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

[ec at cs.brown.edu]

We are just releasing a new Biomed parser.  On the genia biomed
treebank it significantly outperforms previous work.  If you
go to the Bllip web page at Brown you will (or will shortly)
find a link to it.

Quoting radev at umich.edu:

> Here is a reply by Arzucan Ozgur at Michigan.
>
> Drago
>
> -----------------------------------------------------------------
>
> 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.
>
>
> 9
>
> _______________________________________________
> Corpora mailing list
> Corpora at uib.no
> http://mailman.uib.no/listinfo/corpora
>




----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

_______________________________________________
Corpora mailing list
Corpora at uib.no
http://mailman.uib.no/listinfo/corpora