Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

Guocai Chen; Jieyi Zhao; Trevor Cohen; Cui Tao; Jingchun Sun; Hua Xu; Elmer V. Bernstam; Andrew Lawson; Jia Zeng; Amber M. Johnson; Vijaykumar Holla; Ann M. Bailey; Humberto Lara-Guerra; Beate Litzenburger; Funda Meric-Bernstam; W. Jim Zheng

doi:10.1093/database/bav034

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng

Investigational Cancer Therapeutics

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles.

Original language	English (US)
Article number	bav034
Journal	Database
Volume	2015
DOIs	https://doi.org/10.1093/database/bav034
State	Published - 2015

ASJC Scopus subject areas

Information Systems
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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10.1093/database/bav034

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Chen, G., Zhao, J., Cohen, T., Tao, C., Sun, J., Xu, H., Bernstam, E. V., Lawson, A., Zeng, J., Johnson, A. M., Holla, V., Bailey, A. M., Lara-Guerra, H., Litzenburger, B., Meric-Bernstam, F., & Zheng, W. J. (2015). Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database, 2015, Article bav034. https://doi.org/10.1093/database/bav034

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title = "Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature",

abstract = "Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles.",

author = "Guocai Chen and Jieyi Zhao and Trevor Cohen and Cui Tao and Jingchun Sun and Hua Xu and Bernstam, {Elmer V.} and Andrew Lawson and Jia Zeng and Johnson, {Amber M.} and Vijaykumar Holla and Bailey, {Ann M.} and Humberto Lara-Guerra and Beate Litzenburger and Funda Meric-Bernstam and Zheng, {W. Jim}",

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year = "2015",

doi = "10.1093/database/bav034",

language = "English (US)",

volume = "2015",

journal = "Database",

issn = "1758-0463",

publisher = "Oxford University Press",

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AU - Chen, Guocai

AU - Zhao, Jieyi

AU - Cohen, Trevor

AU - Tao, Cui

AU - Sun, Jingchun

AU - Xu, Hua

AU - Bernstam, Elmer V.

AU - Lawson, Andrew

AU - Zeng, Jia

AU - Johnson, Amber M.

AU - Holla, Vijaykumar

AU - Bailey, Ann M.

AU - Lara-Guerra, Humberto

AU - Litzenburger, Beate

AU - Meric-Bernstam, Funda

AU - Zheng, W. Jim

PY - 2015

Y1 - 2015

N2 - Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles.

AB - Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles.

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Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

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ASJC Scopus subject areas

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