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Re: [ontolog-forum] ontology on ontologies

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Peter Yim <peter.yim@xxxxxxxx>
Date: Thu, 4 Nov 2010 17:47:49 -0700
Message-id: <AANLkTim7uKojJSpusFJoznKsEQJE92cPXUZoRj_+XbQT@xxxxxxxxxxxxxx>
Jeff and All,    (01)

> [YZ]  I'll try to dial-in for the next OOR meeting to better understand the 
>current status.    (02)

[ppy]  great. We'll look forward to have you with us. The next OOR
session is scheduled for Fri 2010.11.19 - please mark your calendar
(for now,) and refer to developing details on the session page at:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_11_19    (03)

> [YZ]  What are the places populated with multiple ontologies for convenient 
>search?    (04)

[ppy]  we are talking about ontology repositories here. Of course,
most ontology repository implementations aim at providing much more
than just "hosting" and "search." - ref.
http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008_Communique    (05)

As BarrySmith and JieZheng have indicated, the premier repository for
biomedical related ontologies would be the NCBO (US-NIH funded
National Center for Biomedical Ontology) "BioPortal" - at:
http://bioportal.bioontology.org/ontologies ... whose
donation/contribution of their open source software work formed the
codebase for the OOR implementation.    (06)

> [YZ]  "subject: ontology on ontologies"    (07)

[ppy]  I noticed you changed the subject line to "ontology on
ontologies." The discussion on the thread so far, actually addressed
the question of "repositories for ontologies." ... If you are really
looking for the "ontology on ontologies," you may find it interesting
to look over the proceedings of "OntologySummit2007 - Ontology,
Taxonomy, Folksonomy: Understanding the Distinctions" - see:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007 ;
http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Framework_Session#nid10HH    (08)

Regards.  =ppy
--    (09)

On Thu, Nov 4, 2010 at 3:45 PM, Zhuk, Yefim <Yefim.Zhuk@xxxxxxxxxxxxx> wrote:
> Peter,
> I'll try to dial-in for the next OOR meeting to better understand the current 
> Thank you!
> Jeff (Yefim)    (010)

> -----Original Message-----
> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx 
>[mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Peter Yim
> Sent: Thursday, November 04, 2010 3:43 PM
> To: [ontolog-forum]
> Subject: Re: [ontolog-forum] Need suggestions developing cardiac 
>disease/phenotype ontology
>> [MB]  This is what the Open Ontology
>> Repository project is about.
> [ppy]  Yes, indeed ... thank you very much, Mike.
> See: http://OpenOntologyRepository.org
> or: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository
> ... this is a global community initiative (incubated at the Ontolog
> collaborative work environment), and a work-in-progress, obviously. I
> will take the opportunity to make a call, one more time, for members
> of this community to get involved!
> Thanks & regards.  =ppy
> Regards.  =ppy
> Peter P. Yim
> Co-convener,
> Ontolog Forum
> http://ontolog.cim3.net/wiki/
> Co-convener,
> OpenOntologyRepository (OOR) Initiative
> http://OpenOntologyRepository.org
> --    (011)

> On Thu, Nov 4, 2010 at 7:48 AM, Mike Bennett <mbennett@xxxxxxxxxxxxxxx> wrote:
>> Hi Jeff,
>> Nice to see you in here. This is what the Open Ontology
>> Repository project is about. I'll let others describe it in
>> detail since the calls are usually at a time I can't manage and
>> I'm a bit out of the loop, but this will be a repository in which
>> ontologies can be placed for public search, and we can start to
>> address some of the questions around ontology interoperability
>> which I know you're interested in.
>> Mike    (012)

>> On 04/11/2010 14:39, Zhuk, Yefim wrote:
>>> Mike and Barry,
>>> What are the places populated with multiple ontologies for convenient 
>>> Thank you,
>>> Jeff (Yefim) Zhuk    (013)

>>> -----Original Message-----
>>> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx 
>[mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Barry Smith
>>> Sent: Thursday, November 04, 2010 10:29 AM
>>> To: [ontolog-forum] ; Pradeep Kumar S; [ontolog-forum]
>>> Subject: Re: [ontolog-forum] Need suggestions developing cardiac 
>disease/phenotype ontology
>>> Mike leaves out one important step:
>>> 0. Find out what already exists in the relevant domain, and use what
>>> has already been created as far as possible.
>>> In this case the first places to look will include:
>>> http://www.bioontology.org/wiki/index.php/PATO:Phenotypes_in_OWL
>>> BS    (014)

