title: GeneWeaver: a web-based system for integrative functional genomics.
abstract: High-throughput genome technologies have produced a wealth of data on the association of genes and gene products to biological functions. Investigators have discovered value in combining their experimental results with published genome-wide association studies, quantitative trait locus, microarray, RNA-sequencing and mutant phenotyping studies to identify gene-function associations across diverse experiments, species, conditions, behaviors or biological processes. These experimental results are typically derived from disparate data repositories, publication supplements or reconstructions from primary data stores. This leaves bench biologists with the complex and unscalable task of integrating data by identifying and gathering relevant studies, reanalyzing primary data, unifying gene identifiers and applying ad hoc computational analysis to the integrated set. The freely available GeneWeaver (http://www.GeneWeaver.org) powered by the Ontological Discovery Environment is a curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes. Thus, large numbers of independently published genomic results can be organized into new conceptual frameworks driven by the underlying, inferred biological relationships rather than a pre-existing semantic framework. An empirical 'ontology' is discovered from the aggregate of experimental knowledge around user-defined areas of biological inquiry.
authors.affiliation: School of Engineering & Computer Science, Baylor University, Waco, TX 76798, USA.
authors.forename: Erich J
authors.initials: EJ
authors.lastname: Baker
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Jay
authors.forename: Jason A
authors.initials: JA
authors.lastname: Bubier
authors.forename: Michael A
authors.initials: MA
authors.lastname: Langston
authors.forename: Elissa J
authors.initials: EJ
authors.lastname: Chesler
mesh_terms: D003196:Computer Graphics; D030541:Databases, Genetic; D005796:Genes; D023281:Genomics / Q000379:methods*; D020407:Internet; D012984:Software; D018511:Systems Integration
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D840-5
references.pmid: 18978021
references.citation: PLoS Comput Biol. 2008 Jan;4(1):e2
references.pmid: 18179280
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D445-8
references.pmid: 17984084
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62
references.pmid: 17151068
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D842-8
references.pmid: 21051359
references.citation: Nat Genet. 2004 Sep;36(9):921-4
references.pmid: 15340423
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6368-73
references.pmid: 16618939
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Curr Opin Drug Discov Devel. 2010 May;13(3):310-6
references.pmid: 20443164
references.citation: Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):390-399
references.pmid: 20052305
references.citation: Cell. 2004 Jul 9;118(1):31-44
references.pmid: 15242642
references.citation: Neuroinformatics. 2003;1(4):299-308
references.pmid: 15043217
references.citation: Nat Biotechnol. 2011 Apr;29(4):361-7
references.pmid: 21441928
references.citation: Nucleic Acids Res. 1998 Jan 1;26(1):73-9
references.pmid: 9399804
references.citation: BMC Genomics. 2009 Jul 07;10 Suppl 1:S6
references.pmid: 19594883
references.citation: Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6544-9
references.pmid: 20308572
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7
references.pmid: 19910365
references.citation: Genome Biol. 2003;4(5):P3
references.pmid: 12734009
references.citation: Environ Health Perspect. 2003 May;111(6):793-5
references.pmid: 12760826
references.citation: Summit Transl Bioinform. 2009 Mar 01;2009:56-60
references.pmid: 21347171
references.citation: Genome Res. 2010 Sep;20(9):1180-90
references.pmid: 20688780
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1067-72
references.pmid: 20864448
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5
references.pmid: 19920128
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D768-72
references.pmid: 17991680
references.citation: J Biomed Inform. 2011 Dec;44 Suppl 1:S5-S11
references.pmid: 21397722
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D760-5
references.pmid: 17099226
references.citation: BMC Bioinformatics. 2014 Apr 15;15:110
references.pmid: 24731198
references.citation: Neuroinformatics. 2008 Sep;6(3):149-60
references.pmid: 18946742
references.citation: BMC Bioinformatics. 2006 Mar 28;7:176
references.pmid: 16569235
references.citation: PLoS Comput Biol. 2010 Nov 11;6(11):e1000991
references.pmid: 21085640
references.citation: Genomics. 2009 Dec;94(6):377-87
references.pmid: 19733230
references.citation: Genome Biol. 2005;6(1):R7
references.pmid: 15642099
references.citation: Curr Opin Pharmacol. 2010 Oct;10(5):594-600
references.pmid: 20817606
references.citation: Cell. 2010 Nov 12;143(4):628-38
references.pmid: 21074052