[Fwd: Message from Declan Butler, Nature]

[Pankaj Jaiswal]

Hi Susan and Lincoln, 

You might as well have some suggestions.

-pankaj

"Declan Butler, Nature" wrote:
> 
> Dear all
> My apologies if the subject of this message is tangential to the purpose of
> your list. I'm finishing a broad piece tonight for Nature on the future of
> the electronic literature; this will be followed up later by a more detailed
> feature on the 'scientific publication of the future.' I'm keen to include
> GO as an ontology-based approach to knowledge management, as a key example
> of the changes underway towards a structured approach to information, and
> unification. I appreciate that much of the GO ontology work is clearly
> focussed on resolving nomenclature problems, and transferring annotations
> among biological databases, but what I'm trying to figure out is how to get
> across to readers what the potential impact might also eventually be on the
> literature side of things -- acknowledging that the line between literature
> and databases is set to become increasingly blurred :-).
> 
> Say for example, that publishers began tagging genes and proteins in papers
> to their GO terms; in principle this might allow data mining of papers to
> cluster papers according to GO hierarchies, for example. So what I want to
> get across to the reader at the bench is, given an electronic literature
> that is more akin to a database, what your ontology based approach might
> mean for them in practical terms; ie how might GO be used to allow queries
> that are not now possible in analysing the literature. For example, say you
> searched/mined the literature for a subset of genes that otherwise by their
> name (and their synonyms), have nothing in common, but which we combine in a
> search because we have selected them as belonging to a GO annotation for a
> process, molecular function, or location, eg genes involved in DNA repair.
> Might this allow us to group apparently unrelated papers -- say on DNA
> repair -- that would not be possible were we just searching on gene names
> alone? Or have I misunderstood something, and this approach is fundamentally
> flawed?; let me know.
> 
> What difference might this make to their research/use of the literature?
> More broadly how, if at all, do you see GO and the evolution of other
> ontology/database-driven systems changing the very nature of the scientific
> 'paper' (should publishers be thinking of adding GO terms/metadata from
> various ontologies (eg source tissue/experimental conditions) to papers?).
> How, why, benefits, problems? What might the impact be?
> 
> Given the short notice, even a few bullet points of thoughts by return mail
> would be useful; longer responses later would be welcome; I know the general
> area fairly well, but am endeavouring to make it tangible to readers, so I
> need good grassroots examples and input, and I thought best to go straight
> to the sources of expertise. So any thoughts welcome.
> 
> In passing, I've been following the discussion re PICS etc; given that RDF
> has largely superceded PICS, how does GO feel it should be interacting with
> the W3C, eg given the announcement of the latter this month of the launch of
> a Web Ontology Working Group (see http://www.w3.org/2001/sw/ ); any
> implications for GO? Is there a case for bringing GO, other biological
> ontologies, within the broader chapel of W3C?
> 
> All the best
> Declan
> 
> Declan Butler
> European correspondent, Nature,
> & Editor, Nature Yearbook of Science and Technology.
> Tel: 33 1 43 27 42 13
> Fax: 33 1 43 20 51 52
> d.butler at nature-france.com
> 
> Nature Publishing Group
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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
**************************************************************