An ontology approach to comparative phenomics in plants

Plant Methods
Anika OellrichEva Huala

Abstract

Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be u...Continue Reading

References

Jan 10, 2003·Nucleic Acids Research·Iris TzafrirDavid Meinke
Feb 15, 2003·Plant Physiology·David W MeinkeIris Tzafrir
Jan 12, 2005·Genome Biology·Georgios V GkoutosDuncan Davidson
May 13, 2005·Plant Physiology·Peifen ZhangSeung Y Rhee
May 17, 2005·Genome Biology·Barry SmithCornelius Rosse
Mar 9, 2007·Bioinformatics·Ewa Urbanczyk-Wochniak, Lloyd W Sumner
Jul 25, 2007·Bioinformatics·Christopher J MungallUNKNOWN FlyBase Consortium
Dec 20, 2007·Nucleic Acids Research·UNKNOWN Rice Annotation ProjectManuel Echeverria
Mar 5, 2008·BMC Bioinformatics·Philip GrothUlf Leser
Apr 26, 2008·Science·Philip N Benfey, Thomas Mitchell-Olds
Aug 6, 2008·BMC Bioinformatics·Meeta Mistry, Paul Pavlidis
Aug 4, 2009·PLoS Computational Biology·Catia PesquitaFrancisco M Couto
Dec 4, 2009·PLoS Biology·Nicole L WashingtonSuzanna E Lewis
Jan 13, 2010·Genome Biology·Christopher J MungallMichael Ashburner
Jul 1, 2010·Analytical Chemistry·Royce Murray
Oct 12, 2010·Methods in Molecular Biology·Pankaj Jaiswal
Oct 12, 2010·Nucleic Acids Research·Aureliano BombarelyLukas A Mueller
Oct 26, 2010·Bioinformatics·Robert HoehndorfDietrich Rebholz-Schuhmann
Feb 24, 2011·Bioinformatics·Robert HoehndorfGeorgios V Gkoutos
Jun 1, 2011·Database : the Journal of Biological Databases and Curation·Mary L SchaefferCarolyn J Lawrence
Jul 9, 2011·Nucleic Acids Research·Robert HoehndorfGeorgios V Gkoutos
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Nov 22, 2011·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel S Rokhsar
Dec 14, 2011·PloS One·Rosanna MurallaDavid Meinke
Jun 28, 2012·Zeitschrift Für Angewandte Ichthyologie = Journal of Applied Ichthyology·By Paula MabeeMonte Westerfield
Jul 21, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Georgios V GkoutosRobert Hoehndorf
Aug 1, 2012·American Journal of Botany·Ramona L WallsDennis W Stevenson
Sep 11, 2012·Briefings in Bioinformatics·Robert HoehndorfGeorgios V Gkoutos
Sep 22, 2012·Trends in Plant Science·David W Meinke
Nov 28, 2012·Nucleic Acids Research·Janna HastingsChristoph Steinbeck
Dec 12, 2012·Plant & Cell Physiology·Laurel CooperPankaj Jaiswal
Mar 19, 2013·Bioinformatics·Samuel CrosetDietrich Rebholz-Schuhmann
Mar 28, 2013·TheScientificWorldJournal·Mingxin GanRui Jiang
May 11, 2013·Database : the Journal of Biological Databases and Curation·Damian SmedleyChristopher Mungall
Oct 26, 2013·Bioinformatics·Robert HoehndorfMichel Dumontier

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Citations

Oct 4, 2015·Nucleic Acids Research·Carson M AndorfCarolyn J Lawrence-Dill
Dec 30, 2015·PeerJ·Anne E ThessenPaula M Mabee
Jun 6, 2015·Journal of Experimental Botany·Paweł KrajewskiStephan Weise
Sep 21, 2017·Biotechnology & Genetic Engineering Reviews·Sudip DasJulia S Yumnam
Sep 26, 2019·NPJ Science of Food·Thomas BakerJohannes Keizer
Nov 16, 2016·Journal of Biomedical Semantics·Robert HoehndorfClaus Weiland
Jun 20, 2019·Frontiers in Plant Science·Ramona L WallsPankaj Jaiswal
Jan 31, 2020·Frontiers in Plant Science·Ian R Braun, Carolyn J Lawrence-Dill
Nov 25, 2020·PLoS Computational Biology·Anne E ThessenMelissa A Haendel
Mar 20, 2020·Cell·Claire D McWhiteEdward M Marcotte
May 14, 2018·Current Opinion in Plant Biology·Patricia Lu-IrvingKatrina M Dlugosch
Nov 27, 2017··Eugene ZhangLaurel Cooper

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Software Mentioned

hmmscan
OWL
Gramene
OWL EL
Phytozome10
AraCyc
BioCyc
- PTHREADS
hmmbuild HMMer
Oryzacyc

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