link to the EBI resource you provided. Is there
>>>>> another way to access that information.
>>>>>
>>>>> 2. I think that the discussion whether "minimum" information
>>>>> ontologies are a good thing or not is an important one for the OBO
>>>>> community. So, I suggest having that discussion in a separate e-mail
>>>>> thread. This not only an issue about this specific ontology, but of general
>>>>> interest to the community.
>>>>>
>>>>> 3. A little bit of background regarding MPIO. There is a W3C HCLS
>>>>> Interest Group for representing drug-drug interactions. The IG consists of
>>>>> 46 international experts in the field. They suggested the minimum
>>>>> information based on their experience. The IG proposed implementing the
>>>>> minimum information as an OWL file re-using pre-existing ontologies, namely
>>>>> DINTO and DIDEO (both are listed on the OBO Foundry homepage). The process
>>>>> of putting together MPIO actually lead to resolving representational gaps
>>>>> and  issues between those two ontologies and thus furthered orthogonality.
>>>>> There is no claim by the IG that what they as an expert group consider
>>>>> minimum will cater to the needs of all individuals, however, the name of
>>>>> the artifact they created is that of a minimum information model.
>>>>>
>>>>> Best,
>>>>> Mathias
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Oct 3, 2017 at 6:14 AM, Erick Antezana <
>>>>> eri...@gm...> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> In general, I am not fan of "minimum" information ontologies. What is
>>>>>> minimum (that is, sufficient) for you might be non-minimum for others
>>>>>> (non-sufficient). It is not that easy to find a trade-off to satisfy
>>>>>> defined needs of certain communities. Users might end up "adopting"
>>>>>> terms/concepts (with empty values/non sense) that don't use at all...
>>>>>>
>>>>>> On the other hand, I support metatada standards delineating minimum
>>>>>> information that should be captured in a particular domain (e.g. MIAPPE),
>>>>>> but that is something else... Nonetheless, in the case of ontologies, I
>>>>>> would prefer to avoid working with an ontology telling me what is minimum,
>>>>>> especially if that ontology is a domain ontology.
>>>>>>
>>>>>> BTW, what's the relation in between MPIO and MI (
>>>>>> ftp://ftp.ebi.ac.uk/pub/databases/intact/current/cv) ?
>>>>>>
>>>>>> cheers,
>>>>>> Erick
>>>>>>
>>>>>> On 2 October 2017 at 16:36, Mathias Brochhausen <
>>>>>> mbr...@gm...> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I want to request a PURL and the namespace "MPIO" for the Minimum
>>>>>>> PDDI (Potential Drug-Drug Interaction) Information Ontology. I will add an
>>>>>>> issue tracker with all the required information to the OBO Foundry issue
>>>>>>> tracker.
>>>>>>>
>>>>>>> MPIO is a minimum information ontology for drug-drug interaction
>>>>>>> information. It is part of a W3C Health effort to standardize information
>>>>>>> on drug-drug interactions. It is bridging the gaps between two existing
>>>>>>> ontologies regarding drug-drug interactions and drug-drug interaction
>>>>>>> evidence, DINTO and DIDEO.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Mathias
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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