[Corpora-List] [BioNLP] Dependency parsing of biomedical texts (fwd)

[radev at umich.edu]

Here is a reply by Arzucan Ozgur at Michigan.

Drago

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Some of the dependency parsers used in the BioNLP domain are Minipar,  
Link Parser, Charniak Parser, and Stanford Parser.

We have used the Stanford Parser to extract protein interactions from  
text and achieved good performance:
- Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. Semi-supervised  
classification for extracting protein interaction sentences using  
dependency parsing. In Proceedings of the Conference of Empirical  
Methods in Natural Language Processing (EMNLP '07), Prague, Czech  
Republic, June 28-30 2007.
http://acl.ldc.upenn.edu/D/D07/D07-1024.pdf

- Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. Extracting  
interacting protein pairs and evidence sentences by using dependency  
parsing and machine learning techniques . In Proceedings of the  
Second BioCreAtIvE Challenge Workshop - Critical Assessment of  
Information Extraction in Molecular Biology, Madrid, Spain, ISBN  
84-933255-6-2, April 23-25 2007.

The following paper compares the Stanford Parser with Minipar and  
Link Parser:
- Marie-Catherine de Marneffe, Bill MacCartney and Christopher D.  
Manning. 2006. Generating Typed Dependency Parses from Phrase  
Structure Parses. In LREC 2006.

The following paper compares Link Grammar and Connexor Machinese  
Syntax in the biomedical domain:
- Pyysalo S, Ginter F, Pahikkala T, Boberg J, Järvinen J, Salakoski  
T :Evaluation of two dependency parsers on biomedical corpus targeted  
at protein-protein interactions.
International Journal of Medical Informatics 2006, 75(6):430-442.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1764446

Other relevant papers are:
- Grover C, Lapata M, Lascarides A :A comparison of parsing  
technologies for the biomedical domain.
Natural Language Engineering 2005, 11:27-65.

- Lease M, Charniak E :Parsing Biomedical Literature. In Proceedings  
of the Second International Joint Conference on Natural Language  
Processing (IJCNLP'05).

- Andrew B Clegg and Adrian J Shepherd, Benchmarking natural-language  
parsers for biological applications using dependency graphs, BMC  
Bioinformatics 2007, 8:24.


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