At 10:39 AM 11/4/2010, Zhuk, Yefim wrote:
>Mike and Barry,
>
>What are the places populated with multiple ontologies for convenient search? (01)
http://obofoundry.org
http://bioportal.bioontology.org/ (02)
The former is attempting to impose more stringent quality control.
BS (03)
>Thank you,
>
>Jeff (Yefim) Zhuk
>
>-----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://wiki.geneontology.org/index.php/Cardiovascular>http://wiki.geneontology.org/index.php/Cardiovascular
>
>
>
>
>http://www.bioontology.org/wiki/index.php/PATO:Phenotypes_in_OWL
>
>BS
>
>
>
>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 follows:
> >
> >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 taxonomy?
> >
> >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 meaning.
> >
> >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
> >>
> >>
> >>
> >>
> >>
> >>
> >>
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> >--
> >Mike Bennett
> >Director
> >Hypercube Ltd.
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