What you begin to confront is the fact that if the ontologies were
isolated both in terms of not using a shared foundational ontology, there were
likely also isolated in the sense of not sharing "best practices" for
ontology construction: -
many definitions are imprecise, circular, or - in fact - non-existent -
the same is true for relations - they are used in an imprecise, inconsistent,
or incommensurate manner (a big problem initially for GO) - mixing
"is_a" with the MANY KINDS of "part of" can be a semantic
data integration nightmare**. -
loosely defined and used lexical facets associated with nodes in the ontology -
e.g., acronyms, abbreviations, and misspellings may get used indiscriminately
as synonyms - sometimes that's valid, and sometimes its not. -
plurals and pre-coordinated descriptions cutting across knowledge domains may
appear in the graph - which can limit computability at fine-grained levels. [VK] So, I am in agreement with the fact that best practices
need to be evolved for creating biomedical ontologies in general. Foundational
ontologies could be an aspect of these best practices, but it is going to be tricky. Past efforts at creating a global ontology (Cyc)
haven’t been particularly useful. I think in order to get a set of
primitives that characterize the entire range of biomedical activity one has to
be at a very high level of abstraction, leading to lack of utility for
interoperation for instance. If however, done right, it has great potential to
be useful. Can you provide a concrete example where having a
foundational ontology helped create a “better” ontology and in turn
enabled greater interoperation? Probably, the right way to get there is to iterate over a
broad set of use cases as suggested by Alan Rector. Another aspect of best practices is the ontology building
process, an excellent example being the flowchart you refer to in slide 19
below. The problems above can be a big problem if more than one ontology is
required that have overlapping domains. These inconsistencies need to be
disambiguated or reconciled in some way, and in doing so, you may invalidate
mappings made to data model elements. [VK] Can we have some concrete examples of the types of
things you are referring to the above. What are the types of inconsistencies
observed? How can they be reconciled? How does this result in invalidating some of the mappings. A concrete use case illustrating this will help us do a
better job of creating ontologies and mappings for the Parkinson’s
Disease use Case… Don't get me wrong. It may sound like I'm slamming GO here.
I'm not. I've great admiration and respect for their experience and their
efforts. Most commendable of all is the fact that they've gradually
learned a lot - both from the school of hard knocks and from the C.S., library
science, and ontological philosophy fields that can helped them to develop
better shared practices both for ontology creation, curation, and
use. To my mind, the 25 slides prepared by Suzi Lewis & Michael
Ashburner (slides 11 - 37) in the following presentation summing up the hard
won lessons of the GO Consortium do a better job at establishing such guidelines
than anything else I've seen anywhere: Principles for Building Biomedical Ontologies http://www.geneontology.org/teaching_resources/presentations/2005-10_ISMB_Ontology-Building_various.ppt I'd specifically draw attention to the procedural flowchart on slide 19
as being an excellent foundation from which to build more specific guidelines,
some of which can be culled from other portions of the presentation. [VK] The flowchart on slide 19 is very valuable. It will be
great to understand how having a foundational ontology can help facilitate the
process described in the flow chart? There have also been many successes that have made it very clear,
ontologies are an extremely important part of biomedical KE/KR/KD and
semantically-driven data federation. [VK] Would be great to post examples of these successes on
the Wiki, Success stories will be very important to all of us to learn from. Regards, ---Vipul This email and any accompanying attachments are confidential. This information is intended solely for the use of the individual to whom it is addressed. Any review, disclosure, copying, distribution, or use of this email communication by others is strictly prohibited. If you are not the intended recipient please notify us immediately by returning this message to the sender and delete all copies. Thank you for your cooperation. |
- RE: [HCLS] Bridging Ontologies - with Foundational Ontolog... Kashyap, Vipul
- RE: [HCLS] Bridging Ontologies - with Foundational On... Kashyap, Vipul
- RE: [HCLS] Bridging Ontologies - with Foundational On... Kashyap, Vipul
- RE: [HCLS] Bridging Ontologies - with Foundational On... Kashyap, Vipul