>>> At 10:08 AM 11/4/2010, Mike Bennett wrote:
>>>> Hi Pradeep,
>>>> Here's how I tend to look at creating an ontology. Assuming the
>>>> ontology is intended as a conceptual model of the reality itself,
>>>> and is not constrained by any specific application requirement (i.e.
>>>> it's a model of the problem and not the solution), I would proceed as 
>>>> 1. Have a strict taxonomic hierarchy in which something sits below
>>>> something else if it is a "kind" of that thing, that is it inherits
>>>> all the facts defined for that thing above, and its parents and so on;
>>>> 2. If there are multiple ways of classifying things in the problem
>>>> domain, consider honoring all that are relevant (for example, a
>>>> whale is both a Mammal and a MarineAnimal). However, you may wish to
>>>> consider that while reality and therefore ontology support multiple
>>>> inheritance, most of the applications that use this information will
>>>> not. Having multiple taxonomies will enable you to develop (and map
>>>> against) different applications which classify the diseases in
>>>> different ways. So you should be able to achieve a taxonomy for any
>>>> application that you need to deal with.
>>>> 3. At the top of your hierarchy have what sort of "Thing" everything
>>>> is, that is "DiseasePhenotype" I would imagine. If there is a
>>>> separate way of classifying the diseases (genotype?) then put a
>>>> separate top level term, with an even more general term above that
>>>> (e.g. Disease).
>>>> 4. Finally the facts (properties). For every new kind of thing
>>>> (every disease) ask yourself two questions:
>>>>   - what sort of thing is it? (this determines where it goes in the
>>>> taxonomy e.g. is it a neurone related or muscle related condition);
>>>>   - what facts distinguish it from other things in that part of the 
>>>> This latter gives you the necessary facts that define that that
>>>> thing is what it is.
>>>> There may be other, incidental facts. In financial securities we
>>>> have lots of facts that always apply to a given kind of security so
>>>> it's not always obvious which one is a necessary, defining fact. For
>>>> example exchange traded options are distinguished by the fact that
>>>> they are traded on an exchange, and also by the fact that they have
>>>> specific, standardized legal terms. So don't worry too much about
>>>> distinguishing necessary from incidental facts since the main
>>>> semantics notations don't have a means to put that in anyway. Just
>>>> make sure you have captured the necessary facts that give a thing its 
>>>> If no facts distinguish something from something else, you have a
>>>> synonym (at least at the level of detail you have considered
>>>> appropriate for this particular ontology). Rather than have separate
>>>> classes for each word or disease name that exists, you should
>>>> consider having one class for each meaning, and then identify
>>>> synonymous words in a separate "synonym" tag. Unfortunately there
>>>> isn't a synonym tag in OWL (people seem happy to have a class per
>>>> word and use equivalence relations, which is unnecessary and I would
>>>> suggest counter productive). So either use RDFS Label or find some
>>>> way of identifying particular RDFS Labels as "synonym". Here you
>>>> might also want to have separate synonym tags with a language
>>>> marker, so you have all your Latin terms.
>>>> Ultimately the questions of what amount of relationships / facts to
>>>> put in, is a judgement call based on what level of detail of terms
>>>> you need in any applications you will develop from this ontology, or
>>>> what level of detail exists in databases, data feeds and
>>>> applications that you wish to relate to with this ontology, for
>>>> example if you are using it for integration of disparate systems or
>>>> to create a common messaging language.
>>>> What I found is that once you get an initial draft in place and
>>>> present this to the business subject matter experts to review (I
>>>> hope you will be doing this, since it's their knowledge), they will
>>>> tend to let you know about additional facts and levels of detail
>>>> that are relevant to a given application or to their view of the
>>>> business domain. For example when we looked at legal entities, we
>>>> had 4 terms for kinds of relationships among entities, but the
>>>> business experts identified up to 4 possible shades of meaning for
>>>> each of these, that they considered relevant, for instance for
>>>> different levels of control and different kinds of control that one
>>>> legal entity has over another.
>>>> So once you have got your ontology into the hands of the business
>>>> domain experts they will pretty much fine tune the level of detail
>>>> for you. The key is making sure that it is structured, and can be
>>>> presented and explained, in simple set theory logic with the
>>>> necessary defining facts in place.
>>>> Hope this helps,
>>>> Mike Bennett
>>>> On 04/11/2010 13:38, Pradeep Kumar S wrote:
>>>>> Dear all,
>>>>> I hope this is the right place to request for some help I need
>>>>> developing a cardiac disease/phenotype ontology.
>>>>> I have been curating list of phenotype/disease terms from
>>>>> biomedical literatures for past 1year.
>>>>> Now the collection has grown to about  ~1200 terms. I have the
>>>>> following attributes curated along with the terms:
>>>>> 1. Term name
>>>>> 2. Source ( web, reference of book or paper)
>>>>> 3. Some times definition and the context in which it was curated.
>>>>> I request experts here to suggest me how to proceed further from
>>>>> list of terms to making a good ontology?
>>>>> Specifically I need to know:
>>>>> 1.     how many relationships should I consider initially. Putting
>>>>> terms under hierarchy like a taxonomy will be the easiest. But how
>>>>> to incorporate other plausible relationships. When (how many) would
>>>>> it get very complex?
>>>>> 2.     Basically I want to render a ontology that could be used by
>>>>> data mining tools and serve biological community in their data analysis.
>>>>> Any suggestions from experts here will be highly appreciated.  Also
>>>>> please point me to any websites/literature/books that would be of help.
>>>>> Thanking you,
>>>>> --Pradeep    (015)

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