A graph-search framework for associating gene identifiers with documents

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Cohen, William W ^a,b   Minkov, Einat ^a  

^a Carnegie Mellon University   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATION METHOD; ENGINEERED COMPONENTS; GRAPH-BASED METHODS; NAMED ENTITY RECOGNITION; PERFORMANCE MEASURE; RANKING APPROACH; SEMI-AUTOMATED SYSTEMS; SOURCES OF INFORMATIONS;

GRAPHIC METHODS;

GENES;

ACCURACY; ANALYTIC METHOD; ARTICLE; AUTOMATION; BIOINFORMATICS; DATA BASE; ERROR; GENE IDENTIFICATION; INFORMATION TECHNOLOGY; PREDICTION; SCIENTIFIC LITERATURE; ANIMAL; AUTOMATED PATTERN RECOGNITION; BIOLOGY; COMPUTER GRAPHICS; GENETIC DATABASE; MOUSE; PROCEDURES;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, GENETIC; MICE; PATTERN RECOGNITION, AUTOMATED;

EID: 33750362799     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-440     Document Type: Article

References (33)

1. MGI: Mouse Genome Informatics [http://www.informatics.jax.org/]
2. FlyBase: A Database of the Drosophila Genome [http://flybase.bao.indiana.edu/]
3. Cohen AM, Hersh WR: The TREC 2004 genomics track categorization task: classifying full text biomedical documents. Journal of Biomedical Discovery and Collaboration 2006, 1(4):1-15.
4. Consortium TGO: Gene Ontology: tool for the unification of biology. Nature Genetics 2000, 25:25-29.
5. Hirschman L, Yeh A, Blaschke C, Valencia A: Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 2005, 6 Suppl 1:S1.
6. Hirschman L, Colosimo M, Morgan A, Yeh A: Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 2005, 6 Suppl 1:S11.
7. Yeh A, Morgan A, Colosimo M, Hirschman L: BioCreAtIvE Task 1A: gene mention finding evaluation. BMC Bioinformatics 2005, 6 Suppl 1:S2.
8. Leser U, Hakenberg J: What makes a gene name? Named entity recognition in the biomedical literature. Briefings in Bioinformatics 2005, 6:357-369.
9. Cohen AM, Hersh WR: A survey of current work in biomedical text mining. Briefings in Bioinformatics 2005, 6:57-71.
10. Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW: Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Artificial Intelligence in Medicine (Special Issue on Summarization and Information Extraction from Medical Documents) 2004, 33(2):139-155.
11. Humphreys K, Demetriou G, Gaizauskas R: Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures. Proceedings of the Pacific Symposium on Biocomputing (PSB) 2000:502-513.
12. Rindflesch T, Tanabe L, Weinstein JN, Hunter L: EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature. Proceedings of the Pacific Symposium on Biocomputing (PSB) 2000:514-525.
13. Craven M, Kumlien J: Constructing Biological Knowledge Bases by Extracting Information from Text Sources. In Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB-99) AAAI Press; 1999:77-86.
14. Minorthird: Methods for Identifying Names and Ontological Relations in Text using Heuristics for Inducing Regularities from Data 2004 [http://minorthird.sourceforge.net].
15. Franzén K, Eriksson G, Olsson F, Lidén LAP, Coster J: Protein names and how to find them. International Journal of Medical Informatics 2002, 67(1-3):49-61.
16. Collins M: Discriminative Training Methods for Hidden Markov Models: Theory and Experiments with Perceptron Algorithms. Empirical Methods in Natural Language Processing (EMNLP) 2002.
17. Altun Y, Tsochantaridis I, Hofmann T: Hidden Markov Support Vector Machines. Proceedings of the 20th International Conference on Machine Learning (ICML) 2003.
18. Sha F, Pereira F: Shallow parsing with conditional random fields. Proceedings of HLT-NAACL 2003.
19. Minkov E, Wang RC, Tomasic A, Cohen W: NER Systems that Suit User's Preferences: Adjusting the Recall-Precision Trade-off for Entity Extraction. HLT/NAACL 2006. [To appear]
20. Kou Z, Cohen WW, Murphy RF: High-recall protein entity recognition using a dictionary. Bioinformatics 2005, 21 Suppl 1:i266-73.
21. Cohen WW, Ravikumar P, Fienberg SE: A Comparison of String Distance Metrics for Name-Matching Tasks. Proceedings of the IJCAI-2003 Workshop on Information Integration on the Web (IIWeb-03) 2003.
22. Zhai C, Cohen WW, Lafferty JD: Beyond independent relevance: methods and evaluation metrics for subtopic retrieval. SIGIR 2003: Proceedings of the 26th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, ACM 2003:10-17.
23. Kondor RI, Lafferty J: Diffusion Kernels on Graphs and Other Discrete Structures. Proceedings of the ICML 2002.
24. Minkov E, Cohen WW, Ng AY: Contextual Search and Name Disambiguation in Email Using Graphs. ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR) 2006.
25. Freund Y, Schapire RE: Large Margin Classification Using the Perceptron Algorithm. Computational Learning Theory 1998:209-217.
26. Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005, 6 Suppl 1:S14.
27. Fundel K, Guttner D, Zimmer R, Apostolakis J: A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 2005, 6 Suppl 1:S15.
28. Crim J, McDonald R, Pereira F: Automatically An- noting Documents with h. BMC Bioinformatics 2005, 6 Suppl 1:S13.
29. Cohen AM: Unsupervised gene/protein entity normalization using automatically extracted dictionaries. Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics (BioLink-2005) 2005:17-24.
30. Cohen WW, Ravikumar P: SecondString: An Open-source Java Toolkit of Approximate String-Matching Techniques. 2003 [http://secondstring.sourceforge.net].
31. Cohen WW, Wang R, Murphy RF: Understanding Captions in Biomedical Publications. Proceedings of The Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2003), Washington, DC 2003.
32. Hatcher E, Gospodnetić O: Lucene in Action. Manning 2005.
33. Sleepycat Software [http://www.sleepycat.com]