[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): 

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 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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