In search of protein locations

Catherine Blake; Wu Zheng

In search of protein locations

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

We present a bootstrapping approach to infer new proteins, locations and protein-location pairs by combining UniProt seed protein-location pairs with dependency paths from a large collection of text. Of the top 20 system proposed protein-location pairs, 18 were in UniProt or supported by online evidence. Interestingly, 3 of the top 20 locations identified by the system were in the UniProt description, but missing from the formal ontology.

Original language	English (US)
Title of host publication	2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics
Subtitle of host publication	Human Language Technologies, ACL-HLT 2011 - Proceedings
Editors	Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Jun'ichi Tsujii, Jun'ichi Tsujii, Bonnie Webber
Publisher	Association for Computational Linguistics (ACL)
Pages	101-102
Number of pages	2
ISBN (Electronic)	9781932432916
State	Published - 2011
Event	2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Portland, United States Duration: Jun 23 2011 → Jun 24 2011

Publication series

Name	2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings

Conference

Conference	2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011
Country/Territory	United States
City	Portland
Period	6/23/11 → 6/24/11

ASJC Scopus subject areas

Language and Linguistics
Computer Science Applications
Information Systems
Software
Biomedical Engineering
Health Informatics

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Blake, C., & Zheng, W. (2011). In search of protein locations. In K. B. Cohen, D. Demner-Fushman, S. Ananiadou, J. Pestian, J. Tsujii, J. Tsujii, & B. Webber (Eds.), 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings (pp. 101-102). (2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings). Association for Computational Linguistics (ACL).

In search of protein locations. / Blake, Catherine; Zheng, Wu.
2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings. ed. / Kevin Bretonnel Cohen; Dina Demner-Fushman; Sophia Ananiadou; John Pestian; Jun'ichi Tsujii; Jun'ichi Tsujii; Bonnie Webber. Association for Computational Linguistics (ACL), 2011. p. 101-102 (2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Blake, C & Zheng, W 2011, In search of protein locations. in KB Cohen, D Demner-Fushman, S Ananiadou, J Pestian, J Tsujii, J Tsujii & B Webber (eds), 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings. 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings, Association for Computational Linguistics (ACL), pp. 101-102, 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011, Portland, United States, 6/23/11.

Blake C, Zheng W. In search of protein locations. In Cohen KB, Demner-Fushman D, Ananiadou S, Pestian J, Tsujii J, Tsujii J, Webber B, editors, 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings. Association for Computational Linguistics (ACL). 2011. p. 101-102. (2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings).

Blake, Catherine ; Zheng, Wu. / In search of protein locations. 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings. editor / Kevin Bretonnel Cohen ; Dina Demner-Fushman ; Sophia Ananiadou ; John Pestian ; Jun'ichi Tsujii ; Jun'ichi Tsujii ; Bonnie Webber. Association for Computational Linguistics (ACL), 2011. pp. 101-102 (2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 - Proceedings).

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title = "In search of protein locations",

abstract = "We present a bootstrapping approach to infer new proteins, locations and protein-location pairs by combining UniProt seed protein-location pairs with dependency paths from a large collection of text. Of the top 20 system proposed protein-location pairs, 18 were in UniProt or supported by online evidence. Interestingly, 3 of the top 20 locations identified by the system were in the UniProt description, but missing from the formal ontology.",

author = "Catherine Blake and Wu Zheng",

note = "This material is based in part upon work supported by the National Science Foundation under Grant IIS-0812522. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not nec- essarily reflect the views of the National Science Foundation.; 2011 Workshop on Biomedical Natural Language Processing, BioNLP 2011 at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL-HLT 2011 ; Conference date: 23-06-2011 Through 24-06-2011",

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In search of protein locations

Abstract

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ASJC Scopus subject areas

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