Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

Journal of Biomedical Semantics

Volumn 2, Issue 5, 2011, Pages

  Kim, Jung Jae ^a   Rebholz Schuhmann, Dietrich ^b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84869405581     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-2-S5-S3     Document Type: Article

References (17)

1. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I: Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics. 2004, 20 (5): 604-611. 10.1093/bioinformatics/btg452.
2. Cimiano P, Reyle U, Saric J: Ontology-based discourse analysis for information extraction. Data & Knowledge Engineering. 2005, 55: 59-83. 10.1016/j.datak.2004.11.009.
3. Saric J, Jensen LJ, Rojas I: Large-scale extraction of gene regulation for model organisms in an ontological context. Silico Biology. 2005, 5: 21-32.
4. Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren PV, Cohen KB: OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics. 2008, 9: 78-10.1186/1471-2105-9-78.
5. Kim JD, Ohta T, Pyysalo S, Kano Y, Tsujii J: Overview of BioNLP'09 shared task on event extraction. Proceedings of the Workshop on BioNLP: Shared Task. 2009, 1-9.
6. Gaizauskas R, Demetriou G, Artymiuk PJ, Willett P: Protein structures and information extraction from biological texts: The PASTA system. Bioinformatics. 2003, 19: 135-143. 10.1093/bioinformatics/19.1.135.
7. Narayanaswamy M, Ravikumar KE, Vijay-Shanker K: Beyond the clause: extraction of phosphorylation information from medline abstracts. Bioinformatics. 2005, 21 (Suppl. 1): i319-i327.
8. Culotta A, McCallum A, Betz J: Integrating probabilistic extraction models and data mining to discover relations and patterns in text. Proceedings of Human Language Technology Conference of the North American Chapter of the Association of Computational Linguistics. 2006, 296-303.
9. Beisswanger E, Lee V, Kim JJ, Rebholz-Schuhmann D, Splendiani A, Dameron O, Schulz S, Hahn U: Gene Regulation Ontology (GRO): Design Principles and Use Cases. Studies in Health Technology and Informatics. 2008, 136: 9-14.
10. Hahn U, Tomanek K, Buyko E, Kim JJ, Rebholz-Schuhmann D: How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions. Proceedings of BioNLP. 2009, 2009: 37-45.
11. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R: The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Research. 2009, 37: D396-D403. 10.1093/nar/gkn803.
12. Rodríguez-Penagos C, Salgado H, Martínez-Flores I, Collado-Vides J: Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics. 2007, 8: 293-10.1186/1471-2105-8-293.
13. Kim JJ, Pezik P, Rebholz-Schuhmann D: MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline. Bioinformatics. 2008, 24 (11): 1410-1412. 1093/bioinformatics/btn117.
14. Kim JJ, Chae YS, Choi KS: Phrase-Pattern-based Korean to English Machine Translation using Two Level Translation Pattern Selection. Proceedings of 38th Association for Computational Lingusitics (ACL). 2000, 31-36.
15. Sagae K, Miyao Y, Tsujii J: HPSG parsing with shallow dependency constraints. Proceedings of the 45th Annual Meeting of the Association of Computational Linguistics Prague, Czech Republic. 2007, 624-631.
16. Browning DF, Busby SJW: The regulation of bacterial transcription initiation. Nature Reviews Microbiology. 2004, 2: 57-65. 10.1038/nrmicro787.
17. Motik B, Sattler U, Studer R: Query answering for OWL-DL with rules. Web Semantics: Science, Services and Agents on the World Wide Web. 2005, 3: 41-60.