Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Draft evidence code ontology

Michael Ashburner (Genetics) ma11 at
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.

Envelope-to: m.ashburner at
Delivery-date: Mon, 22 Mar 2004 20:48:49 +0000
Date: Mon, 22 Mar 2004 21:48:38 +0100
To: m.ashburner at
Subject: Evidence Ontology - Bioinformatics tools suggestion
Mime-Version: 1.0
Content-Disposition: inline
User-Agent: Mutt/1.3.28i
From: Steffen Moeller <moeller at>
X-Cam-AntiVirus: No virus found
X-Cam-SpamDetails: scanned, SpamAssassin (score=-2.5, USER_AGENT_MUTT -2.49)

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

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


* 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)

This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at
Subscribing   send   "subscribe"   to   gofriends-request at
Unsubscribing send   "unsubscribe"  to  gofriends-request at

More information about the go-friends mailing list