Biomedical discovery acceleration, with applications to craniofacial development.

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navi...

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Autores principales:	Sonia M Leach, Hannah Tipney, Weiguo Feng, William A Baumgartner, Priyanka Kasliwal, Ronald P Schuyler, Trevor Williams, Richard A Spritz, Lawrence Hunter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ec376e5f2e2045d18f42ca99e9b6c126
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spelling	oai:doaj.org-article:ec376e5f2e2045d18f42ca99e9b6c1262021-11-25T05:41:45ZBiomedical discovery acceleration, with applications to craniofacial development.1553-734X1553-735810.1371/journal.pcbi.1000215https://doaj.org/article/ec376e5f2e2045d18f42ca99e9b6c1262009-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19325874/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.Sonia M LeachHannah TipneyWeiguo FengWilliam A BaumgartnerPriyanka KasliwalRonald P SchuylerTrevor WilliamsRichard A SpritzLawrence HunterPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 3, p e1000215 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Sonia M Leach Hannah Tipney Weiguo Feng William A Baumgartner Priyanka Kasliwal Ronald P Schuyler Trevor Williams Richard A Spritz Lawrence Hunter Biomedical discovery acceleration, with applications to craniofacial development.
description	The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.
format	article
author	Sonia M Leach Hannah Tipney Weiguo Feng William A Baumgartner Priyanka Kasliwal Ronald P Schuyler Trevor Williams Richard A Spritz Lawrence Hunter
author_facet	Sonia M Leach Hannah Tipney Weiguo Feng William A Baumgartner Priyanka Kasliwal Ronald P Schuyler Trevor Williams Richard A Spritz Lawrence Hunter
author_sort	Sonia M Leach
title	Biomedical discovery acceleration, with applications to craniofacial development.
title_short	Biomedical discovery acceleration, with applications to craniofacial development.
title_full	Biomedical discovery acceleration, with applications to craniofacial development.
title_fullStr	Biomedical discovery acceleration, with applications to craniofacial development.
title_full_unstemmed	Biomedical discovery acceleration, with applications to craniofacial development.
title_sort	biomedical discovery acceleration, with applications to craniofacial development.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/ec376e5f2e2045d18f42ca99e9b6c126
work_keys_str_mv	AT soniamleach biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT hannahtipney biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT weiguofeng biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT williamabaumgartner biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT priyankakasliwal biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT ronaldpschuyler biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT trevorwilliams biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT richardaspritz biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment AT lawrencehunter biomedicaldiscoveryaccelerationwithapplicationstocraniofacialdevelopment
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Biomedical discovery acceleration, with applications to craniofacial development.

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