[BioNLP] dataset of phenotypic information for plants

Martin Krallinger mkrallinger at cnio.es
Wed Oct 21 09:29:44 EDT 2009


Hi Sofie,

we have implemented a sentence retrieval system for leaf development as 
part of
PLAN2L (Plant annotation to literature): 
http://zope.bioinfo.cnio.es/plan2l/plan2l.html

Martin Krallinger, Carlos Rodriguez-Penagos, Ashish Tendulkar and 
Alfonso Valencia: PLAN2L: a web tool for integrated text mining and 
literature-based bioentity relation extraction. Nucl. Acids Res., Web 
Server Issue, 2009.

In case you are interested I provide you more detailed feedback on the 
used strategy, maybe soem
of our data could be useful for you too.

Best regards,

Martin


--------------------------------------------------
Martin Krallinger
Structural Biology and Biocomputing Group,
Spanish National Cancer Research Center (CNIO)
E-28029 Madrid, Spain
Tel.: +(34)917 328 000
Fax:  +(34)912 246 980
e-mail: mkrallinger at cnio.es
--------------------------------------------------

> is anybody aware of existing datasets consisting of phenotypic 
> information such as leaf development linked to genes?
>
> We would want to extract sentences like this one : "In Arabidopsis, 
> deletion of the PEAPOD (PPD) locus increases leaf lamina size and 
> results in dome-shaped rather than flat leaves." and convert them to a 
> machine-readable format in an event-style sort of annotation.
>
> I would be very grateful for any pointers on this subject!
>
> Best regards,
> Sofie
>
>   


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