Clarifying the 'confusion' - RE: Summary of discussion

[Vincent, Leszek]

Hi Pankaj (& colleagues elsewhere)

It's good to 'hear' that you folk are looking into what can be done with your Gramene ontology browser so that the arrangement of biologically sequenced relationships are somehow maintained when the ontology database is viewed with the browser. 

My struggle is that the alphabetic & numeric sequencing of terms (concepts) in DAG-Edit adds somewhat to the complexity of applying the True Path Rule (TPR). When applying the TPR you will appreciate that complex networks of concept-relationships & associations are worked through in our thinking. Similarly when we construct a representation of putative relationships in a DAG a lot of implicit & explicit biology is surveyed at the conceptual level & the subsequent representation of this in the DAG is a very information-rich product. So, having this complexity reorganised via alphabetic & numeric criteria really impacts (adversely) my biological-systems thinking when applying the TPR & adding to existing DAG material. This is where 'confusion' originates for me. Hopefully we can overcome this challenge in DAG-Edit & avoid it in the browser(s) of ontology - if at all possible - without adversely affecting other arrangements of good fruit at the software-level. 

Regards,
- Leszek
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P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228; 
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
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> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Sunday, May 19, 2002 6:11 PM
> To: gramene at brie.cshl.org; Michael Ashburner (Genetics)
> Cc: curator at acoma.Stanford.EDU; ware at cshl.org; Coe, Edward H.;
> lreiser at acoma.Stanford.EDU; lstein at cshl.org;
> maryp at teosinte.agron.missouri.edu; r.bruskiewich at cgiar.org;
> rhee at acoma.Stanford.EDU; smundodi at acoma.Stanford.EDU; 
> srm4 at cornell.edu;
> tberardi at acoma.Stanford.EDU; V.ULAT at cgiar.org; Vincent, Leszek;
> sprig-cvo_dev at bioinformatics.org
> Subject: Re: Summary of discussion
> 
> "Michael Ashburner (Genetics)" wrote:
> 
> > 
> > >- DAG-Edit arranges terms in alphabetic & numerical order ...
> > 
> > .. this was discussed at he recent GO meeting in CSHLs, I 
> _think_ John Richter
> > was going to do something about this, but I am not sure.
> >
> 
> Please do not confuse with the representation of alphabetic & 
> numerical order of
> terms in DAG edit software Vs the Web browser we have. The 
> ontology browser we
> have works out of an ontology database and the concepts are 
> different compared
> to DAG edit. They are different issues to be dealt with. I 
> will see what can be
> done with the ontology browser.
> 
> Pankaj
>