BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature

With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of...

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Main Authors: SARMA, Moushumi Sen, Arcoleo, David, Khetani, Radhika S., CHEE, Brant, Ling, Xu, He, Xin, JIANG, Jing, MEI, Qiaozhu, ZHAI, ChengXiang, Schatz, Bruce
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Language:English
Published: Institutional Knowledge at Singapore Management University 2011
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Online Access:https://ink.library.smu.edu.sg/sis_research/1379
https://ink.library.smu.edu.sg/context/sis_research/article/2378/viewcontent/nar.gkr285.full.pdf
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Institution: Singapore Management University
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spelling sg-smu-ink.sis_research-23782013-07-29T02:53:10Z BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature SARMA, Moushumi Sen Arcoleo, David Khetani, Radhika S. CHEE, Brant Ling, Xu He, Xin JIANG, Jing MEI, Qiaozhu ZHAI, ChengXiang Schatz, Bruce With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available atwww.beespace.illinois.edu/bstwmaterials.php. 2011-05-01T07:00:00Z text application/pdf https://ink.library.smu.edu.sg/sis_research/1379 info:doi/10.1093/nar/gkr285 https://ink.library.smu.edu.sg/context/sis_research/article/2378/viewcontent/nar.gkr285.full.pdf http://creativecommons.org/licenses/by-nc-nd/4.0/ Research Collection School Of Computing and Information Systems eng Institutional Knowledge at Singapore Management University gene function biological literature software curation conceptual spaces semantic indexing Bioinformatics Computer Sciences
institution Singapore Management University
building SMU Libraries
continent Asia
country Singapore
Singapore
content_provider SMU Libraries
collection InK@SMU
language English
topic gene function
biological literature
software
curation
conceptual spaces
semantic indexing
Bioinformatics
Computer Sciences
spellingShingle gene function
biological literature
software
curation
conceptual spaces
semantic indexing
Bioinformatics
Computer Sciences
SARMA, Moushumi Sen
Arcoleo, David
Khetani, Radhika S.
CHEE, Brant
Ling, Xu
He, Xin
JIANG, Jing
MEI, Qiaozhu
ZHAI, ChengXiang
Schatz, Bruce
BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
description With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available atwww.beespace.illinois.edu/bstwmaterials.php.
format text
author SARMA, Moushumi Sen
Arcoleo, David
Khetani, Radhika S.
CHEE, Brant
Ling, Xu
He, Xin
JIANG, Jing
MEI, Qiaozhu
ZHAI, ChengXiang
Schatz, Bruce
author_facet SARMA, Moushumi Sen
Arcoleo, David
Khetani, Radhika S.
CHEE, Brant
Ling, Xu
He, Xin
JIANG, Jing
MEI, Qiaozhu
ZHAI, ChengXiang
Schatz, Bruce
author_sort SARMA, Moushumi Sen
title BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
title_short BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
title_full BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
title_fullStr BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
title_full_unstemmed BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature
title_sort beespace navigator: exploratory analysis of gene function using semantic indexing of biological literature
publisher Institutional Knowledge at Singapore Management University
publishDate 2011
url https://ink.library.smu.edu.sg/sis_research/1379
https://ink.library.smu.edu.sg/context/sis_research/article/2378/viewcontent/nar.gkr285.full.pdf
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