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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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Autores principales: Sen Sarma, Moushumi, Arcoleo, David, Khetani, Radhika S., Chee, Brant, Ling, Xu, He, Xin, Jiang, Jing, Mei, Qiaozhu, Zhai, ChengXiang, Schatz, Bruce
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125736/
https://www.ncbi.nlm.nih.gov/pubmed/21558175
http://dx.doi.org/10.1093/nar/gkr285
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author Sen Sarma, Moushumi
Arcoleo, David
Khetani, Radhika S.
Chee, Brant
Ling, Xu
He, Xin
Jiang, Jing
Mei, Qiaozhu
Zhai, ChengXiang
Schatz, Bruce
author_facet Sen Sarma, Moushumi
Arcoleo, David
Khetani, Radhika S.
Chee, Brant
Ling, Xu
He, Xin
Jiang, Jing
Mei, Qiaozhu
Zhai, ChengXiang
Schatz, Bruce
author_sort Sen Sarma, Moushumi
collection PubMed
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 at www.beespace.illinois.edu/bstwmaterials.php.
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spelling pubmed-31257362011-07-05 BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature Sen Sarma, Moushumi Arcoleo, David Khetani, Radhika S. Chee, Brant Ling, Xu He, Xin Jiang, Jing Mei, Qiaozhu Zhai, ChengXiang Schatz, Bruce Nucleic Acids Res Articles 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 at www.beespace.illinois.edu/bstwmaterials.php. Oxford University Press 2011-07-01 2011-05-09 /pmc/articles/PMC3125736/ /pubmed/21558175 http://dx.doi.org/10.1093/nar/gkr285 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Sen Sarma, Moushumi
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
title 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_short 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
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125736/
https://www.ncbi.nlm.nih.gov/pubmed/21558175
http://dx.doi.org/10.1093/nar/gkr285
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