Benchmarking natural-language parsers for biological applications using dependency graphs

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Clegg, Andrew B ^a   Shepherd, Adrian J ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL APPLICATIONS; BIOLOGICAL EVALUATION; DEPENDENCY GRAPHS; INTERMEDIATE REPRESENTATIONS; NATURAL LANGUAGE PROCESSING; PERFORMANCE MEASURE; PROCESSING TECHNIQUE; SEMANTIC RELATIONSHIPS;

BIOINFORMATICS; ERRORS; GENE EXPRESSION; NATURAL LANGUAGE PROCESSING SYSTEMS; TOOLS; TREES (MATHEMATICS);

SEMANTICS;

TRANSCRIPTION FACTOR GATA 1;

ACCESS TO INFORMATION; ACCURACY; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; GENE EXPRESSION; HUMAN; INFORMATION PROCESSING; MACROPHAGE; MONOCYTE; NATURAL LANGUAGE PROCESSING; NONHUMAN; SEMANTICS; ALGORITHM; ANIMAL; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA BASE; DEVICES; INFORMATION RETRIEVAL; LANGUAGE; PROCEDURES; QUALITY CONTROL; REPRODUCIBILITY; STANDARDS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BENCHMARKING; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; LANGUAGE; MODELS, STATISTICAL; NATURAL LANGUAGE PROCESSING; PROGRAMMING LANGUAGES; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 33847095048     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-24     Document Type: Article

References (54)

