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suggestions requested for plant trait ontology

Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
Tue Aug 21 13:23:10 PDT 2001


I also dislike option 1 for the same reasons as Michael.

However, option 2 worries me in that if I understand your solution there
appears to be useful information burried in free text.

It seems to me that there are actually 3 classes of concept here:
diseases, susceptibility scores, and the actual phenotypes.

So what about 3 subgraphs: one minimal one for diseases, another with 10
entries (one per score) - these two subgraphs should be orthogonal - and a
final subgraph of phenotypes. Each phenotype node should have two parents,
one from disease, one from score. This way you're representing the
knowledge that not all scores can be applied to all diseases. This is
similar to the way GO is headed with anatomy + development.

The nodes should be named unambiguously eg leaf-blast-3

This still isn't ideal - the GO database wasn't designed with quantative
data in mind, so it will be impossible to do quantitive queries (eg find
me everything susceptible (threshold X) to disease Y). Although with 10
scores this could be hacked (either at the application level or by adding
less-than/more-than arcs between score nodes). This is the kind of thing
that will spur us to make the database more generic and useful to wider
groups of people.

This is a slightly experimental suggestion; it may be best to stick with
option 2, effectively making TO a disease ontology, but you effectively
lose scale information.

On Tue, 21 Aug 2001, Pankaj Jaiswal wrote:

> Dear Michael
> 
> Thanks for the suggestions. We are also worried about the scoring system, since
> there is a generic way of evaluation by scoring from 0-9, however all the 10
> scores (0-9), are not scored for each disease (important thing  here is to note
> that traits will cover not only the damage by pathogens, but will also include
> response to environmental stress and plant's own characteristics, eg.
> morphology/anatomy/growth and again each of these sub-sub instances has a score 
> 0-9 for evaluation). some may have all 10 other only 1,3,5,7,9 or else only
> 1,5,9 and so on. From my options the no. 2 seems fine, but that never represents
> the usage of the CV/O with respect to resistance or susceptibility. DO you think
> that for each disease i can have the susceptibility and resistance nodes and
> their definitions will suggest the respective infectivity score, if one wants to
> evaluate.
> 
>  
> -pankaj
> 
> 
> "Michael Ashburner (Genetics)" wrote:
> > 
> > Pankaj
> > 
> > I do not like option 1 at all (over and above the fact that each term
> > must be lexically unique, it suffers from mixing chalk (the diseases)
> > and cheese (the scoring system).  It is a very good principle that
> > within a DAG all terms should belong to the same "semantic family"
> > - if I may create a phrase.  So, option 2 it should be.  I thought of
> > creating a separate "score" DAG but think that would be too cumbersome -
> > especially as the scores are disease specific.
> > 
> > Michael
> > 
> > --
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> -- 
> 
> **************************************************************
> Pankaj Jaiswal, Ph.D.                                   
> Postdoctoral Associate
> Dept. of plant Breeding                             
> Cornell University                                   
> Ithaca, NY-14853, USA   
> 
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org   http://ars-genome.cornell.edu/rice
> **************************************************************
> 
> 
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