Extending ontologies by finding siblings using set expansion techniques

Bioinformatics

Volumn 28, Issue 12, 2012, Pages

  Fabian, Götz ^a   Wächter, Thomas ^a   Schroeder, Michael ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DATA MINING; INTERNET; MEDICAL SUBJECT HEADINGS; METHODOLOGY; NOMENCLATURE;

ALGORITHMS; DATA MINING; INTERNET; MEDICAL SUBJECT HEADINGS; TERMINOLOGY AS TOPIC;

EID: 84863509763     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts215     Document Type: Article

References (27)

1. Ashburner, M. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
2. Balog, K. et al. (2011) Overview of the TREC 2010 entity track. Proceedings of the Nineteenth Text REtrieval Conference (TREC 2010), Gaithersburg, Maryland, USA.
3. Bodenreider, O. (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res., 32, D267-D270.
4. Brunzel, M. and Spiliopoulou, M. (2006) Discovering Multi Terms and Co-hyponymy from XHTML Documents with XTREEM. Knowledge Discovery from XML Documents. Lecture Notes in Computer Science, Springer Berlin/Heidelberg. Vol. 3915, pp. 22-32. doi: 10.1007/11730262_5.
5. Côté, R.G. et al. (2008) The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res., 36, W372-W376.
6. Day-Richter, J. et al. (2007) OBO-Edit-an ontology editor for biologists. Bioinformatics, 23, 2198-2200.
7. Doms, A. and Schroeder, M. (2005) GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res., 33, W783-W786.
8. Etzioni, O. et al. (2005) Unsupervised named-entity extraction from the Web: an experimental study. Artif. Intell., 165, 91-134.
9. Frantzi, K. et al. (2000) Automatic recognition of multi-word terms: the C-value/NCvalue Method. Int. J. Digit. Libr., 3, 115-130.
10. Hearst, M. (1992) Automatic acquisition of hyponyms from large text corpora. Proceedings of the 14th Conference on Computational Linguistics. Nantes, France. Vol. 2, pp. 539-545.
11. Howe, D. et al. (2008) Big data: the future of biocuration. Nature, 455, 47-50.
12. Kozareva, Z. et al. (2008) Semantic class learning from the web with hyponym pattern linkage graphs. In Proceedings of ACL-08: HLT, Columbus, OH, USA. pp. 1048-1056.
13. Lin, D. et al. (2001) Induction of semantic classes from natural language text. In Proceedings of the Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Francisco, CA, USA. pp. 317-322.
14. Liu, K. et al. (2011) Natural language processing methods and systems for biomedical ontology learning. J. Biomed. Inform., 44, 163-179.
15. Ogren, P.V. et al. (2004) The compositional structure of gene ontology terms. In Pacific Symposium on Biocomputing, Hawaii, USA. pp. 214-225.
16. Pantel, P. et al. (2009) Web-scale distributional similarity and entity set expansion. In Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing, Singapore. pp. 938-947.
17. Pa̧sca, M. (2004) Acquisition of categorized named entities for web search. In Proceedings of the Thirteenth ACM International Conference on Information and Knowledge Management, Washington, DC, USA. pp. 137-145.
18. Schober, D. et al. (2009) Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics, 10, 125.
19. Shi, S. et al. (2008) Pattern-based semantic class discovery with multi-membership support. In Proceeding of the 17th ACM Conference on Information and Knowledge Management, Napa Valley, California, USA. pp. 1453-1454.
20. Shi, S. et al. (2010) Corpus-based semantic class mining: distributional vs. pattern-based approaches. In Proceedings of the 23rd International Conference on Computational Linguistics, Beijing, China. pp. 993-1001.
21. Shinzato, K. et al. (2004) Acquiring hyponymy relations from web documents. Proc. HLT-NAACL, 2004, 73-80.
22. Wächter, T. and Schroeder, M. (2010) Semi-automated ontology generation within OBOEdit. Bioinformatics, 26, i88-i96.
23. Wang, R. and Cohen, W. (2007) Language-independent set expansion of named entities using the web. 2007 Seventh IEEE International Conference on Data Mining, pp. 342-350.
24. Whetzel, P.L. et al. (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics, 22, 866-873.
25. Whetzel, P.L. et al. (2011) BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res., 39, W541-W545.
26. Yao, L. et al. (2011) Benchmarking ontologies: bigger or better? PLoS Comput. Biol., 7, e1001055.
27. Zhang, H. et al. (2009) Employing topic models for pattern-based semantic class discovery. Proceedings of ACL/AFNLP 2009, pp. 459-467