« Previous
Next »
Artificial Intelligence in Medicine
Volume 39, Issue 2
, Pages 127-136
, February 2007
Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach
References
- . Relation mining over a corpus of scientific literature. In: Proceedings of the 10th Conference on Artificial Intelligence in Medicine, LNAI 3581. Aberdeen, Scotland: Springer Verlag; 2005;p. 550–559
- . An environment for relation mining over richly annotated corpora: the case of GENIA. In: Proceedings of the second international symposium on semantic mining in biomedicine. 2006;p. 68–75
- . Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics. 2004;20(5):604–611
- . The daily rhythms of genes, cells and organs. Biological clocks and circadian timing in cells. EMBO Rep. 2005;6:9–13
- . All in good time: the Arabidopsis Circadian Clock. Trends Plant Sci. 2000;5(12):517–522
- . GENIA corpus—a semantically annotated corpus for bio-textmining. Bioinformatics. 2003;19(1):180–182
- Kaljurand K, Rinaldi F, Schneider G. Prolog-based query interface to syntactic dependencies extracted from biomedical literature. Technical report IFI-2006.04. University of Zurich; 2006.
- . Multilayer Annotations in PARMENIDES. In: Handschuh S, Koivunen M, Dieng R, Staab S editor. Proceedings of the K-CAP2003 workshop on knowledge markup and semantic annotation. 2003;p. 33–40
- . A maximum entropy approach to identifying sentence boundaries. In: Proceedings of the fifth conference on applied natural language processing. Washington, DC: University of Pennsylvania; 1997;p. 16–19
- . Building a large annotated corpus of English: the Penn treebank. Comput Linguist. 1993;19:313–330
- . A maximum entropy part-of-speech tagger. In: Brill E, Church K editor. Proceedings of the empirical methods in natural language processing conference. University of Pennsylvania; 1996;p. 133–142
- . Applied morphological processing of English. Nat Lang Eng. 2001;7(3):207–223
- . Automatic rule induction for unknown word guessing. Comput Linguist. 1997;23(3):405–423
- . Extracting and using trace-free functional dependencies from the Penn treebank to reduce parsing complexity. In: Nivre J, Hinrichs E editor. Proceedings of the second workshop on treebanks and linguistic theories (TLT 2003), vol. 9 of Mathematical Modelling in Physics, Engineering and Cognitive Science. 2003;p. 153–164
- . Fast, deep-linguistic statistical minimalist dependency parsing. In: Kruijff G, Duchier D editor. Proceedings of the COLING-2004 workshop on recent advances in dependency grammars. 2004;p. 33–40
- M. Collins, Head-statistical models for natural language processing. PhD Thesis. Philadelphia, USA: University of Pennsylvania; 1999.
- . Recognition and parsing of context-free languages in time
. Inform Contr. 1967;10:189–208 - http://www.cs.york.ac.uk/aig/lll/lll05/(accessed: May 10, 2006) In: Cussens J, Nédellec C editor. Proceedings of the workshop on learning language in logic (LLL05). 2005;
- . Parser evaluation: using a grammatical relation annotation scheme. In: Abeillé A editors. Treebanks: building and using parsed corpora. Dordrecht: Kluwer; 2003;p. 299–316
- . Dependency-based evaluation of MINIPAR. In: Proceedings of the workshop on the evaluation of parsing systems. 1998;
- . Using grammatical relations to compare parsers. In: Proceedings of the EACL ’03. 2003;p. 291–296
- . Event extraction from biomedical papers using a full parser. In: Proceedings of Pacific symposium on biocomputing. River Edge, NJ: World Scientific Publishing; 2001;p. 408–419
- . Corpus-oriented grammar development for acquiring a head-driven phrase structure grammar from the Penn treebank. In: Proceedings of IJCNLP-04. 2004;p. 684–693
- . GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics. 2001;17(1):74–82
- . Information extraction from biological texts: the PASTA system. Bioinformatics. 2003;19:135–143
- . MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics. 2003;19(13):1699–1706
- . Learning biological interactions from medline abstracts. In: Cussens J, Nédellec C editor. Proceedings of the workshop on learning language in logic (LLL05). 2005;p. 53–58
- . Automatically acquiring a linguistically motivated genic interaction extraction system. In: Cussens J, Nédellec C editor. Proceedings of the workshop on learning language in logic (LLL05). 2005;p. 46–52
☆ A preliminary version of the system described in this paper has been presented in [1]. Recent results obtained after the submission of this paper are described in [2]. All URLs mentioned in this paper have been accessed and verified on 10 May 2006.
☆☆ The tools and resources used for the work described in this paper are freely available for research purposes. The DepGENIA corpus can be downloaded from the OntoGene web site (http://www.ontogene.org/). The Pro3Gres parser and the OntoGene text mining system can be obtained by contacting the authors of this paper.
PII: S0933-3657(06)00137-0
doi: 10.1016/j.artmed.2006.08.005
« Previous
Next »
Artificial Intelligence in Medicine
Volume 39, Issue 2
, Pages 127-136
, February 2007
