[MOBY-l] Attn. all those interested in the Service Ontology

[Mark Wilkinson]

This gem has been floating around the GO-friends mailing list.  If they
have a bioinformatics tools ontology already, we should be using it and
working with them to extend it.  It seems to be at exactly the level of
resolution that we require for our Service Ontology...

M


-----Forwarded Message-----
> From: Michael Ashburner (Genetics) <ma11 at gen.cam.ac.uk>
> To: ma11 at gen.cam.ac.uk, midori at ebi.ac.uk
> Cc: gofriends at genome.stanford.edu, ref26 at gen.cam.ac.uk
> Subject: [MISC] Re: Draft evidence code ontology
> Date: Mon, 31 May 2004 14:14:07 +0100
> 
> I should also add that I did not take into account this very useful
> email from Steffen Moeller, tho I would like to.
> Michael
> 
> 
> Envelope-to: m.ashburner at gen.cam.ac.uk
> Delivery-date: Mon, 22 Mar 2004 20:48:49 +0000
> Date: Mon, 22 Mar 2004 21:48:38 +0100
> To: m.ashburner at gen.cam.ac.uk
> Subject: Evidence Ontology - Bioinformatics tools suggestion
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> From: Steffen Moeller <moeller at pzr3.pzr.uni-rostock.de>
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> 
> Dear Michael,
> 
> below you find my revised suggestion of an ontology for bioinformatics
> tools. I perceive the world as a combination of known sources of
> information and various methods that may be applied to get to this
> source.
> 
> Difficult are cases when the language does not distinguish between the
> approach and the tool. Taking "Blast" as an example, Blast certainly
> is an algorithm with many flavours (PSI-...). This has
> multiple implementations (NCBI and WU spring to mind). The method is a
> pairwise sequence comparison. The implementation is an application.
> 
> Hope to have helped to some extend. If you consider this usable and you
> want me to fill the gaps then please tell me.
> 
> Many greetings
> 
> Steffen
> 
> * in-silco analysis
>   & source-of-information (part-of)
>     + application (is-a)
>       + sequence-analysis (is-a)
> 	+ sequence-comparison (is-a)
>         + structure-prediction (is-a)
>           + fold-prediction  (is-a)
>   	  + transmembrane-topology prediction (is-a)
> 	    - TMHMM (part-of) is-a hidden markov model
> 	    - HMMTOP (part-of) is-a hidden markov model
> 	    - PHD (part-of) is-a neuronal network
> 	  + contact prediction
>       + structure-comparison (is-a)
>       + interaction-prediction (is-a)
>       + visualisation (is-a)
>     + databases (is-a)
>       + literature (is-a)
>       + sequence database(is-a)
>         + DNA database (is-a)
> 	  + SNP database (is-a)
>         + RNA database (is-a)
>         + protein database (is-a)
>       + databases connecting other databases (is-a)
>         + protein-interaction (is-a)
> 	+ metabolism (is-a)
>         + abstraction (is-a)
>           + Protein Domain database (is-a)
> 	    + PFAM (instance-of)
> 	    + InterPro (instance-of)
> 	    - Prosite (instance-of) is-a Regular expression, is-a Profile
>   & techniques (part-of)
>     + molecular modeling (is-a)
>     + sequence-similarity (is-a)
>       + direct-comparisons (is-a)
>       	+ pairwise (is-a)
> 	  + global
> 	  + local
> 	+ multiple (is-a)
> 	  + global
> 	  + local
>       + abstraction (is-a)
>         + neuronal network (is-a)
>         + hidden markov model (is-a)
> 	+ Profile (is-a)
> 	+ Weight matrix (is-a)
> 	+ Regular expression (is-a)
> 
> 
> --
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-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre