W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2008

Re: RE: BioRDF Brainstorming

From: <samwald@gmx.at>
Date: Tue, 12 Feb 2008 14:47:52 +0100
Cc: holger.stenzhorn@deri.org
Message-ID: <20080212134752.109250@gmx.net>
To: "Colin Batchelor" <BatchelorC@rsc.org>, public-semweb-lifesci@w3.org

> Good point.  What I was sort of driving at (and failing) was the context 
> in which the facts are mentioned---are they the aim of the paper, 
> background information, mentioned as results and so forth?

In what I see as the ideal scenario, each text/database entry would only be 
annotated with the results and not with background information or the 
citation of secondary sources. The annotations should only consist of what 
the creators of the annotated text/database entry considered to be 'true', and what has not already been stated in other texts/database entries.

For example, article pmid:123 contains the text
"We found that bananas are yellow. This is in conflict with article 
pmid:456, which states that bananas are pink".

Article pmid:123 should only be annotated with 
"banana has_quality yellow . 
pmid:123 in_conflict_with pmid:456 ."
Article pmid:456 should be annotated with 
"banana has_quality pink ."

"banana has_quality pink" should not be re-iterated in the annotation of 

For widely-accepted and deployed biomedical annotation it really does not need to be more complicated than that. Trying to capture the whole narrative of each publication in detail in such a scenario is very hard and might actually make the annotation as a whole less usable, since it becomes harder to understand, query, integrate and maintain.

Matthias Samwald 

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Received on Tuesday, 12 February 2008 13:48:05 UTC

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