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Message from Declan Butler, Nature

Declan Butler, Nature d.butler at
Thu Aug 30 14:34:54 PDT 2001

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 ); any
implications for GO? Is there a case for bringing GO, other biological
ontologies, within the broader chapel of W3C?

All the best

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 Publishing Group
BP 264
3 rue de l'Arrivee
75015 Paris

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