PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. METHODS: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY RESULTS: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. CONCLUSIONS: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. METHODS: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY RESULTS: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. CONCLUSIONS: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
Authors: Martín J Ramírez; Jonathan A Coddington; Wayne P Maddison; Peter E Midford; Lorenzo Prendini; Jeremy Miller; Charles E Griswold; Gustavo Hormiga; Petra Sierwald; Nikolaj Scharff; Suresh P Benjamin; Ward C Wheeler Journal: Syst Biol Date: 2007-04 Impact factor: 15.683
Authors: Sudeshna Das; Lisa Girard; Tom Green; Louis Weitzman; Alister Lewis-Bowen; Tim Clark Journal: Brief Bioinform Date: 2008-12-06 Impact factor: 11.622
Authors: Ryan R Brinkman; Mélanie Courtot; Dirk Derom; Jennifer M Fostel; Yongqun He; Phillip Lord; James Malone; Helen Parkinson; Bjoern Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Larisa N Soldatova; Christian J Stoeckert; Jessica A Turner; Jie Zheng Journal: J Biomed Semantics Date: 2010-06-22
Authors: Christopher J Mungall; Georgios V Gkoutos; Cynthia L Smith; Melissa A Haendel; Suzanna E Lewis; Michael Ashburner Journal: Genome Biol Date: 2010-01-08 Impact factor: 13.583
Authors: Shulamit Avraham; Chih-Wei Tung; Katica Ilic; Pankaj Jaiswal; Elizabeth A Kellogg; Susan McCouch; Anuradha Pujar; Leonore Reiser; Seung Y Rhee; Martin M Sachs; Mary Schaeffer; Lincoln Stein; Peter Stevens; Leszek Vincent; Felipe Zapata; Doreen Ware Journal: Nucleic Acids Res Date: 2008-01 Impact factor: 16.971
Authors: Georg Fuellen; Melanie Boerries; Hauke Busch; Aubrey de Grey; Udo Hahn; Thomas Hiller; Andreas Hoeflich; Ludger Jansen; Georges E Janssens; Christoph Kaleta; Anne C Meinema; Sascha Schäuble; Andreas Simm; Paul N Schofield; Barry Smith; Juergen Sühnel; Julio Vera; Wolfgang Wagner; Eva C Wönne; Daniel Wuttke Journal: Rejuvenation Res Date: 2013-12 Impact factor: 4.663
Authors: Kai R Larsen; Susan Michie; Eric B Hekler; Bryan Gibson; Donna Spruijt-Metz; David Ahern; Heather Cole-Lewis; Rebecca J Bartlett Ellis; Bradford Hesse; Richard P Moser; Jean Yi Journal: J Behav Med Date: 2016-08-01
Authors: J A Blake; M Dolan; H Drabkin; D P Hill; Ni Li; D Sitnikov; S Bridges; S Burgess; T Buza; F McCarthy; D Peddinti; L Pillai; S Carbon; H Dietze; A Ireland; S E Lewis; C J Mungall; P Gaudet; R L Chrisholm; P Fey; W A Kibbe; S Basu; D A Siegele; B K McIntosh; D P Renfro; A E Zweifel; J C Hu; N H Brown; S Tweedie; Y Alam-Faruque; R Apweiler; A Auchinchloss; K Axelsen; B Bely; M -C Blatter; C Bonilla; L Bouguerleret; E Boutet; L Breuza; A Bridge; W M Chan; G Chavali; E Coudert; E Dimmer; A Estreicher; L Famiglietti; M Feuermann; A Gos; N Gruaz-Gumowski; R Hieta; C Hinz; C Hulo; R Huntley; J James; F Jungo; G Keller; K Laiho; D Legge; P Lemercier; D Lieberherr; M Magrane; M J Martin; P Masson; P Mutowo-Muellenet; C O'Donovan; I Pedruzzi; K Pichler; D Poggioli; P Porras Millán; S Poux; C Rivoire; B Roechert; T Sawford; M Schneider; A Stutz; S Sundaram; M Tognolli; I Xenarios; R Foulgar; J Lomax; P Roncaglia; V K Khodiyar; R C Lovering; P J Talmud; M Chibucos; M Gwinn Giglio; H -Y Chang; S Hunter; C McAnulla; A Mitchell; A Sangrador; R Stephan; M A Harris; S G Oliver; K Rutherford; V Wood; J Bahler; A Lock; P J Kersey; D M McDowall; D M Staines; M Dwinell; M Shimoyama; S Laulederkind; T Hayman; S -J Wang; V Petri; T Lowry; P D'Eustachio; L Matthews; R Balakrishnan; G Binkley; J M Cherry; M C Costanzo; S S Dwight; S R Engel; D G Fisk; B C Hitz; E L Hong; K Karra; S R Miyasato; R S Nash; J Park; M S Skrzypek; S Weng; E D Wong; T Z Berardini; E Huala; H Mi; P D Thomas; J Chan; R Kishore; P Sternberg; K Van Auken; D Howe; M Westerfield Journal: Nucleic Acids Res Date: 2012-11-17 Impact factor: 16.971
Authors: Laurel Cooper; Ramona L Walls; Justin Elser; Maria A Gandolfo; Dennis W Stevenson; Barry Smith; Justin Preece; Balaji Athreya; Christopher J Mungall; Stefan Rensing; Manuel Hiss; Daniel Lang; Ralf Reski; Tanya Z Berardini; Donghui Li; Eva Huala; Mary Schaeffer; Naama Menda; Elizabeth Arnaud; Rosemary Shrestha; Yukiko Yamazaki; Pankaj Jaiswal Journal: Plant Cell Physiol Date: 2012-12-05 Impact factor: 4.927