1. Cohen KB Hunter L Natural language processing and systems biology Artificial intelligence methods and tools for systems biology Dordrecht: Kluwer Dubitzky W, Azuaje F 2004
2. Xiao J Su J Zhou G Tan C Protein-Protein Interaction: A Supervised Learning Approach Proceedings of the First International Symposium on Semantic Mining in Biomedicine Hinxton, UK 2005
3. Camon EB Barrell DG Dimmer EC Lee V Magrane M Maslen J Binns D Apweiler R An evaluation of GO annotation retrieval for BioCreAtIvE and GOA BMC Bioinformatics 2005 6 Suppl. 1 (S17) 15960829
4. Domedel-Puig N Wernisch L Applying GIFT, a Gene Interactions Finder in Text, to fly literature Bioinformatics 2005 21 17 3582-3583 10.1093/ bioinformatics/bti578 16014369
5. Rindflesch TC Bisharah L Dimitar H Aronson AR H K Semantic Relations Asserting the Etiology of Genetic Diseases Proceedings of the American Medical Informatics Association Annual Symposium, Hanley and Belfus, Inc 2003
6. Temkin JM Gilder MR Extraction of protein interaction information from unstructured text using a context-free grammar Bioinformatics 2003 19 16 2046-2053 10.1093/bioinformatics/btg279 14594709
7. Ahmed ST Chidambaram D Davulcu H Baral C IntEx: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text Proceedings of the ACL-ISMB Workshop on Linking Biological Literature. Ontologies and Databases: Mining Biological Semantics Detroit: Association for Computational Linguistics 2005 54-61
8. 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 10.1016/j.ijmedinf.2005.06.009 16099201
9. de Marneffe MC MacCartney B Manning CD Generating Typed Dependency Parses from Phrase Structure Parses Proceedings of 5th International Conference on Language Resources and Evaluation (LREC2006) Genoa, Italy 2006
10. Marcus MP Santorini B Marcinkiewicz MA Building a Large Annotated Corpus of English: The Penn Treebank Computational Linguistics 1994 19 2 313-330
11. Sampson G Babarczy A A test of the leaf-ancestor metric for parse accuracy Proceedings of the Beyond PARSEVAL workshop of the third LREC conference Las Palmas, Canary Islands 2002
12. Clegg AB Shepherd AJ Evaluating and integrating treebank parsers on a biomedical corpus Association for Computational Linguistics Workshop on Software CDROM Jansche M, Ann Arbor, MI 2005
13. GENIA Treebank Beta Version http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/ topics/Corpus/GTB.html
14. Mining the Bibliome http://bioie.ldc.upenn.edu/
15. Bikel DM Design of a Multi-lingual, Parallel-processing Statistical Parsing Engine Proceedings of the Human Language Technology Conference 2002 (HLT2002) San Diego 2002
16. Collins M Head-Driven Statistical Models for Natural Language Parsing Phd University of Pennsylvania 1999
17. Klein D Manning CD Fast Exact Inference with a Factored Model for Natural Language Parsing Advances in Neural Information Processing Systems 2002 3-10
18. Klein D Manning CD Accurate Unlexicalized Parsing Proceedings of the 41st Meeting of the Association for Computational Linguistics (ACL'03). Main Volume Sapporo, Japan: ACL 2003
19. Charniak E A Maximum-Entropy-Inspired Parser Tech rep Brown University 1999
20. Lease M Charniak E Parsing Biomedical Literature Proceedings of the Second International Joint Conference on Natural Language Processing (IJCNLP'05) Jeju Island, Korea Dale R, Wong KF, Su J, Kwong OY 2005
21. Friedman C Kra P Rzhetsky A Two biomedical sublanguages: A description based on the theories of Zellig Harris Journal of Biomedical Informatics 2002 35 4 222-235 10.1016/S1532-0464(03)00012-1 12755517
22. Bikel Parser http://www.cis.upenn.edu/~dbikel/software.html
23. Goldin IM Chapman WW Learning to Detect Negation with 'Not' in Medical Texts ACM SIGIR '03 Workshop on Text Analysis and Search for Bioinformatics: Participant Notebook Toronto, Canada: Association for Computing Machinery 2003
24. Mutalik PG Deshpande A Nadkarni PM Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents: A Quantitative Study Using the UMLS Journal of the American Medical Informatics Association 2001 8 6 598-609 130070 11687566
25. Ge N Hale J Charniak E A Statistical Approach to Anaphora Resolution Proceedings of the Sixth Workshop on Very Large Corpora, Hong Kong 1998
26. Gildea D Jurafsky D Automatic labeling of semantic roles Computational Linguistics 2002 28 3 245-288 10.1162/089120102760275983
27. Knight K Marcu D Statistics-based summarization - Step one: Sentence compression Proceedings of the 17th National Conference on Artificial Intelligence (AAAI) Austin, Texas 2000
28. Merlo P Stevenson S Automatic Verb Classification Based on Statistical Distributions of Argument Structure Computational Linguistics 2001 27 3 373-408 10.1162/089120101317066122
