[Hplusroadmap] Gene Ontology, and other OBO Ontologies

[Bryan Bishop]

On Tuesday 10 June 2008, Antonio Marcos wrote:
> For those unfamiliar, OBO = Open Biomedical Ontonologies
> www.obofoundry.org/
> http://oboedit.org/docs/html/An_Introduction_to_OBO_Ontologies.htm

Yep, the ontology databases have been mushrooming:

http://faculty.washington.edu/gennari/Protege-plugins/OBO-import/
http://protege.stanford.edu/community/lists.html
http://protege.stanford.edu/download/ontologies.html
http://protegewiki.stanford.edu/index.php/Protege_Ontology_Library
http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml
http://obofoundry.org/
http://oboedit.org/
http://sbml.org/

And so on. Anyway, yes, it is useful. Specifically see how the biobricks 
guys are formalizing it even more into 'functional parts' that you can 
plug-and-play; the trick is merging (1) the instrumentation side of it 
all (ahem), and (2) also making sure we have good tools to deal with 
those ontologies, data sets, and the majority of databases out there so 
that we can relate it back to the simple tools that we already have, 
and whatever automation we can manage. The majority of the ontologies 
on the obofoundry are models, from what I can remember. Models of 
biological systems. So, what we're talking about is getting some formal 
interfaces so that people can acquire that sort of information from 
physical contexts. And manipulate it. And so on. Other stuff like 
that. :)

- Bryan
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http://heybryan.org/