Journal and Proceedings Articles -- BIONLP.ORG

Updated 5 July 2010
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The mailing list archives are now the place to find pointers to conferences and articles.

October 7th, 2004: Here are two papers from the most recent issue of the IBM Systems Journal, Vol. 43, No. 3, 2004:

September 18th, 2004: This link to some PAKDD 2004 papers on Biomedical Mining contains the titles/authors/abstracts of six papers presented there. The information below was kindly gathered by and contributed by Oriane Matte-Tailliez.

February 2nd, 2004: A lengthy review, "Mining the Biomedical Literature in the Genomic Era: An Overview" by H. Shatkay and R. Feldman appeared in the December 2003 issue of the Journal of Computational Biology, 10 (3) 821-855. A PDF of the paper from Shatkay's site, which she describes as "A somewhat modified preprint version" is available as a PDF file here.

NLP papers from the PSB, ACL and ISMB conferences/workshops:

A 2002 review by Mandell and Majoros on Genomics and NLP: A copy of their paper appeared on the Web but is copyright by the Nature Publishing Group. Use with care. Here is a copy cached on the site. (Posted 7/20/2003)

Two papers from ISMB 2001

A review on biology text mining, abstract and references, from Bioinformatics 12/02

Papers from the session at PSB 2002, January 2002

This first paper is not from the NLP session, but should be of interest:

Ontology Development for a Pharmacogenetics Knowledge Base
D.E. Oliver, D.L. Rubin, J.M. Stuart, M. Hewett, T.E. Klein, and R.B. Altman cached

The remainder are from the NLP session Literature Data Mining for Biology

Session Introduction
L. Hirschman, J.C. Park, J. Tsujii, C. Wu, and L. Wong cached

Mining MEDLINE: Abstracts, Sentences, or Phrases?
J. Ding, D. Berleant, D. Nettleton, and E. Wurtele cached

Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System
U. Hahn, M. Romacker, and S. Schulz cached

Filling Preposition-Based Templates to Capture Information from Medical Abstracts
G. Leroy and H. Chen cached

Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations
J. Pustejovsky, J. Casta–o, J. Zhang, M. Kotecki, and B. Cochran cached

Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector Machines
B.J. Stapley, L.A. Kelley, and M.J.E. Sternberg cached

A Thematic Analysis of the AIDS Literature
W.J. Wilbur cached

Papers from the session at PSB 2001


Session Introduction
J. Tsujii and L. Wong; Pacific Symposium on Biocomputing 6:372-373 (2001). (cached)

Including Biological Literature Improves Homology Search
J.T. Chang, S. Raychaudhuri, and R.B. Altman; Pacific Symposium on Biocomputing 6:374-383 (2001). (cached)

TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology
I. Iliopoulos, A. J. Enright, and C. A. Ouzounis ; Pacific Symposium on Biocomputing 6:384-395 (2001). (cached)

Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar
J. C. Park, H. S. Kim, and J. J. Kim; Pacific Symposium on Biocomputing 6:396-407 (2001). (cached)

Event Extraction from Biomedical Papers Using a Full Parser
A. Yakushiji, Y. Tateisi, Y. Miyao, and J. Tsujii; Pacific Symposium on Biocomputing 6:408-419 (2001). (cached)

An additional paper not in the PSB 2001 NLP session, but is of interest, is: PIES, A Protein Interaction Extraction System
L. Wong; Pacific Symposium on Biocomputing 6:520-531 (2001). (cached)

PSB 2000 had a similar session on NLP:

Session Introduction
T. Tsunoda and L. Wong; Pacific Symposium on Biocomputing 5:488-489 (2000). (cached)

Knowledge Representation and Indexing Using the Unified Medical Language System
K. Baclawski, J. Cigna, M.M. Kokar, P. Mager, and B. Indurkhya; Pacific Symposium on Biocomputing 5:490-501 (2000). (cached)

Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures
K. Humphreys, G. Demetriou and R. Gaizauskas; Pacific Symposium on Biocomputing 5:502-513 (2000). (cached)

EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature
T.C. Rindflesch, Lorraine Tanabe, John N. Weinstein, and L. Hunter; Pacific Symposium on Biocomputing 5:514-525 (2000). (cached)

Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts
B.J. Stapley and G. Benoit; Pacific Symposium on Biocomputing 5:526-537 (2000). (cached)

Automatic Extraction of Protein Interactions from Scientific Abstracts
J. Thomas, D. Milward, C. Ouzounis, S. Pulman, and M. Carroll; Pacific Symposium on Biocomputing 5:538-549 (2000). (cached)

Access to prior years' proceedings of PSB (There were no sessions devoted specifically to NLP in the prior years' conferences.)

From the Bioinformatics Journal, July 2001 (Added 28 July 2001):

The following two articles appeared in the Proceedings of ISMB 2001, published as a special issue of Bionformatics, Vol. 17, Suppplement 1, July 2001. Available to subscribers on-line at

Carol Friedman, Pauline Kra, Hony Yu, Michael Krauthammer and Andry Rzhetsky "GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles", pgs. S74-S82.

Vasileios Hatzivassiloglou, Pablo A. Duboue and Andrey Rzhetsky, "Disambiguating proteins, genes, and RNA in text: a machine learning approach", pgs. S97-S106.