tag:blogger.com,1999:blog-5980104128798509938.post8024624645019780333..comments2010-04-06T21:05:29.263-07:00Comments on The Semantic Web in Life Sciences research: So you think you know ontologies?Cartikhttp://www.blogger.com/profile/06141451252596268391noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-5980104128798509938.post-39652055636657181112007-10-03T17:06:00.000-07:002007-10-03T17:06:00.000-07:00To respond to Ben's critique, it is not my intenti...To respond to Ben's critique, it is not my intention to dismiss the contributions of bio-ontologists to the life sciences. Bio-ontologists are a very rare breed indeed, as they effectively straddle two vastly different areas of expertise, viz. biology and knowledge representation formalisms. This is no mean feat. I know of only a handful of people who fit this description, and I'm lucky enough to work with two of them! Ontologies mean different things to different people. I have talked about ontologies from a formal Computer Science perspective (as that is my background). Ontologies that are being used in the life sciences today, despite their mathematical limitations, are very effective at solving biological problems and are extensively used by biologists. Formal ontologies lag far behind in terms of usage and performance. My intention was to highlight the formal rigor of ontology development, which seems to be commonly overlooked, to potentially detrimental effect. The Soldatova and King paper that I have referred to explains these dangers at length. Referring to Carol Goble's "Capulets and Montagues" analogy, both families need each other. My intention was to highlight the possible dangers of Capulets trying to be Montagues, and vice versa (although I have not alluded to the latter specifically in my post). What is obvious is everyone needs to get along, if we are to get anywhere!Cartikhttps://www.blogger.com/profile/06141451252596268391noreply@blogger.comtag:blogger.com,1999:blog-5980104128798509938.post-48181833144823172312007-10-02T19:03:00.000-07:002007-10-02T19:03:00.000-07:00Ack! A Montague in our midst! From Carole Goble'...Ack! A Montague in our midst! <BR/><BR/>From <A HREF="http://doi.wiley.com/10.1002/cfg.442" REL="nofollow">Carole Goble's famous talk</A> <BR/> <I>"Two households, both alike in dignity, In fair Genomics, where we lay our scene, (One, comforted by its logic's rigour, Claims ontology for the realm of pure, The other, with blessed scientist's vigour, Acts hastily on models that endure), From ancient grudge break to new mutiny, When being drives a fly-man to blaspheme. From forth the fatal loins of these two foes, Researchers to unlock the book of life; Whole misadventured piteous overthrows, Can with their work bury their clans' strife. The fruitful passage of their GO-mark'd love, And the continuance of their studies sage, Which, united, yield ontologies undreamed-of, Is now the hour's traffic of our stage; The which if you with patient ears attend, What here shall miss, our toil shall strive to mend. "</I><BR/><BR/>Wihout those Capulets you Montagues would <BR/>A) have nothing to complain about - and what fun would you have then?<BR/>B) the task of representing all the complexity of biology (which of course you likely don't understand much of) on your shoulders.<BR/><BR/>As another ontology developer that, in many respects, agrees with the ideas in the paper you cite, I have to disagree whole-heartedly with both your dismissal of ontology editors and of bio-ontologists. Both are absolutely fundamental to the advance of the semantic web and, through it, of biology and medicine.<BR/><BR/>I'm in a quoting mood so I'll finish with another one <BR/>"<I>Can't we all just get along..</I>" , stop bashing eachother and get on with it???Benjamin Goodhttps://www.blogger.com/profile/11241205744976358428noreply@blogger.com