tag:blogger.com,1999:blog-16081779.post4994435539767126490..comments2023-10-28T09:24:38.420+01:00Comments on iPhylo: A database of everythingRoderic Pagehttp://www.blogger.com/profile/00269598293846172649noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-16081779.post-38057832933591438502008-02-07T01:35:00.000+00:002008-02-07T01:35:00.000+00:00For the ideas I was mentioning, the way I like to ...For the ideas I was mentioning, the way I like to think about (e.g., trait) ontologies in this context is more along the lines of - user-driven - agile and mass development of controlled vocabularies, not what I imagine you mean by 'big' ontologies. You have come across some interesting work in this regard by Mark Wilkinson (UBC, not NHM), for example<BR/>http://psb.stanford.edu/psb-online/proceedings/psb06/good.pdf and http://hdl.nature.com/10101/npre.2007.945.2<BR/><BR/>But indeed what you're aiming for may not need any ontologies. BTW have you thought about building this on top of Freebase? I just wish the software were available ...Drycafehttps://www.blogger.com/profile/16035210916769593629noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-67574363526877440752008-02-06T22:28:00.000+00:002008-02-06T22:28:00.000+00:00Yep, let me know. It would be a pleasure to help.C...Yep, let me know. It would be a pleasure to help.<BR/><BR/>CheersAnonymoushttps://www.blogger.com/profile/12361293458447621754noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-49177725413006870712008-02-06T17:27:00.000+00:002008-02-06T17:27:00.000+00:00Ironically, after having given TreeBASE such a har...Ironically, after having given TreeBASE such a hard time for not having an ontology (i.e., a taxonomy), I find myself increasingly sceptical about large-scale ontologies. Perhaps it's the result of reading too many books like <A HREF="http://www.amazon.com/Everything-Miscellaneous-Power-Digital-Disorder/dp/0805080430/" REL="nofollow">Everything is miscellaneous</A>, but things like automatic clustering of tags (e.g., <A HREF="http://www.pui.ch/phred/automated_tag_clustering/" REL="nofollow">here</A>) look promising. Your recent post <A HREF="http://blog.evolvingbits.org/2008/02/04/integrating-ontologies-is-a-mess/" REL="nofollow">Integrating ontologies is a mess</A> doesn't fill me with confidence that big ontologies are the way to go. I think global identifiers and linking (perhaps with some very basic semantics, such as <I>x</I> cites <I>y</I>) is the way to go. There's much to be said for keeping things simple...Roderic Pagehttps://www.blogger.com/profile/00269598293846172649noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-20719898471238608812008-02-06T13:08:00.001+00:002008-02-06T13:08:00.001+00:00Hi Rod - very exciting to hear you're pursuing thi...Hi Rod - very exciting to hear you're pursuing this! I have been hatching similar ideas towards a generic, semantics-enabled deployable trait database.<BR/><BR/>The NCBO and affiliated groups have done some significant work in this direction which you might want to check out. <BR/><BR/>More specifically, they have conceived an EAV-based model (meanwhile called EQ-model, as A and V are subsumed into a Quality) for formalizing phenotype descriptions, which we have adopted within PhenoScape (http://phenoscape.org) to formalize evolutionary characters in a compatible way. More to your project, Chris Mungall has done some significant prototype work towards the OBD, a database of any ontology-annotated biological data (http://www.bioontology.org/wiki/index.php/OBD:Main_Page has an overview).Drycafehttps://www.blogger.com/profile/16035210916769593629noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-51421700728210916352008-02-06T13:08:00.000+00:002008-02-06T13:08:00.000+00:00Thanks. I think what I need to do first is get the...Thanks. I think what I need to do first is get the code working properly, and documented sufficiently to make it public. I'll keep you posted.Roderic Pagehttps://www.blogger.com/profile/00269598293846172649noreply@blogger.comtag:blogger.com,1999:blog-16081779.post-56516247404539500752008-02-04T17:32:00.000+00:002008-02-04T17:32:00.000+00:00I would be glad to participate if you need some he...I would be glad to participate if you need some help.<BR/><BR/>Cheers<BR/>PauloAnonymoushttps://www.blogger.com/profile/12361293458447621754noreply@blogger.com