29. Blaheta D Charniak E Assigning function tags to parsed text Proceedings of the 1st Annual Meeting of the North American Chapter of the Association for Computational Linguistics 2000 234-240
30. Bies A Kulick S Mandel M Parallel Entity and Treebank Annotation Proceedings of the Workshop on Frontiers in Corpus Annotations II: Pie in the Sky Ann Arbor, Michigan: Association for Computational Linguistics 2005 21-28
31. Rosario B Hearst M Classifying Semantic Relations in Bioscience Texts Proceedings of the 42nd Meeting of the Association for Computational Linguistics (ACL'04), Main Volume Barcelona, Spain 2004 430-437
32. Shi Z Gu B Popowich F Sarkar A Synonym-based Query Expansion and Boosting-based Re-ranking: A Two-phase Approach for Genomic Information Retrieval Proceedings of the Fourteenth Text REtrieval Conference (TREC 2005) Gaithersburg, Maryland 2005
33. Sanchez O Poesio M Acquisition of Causal Knowledge from Text: Applications to Bioinformatics First International Symposium on Semantic Mining in Biomedicine (SMBM) poster session Hinxton, UK 2005
34. Huang Y Lowe HJ Klein D Cucina RJ Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon Journal of the American Medical Informatics Association 2005 12 3 275-285 1090458 15684131 10.1197/jamia.M1695
35. Finkel J Dingare S Nguyen H Nissim M Manning C Sinclair G Exploiting concepts for biomedical entity recognition: From syntax to the Web Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA) Geneva, Switzerland Collier N, Ruch P, Nazarenko A 2004 88-91
36. Grover C Lapata M Lascarides A A comparison of parsing technologies for the biomedical domain Natural Language Engineering 2005 11 27-65 10.1017/ S1351324904003547
37. Grover C Carroll J Briscoe EJ The Alvey Natural Language Tools grammar (4th release) Technical report 284, Cambridge University 1993 http://www.cl.cam.ac.uk/users/ejb/anlt-gram.pdf
38. Abney S Partial Parsing via Finite-State Cascades Workshop on Robust Parsing. 8th European Summer School in Logic. Language and Information (ESSLI) Carroll J, Prague 1996 8-15
39. Briscoe EJ Carroll J Robust Accurate Statistical Annotation of General Text Proceedings of the Third International Conference on Language Resources and Evaluation (LREC 2002) Las Palmas, Canary Islands 2002 1499-1504
40. Sleator D Temperley D Parsing English with a Link Grammar Proceedings of the Third International Workshop on Parsing Technologies Tilburg, Netherlands 1993
41. Connexor Oy http://www.connexor.com/
42. Franzén K Eriksson G Olsson F Lidén LAP Coster J Protein names and how to find them International Journal of Medical Informatics 2002 67 l-3 49-61 10.1016/S1386-5056(02)00052-7 12460631
43. Tsivtsivadze E Pahikkala T Pyysalo S Boberg J Mylläri A Salakoski T Regularized Least-Squares for Parse Ranking Proceedings of the 6th International Symposium on Intelligent Data Analysis (IDA 2005) Madrid, Spain 2005 464 474
44. Schneider G Rinaldi F Kaljurand K Hess M Steps towards a GENIA Dependency Treebank Proceedings of the Third Workshop on Treebanks and Linguistic Theories (TLT 2004) Tübingen, Germany 2004 137-148
45. Schneider G Dowdall J Rinaldi F A robust and deep-linguistic theory applied to large-scale parsing Coling 2004 Workshop on Robust Methods in the Analysis of Natural Language Data (ROMAND 2004) Geneva 2004
46. Lin D A dependency-based method for evaluating broad-coverage parsers Proceedings of the International Joint Conference on Artificial Intelligence (IJACI-95) Montreal, Quebec 1995
47. Lin D Dependency-Based Evaluation Of Minipar Building and using Parsed Corpora Dordrecht: Kluwer Abeillé A 2003
48. Carroll J Briscoe T Sanfilippo A Parser evaluation: A survey and new proposal Proceedings of the first international conference on language resources and evaluation (LREC) Granada, Spain 1998
49. Carroll J Minnen G Briscoe T Corpus annotation for parser evaluation Proceedings of the EACL workshop on linguistically interpreted corpora (LINC) Bergen, Norway 1999
50. Briscoe T Carroll J Graham J Copestake A Relational evaluation schemes Proceedings of the Beyond PARSEVAL workshop of the third LREC conference Las Palmas, Canary Islands 2002
51. Srinivas B Doran C Hockey BA Joshi A An approach to robust partial parsing and evaluation metrics Proceedings of the Eight European Summer School In Logic. Language and Information Prague, Czech Republic 1996
52. Kübler S Telljohann H Towards a dependency-oriented evaluation for partial parsing Proceedings of the Beyond PARSEVAL workshop of the third LREC conference Las Palmas, Canary Islands 2002
53. Smith L Rindflesch T Wilbur WJ MedPost: A part-of-speech tagger for bioMedical text Bioinformatics 2004 20 14 2320 2321 10.1093/ bioinformatics/bth227 15073016
54. Stanford NLP tools http://nlp.stanford.edu/software/index.shtml