[MOBY-l] further thoughts on atomic services & service description

[David Block]

On Tuesday, November 5, 2002, at 03:18  PM, Andrew D. Farmer wrote:

> Hi Mark-
>
> this seems like an interesting direction to explore. My initial take 
> is that
> you'll always run into cases in which two natural datatypes can have 
> two
> or more natural associations, e.g.:
>         sequences related as orthologs or sequences related as 
> paralogs;
>         references authored by a person or references about a person;
>         genes that encode proteins or genes regulated by proteins;
>         genes associated with GO terms based on experimental evidence 
> vs
>                 genes associated with GO terms based on motif analysis
>         etc., etc.
>
> So at some level, it seems natural that there will be "meaning" 
> attributed
> in some way to the associations that can't be captured by just 
> specifying the
> datatypes on either end of the transformation. (I think the last 
> example
> of GO term-gene associations subclassed by evidence also suggests that 
> one
> could go crazy trying to define ontologies of relationship types...)

You've hit on something here that we are working on at GNF.  We need to 
capture metadata about the edges, not just the nodes, in order to 
understand the network of biological entities.  We have envisioned a 
"relationship ontology", and I have the beginnings of it on my hard 
drive, but we are just using very basic relations in our database right 
now.  I believe this ontology will be helpful in many areas, but it's 
obviously a big project.  Is there interest in fleshing it out?  Does 
anyone have any good ideas for how to get it built?  I'm thinking now 
about some kind of online jamboree in which there is a concerted 
brainstorming effort, followed by some careful editorial work, followed 
by publication of an initial draft, probably through GOBO.

If anyone thinks this is tilting at windmills, let me know why, but I 
need something!

-Dave
--
David Block                                  dblock at gnf.org
GNF - San Diego, CA             http://www.gnf.org
Genome Informatics / Enterprise Programming
Weblog:      http://radio.weblogs.com/0104507/
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