[BioNLP] Comparison of concept identification systems

Krallinger.Martin mkrallinger at cnio.es
Wed Nov 30 12:36:28 EST 2011

Hi Ning Kang,
you might find the IMS task of BioCreative III interesting as it relates to the identification 
of ontology concepts in full text papers. In this case it was on concepts from the Molecular 
Interaction (MI) ontology used for annotation of protein interactions.
The paper describing all the methods and the results, data sets, etc is :
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
<http://www.biomedcentral.com/1471-2105/12/S8/S3> Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W John Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu, et al.
BMC Bioinformatics 2011, 12(Suppl 8):S3 (3 October 2011)

It also provides a summery of the kind of techniques used for this purpose. 

Does anyone know any paper about comparison of performance and usability
for more than 2 biomedical concept identification systems?

I only found some papers compared Metamap and their own system, and did not
find any paper compared more systems together. I am now doing some work for

Btw, besides MetaMap, Watizit, NCBO Annotator(MGREP), are there any other
public available biomedical concept identification systems?

Thank you very much.

Ning Kang
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