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Draft evidence code ontology

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Mon May 31 06:14:07 PDT 2004


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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