Transforming the study of organisms: Phenomic data models and knowledge bases.

PLoS Computational Biology
Anne ThessenMelissa Haendel


The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.


Feb 21, 1998·Nucleic Acids Research·J M CherryD Botstein
Mar 9, 1999·Bioinformatics·M TomitaC A Hutchison
Mar 2, 2002·Science·Eric H DavidsonHamid Bolouri
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Niko BeerenwinkelJoachim Selbig
Apr 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·M CastellanosM L Shuler
Jul 13, 2005·Plant Physiology·Lukas A MuellerSteven D Tanksley
Oct 13, 2005·Plant Physiology·Victoria CarolloOlin D Anderson
Apr 10, 2007·Trends in Ecology & Evolution·Paula M MabeeMonte Westerfield
Jul 25, 2007·Bioinformatics·Christopher J MungallUNKNOWN FlyBase Consortium
Nov 21, 2007·Systematic Biology·Kevin De Queiroz
Sep 1, 1984·Biotechnology and Bioengineering·M M DomachM L Shuler
Jun 24, 2008·Genome Biology·Brian D O'ConnorLincoln D Stein
Jul 17, 2008·Comparative and Functional Genomics·UNKNOWN Plant Ontology Consortium
Jul 17, 2008·Comparative and Functional Genomics·G V GkoutosD Davidson
Mar 13, 2009·Current Biology : CB·Fan LiuManfred Kayser
Jun 2, 2009·Nucleic Acids Research·Natalya F NoyMark A Musen
Dec 4, 2009·PLoS Biology·Nicole L WashingtonSuzanna E Lewis
Dec 17, 2009·Nucleic Acids Research·David GrantRandy C Shoemaker
Jan 13, 2010·Genome Biology·Christopher J MungallMichael Ashburner
Feb 18, 2010·Journal of Forensic Sciences·Robert K ValenzuelaMurray H Brilliant
Mar 10, 2010·Nature Biotechnology·Jeffrey D OrthBernhard Ø Palsson
May 14, 2010·PloS One·James P BalhoffTodd J Vision
Jan 7, 2011·PloS One·Matthew J YoderAndrew R Deans
Feb 12, 2011·Science·O J ReichmanMark P Schildhauer
Jul 9, 2011·Nucleic Acids Research·Robert HoehndorfGeorgios V Gkoutos
Nov 15, 2011·Trends in Plant Science·Robert T Furbank, Mark Tester
Nov 29, 2011·Database : the Journal of Biological Databases and Curation·Sook JungDorrie Main
Dec 23, 2011·Trends in Ecology & Evolution·Andrew R DeansJames P Balhoff
Jan 13, 2012·PloS One·John WieczorekDavid Vieglais
Feb 2, 2012·Genome Biology·Christopher J MungallMelissa A Haendel
Mar 1, 2012·Nature Reviews. Microbiology·Nathan E LewisBernhard O Palsson
Jun 12, 2012·Advances in Bioinformatics·Anne E ThessenDmitry Mozzherin
Jul 24, 2012·Cell·Jonathan R KarrMarkus W Covert
Mar 23, 2013·Nature·David GriggsIan Noble
Oct 22, 2013·Journal of Biomedical Semantics·David Osumi-SutherlandGeorgios V Gkoutos
Feb 27, 2014·Journal of Biomedical Semantics·Ceri E Van SlykeMelissa A Haendel
May 24, 2014·Biodiversity Data Journal·Sarah FaulwetterChristos Arvanitidis
Sep 5, 2014·Science Translational Medicine·Tomasz ZemojtelPeter N Robinson
Oct 31, 2014·Nucleic Acids Research·Mary ShimoyamaHoward Jacob
Dec 5, 2014·BMC Bioinformatics·Alejandra González-BeltránPhilippe Rocca-Serra

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