The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

被引：111

作者：

Cooper, Laurel ^{[1
]}

Walls, Ramona L. ^{[2
]}

Elser, Justin ^{[1
]}

Gandolfo, Maria A. ^{[3
]}

Stevenson, Dennis W. ^{[2
]}

Smith, Barry ^{[4
]}

Preece, Justin ^{[1
]}

Athreya, Balaji ^{[1
]}

Mungall, Christopher J. ^{[5
]}

Rensing, Stefan ^{[6
,7
]}

Hiss, Manuel ^{[6
,7
]}

Lang, Daniel ^{[6
]}

Reski, Ralf ^{[6
,8
]}

Berardini, Tanya Z. ^{[9
]}

Li, Donghui ^{[9
]}

Huala, Eva ^{[9
]}

Schaeffer, Mary ^{[10
,11
]}

Menda, Naama ^{[12
]}

Arnaud, Elizabeth ^{[13
]}

Shrestha, Rosemary ^{[14
]}

Yamazaki, Yukiko ^{[15
]}

Jaiswal, Pankaj ^{[1
]}

机构：

[1] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA

[2] New York Bot Garden, Bronx, NY 10458 USA

[3] Cornell Univ, LH Bailey Hortorium, Dept Plant Biol, Ithaca, NY 14853 USA

[4] SUNY Buffalo, Dept Philosophy, Buffalo, NY 14260 USA

[5] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley Bioinformat Open Source Projects, Berkeley, CA 94720 USA

[6] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany

[7] Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany

[8] Univ Freiburg, FRIAS Freiburg Inst Adv Studies, D-79104 Freiburg, Germany

[9] Carnegie Inst Sci, Dept Plant Biol, Stanford, CA 94305 USA

[10] ARS, USDA, Columbia, MO 65211 USA

[11] Univ Missouri, Div Plant Sci, Dept Agron, Columbia, MO 65211 USA

[12] Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

[13] Biovers Int, Rome, Italy

[14] CIMMYT, Genet Resources Program, Mexico City 06600, DF, Mexico

[15] Natl Inst Genet, Ctr Genet Resource Informat, Mishima, Shizuoka 4118540, Japan

来源：

PLANT AND CELL PHYSIOLOGY | 2013年 / 54卷 / 02期

基金：

美国国家科学基金会;

关键词：

Bioinformatics; Comparative genomics; Genome annotation; Ontology; Plant anatomy; Terpene synthase; SEMANTIC WEB ARCHITECTURE; GENE-EXPRESSION; INTEGRATED INFORMATION; PHYSCOMITRELLA-PATENS; PHYLOGENETIC TREES; INTERACTIVE TREE; DRAFT SEQUENCE; RICE; ANNOTATION; DATABASE;

D O I：

10.1093/pcp/pcs163

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

The Plant Ontology (PO; ext-link-type="uri" xlink:href="http://www.plantontology.org/" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to > 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.

引用

页码：E1 / +

页数：23

共 104 条

[1]

[Anonymous], 2011, Database

[2] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[3]

Arp R., 2008, NATURE PRECEDINGS, V1941, P1, DOI [DOI 10.1038/NPRE.2008.1941.1, 10.1038/npre.2008.1941.1]

[4] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[5] Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana [J].

Aubourg, S ;

Lecharny, A ;

Bohlmann, J .

MOLECULAR GENETICS AND GENOMICS, 2002, 267 (06) :730-745

[6] The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations [J].

Avraham, Shulamit ;

Tung, Chih-Wei ;

Ilic, Katica ;

Jaiswal, Pankaj ;

Kellogg, Elizabeth A. ;

McCouch, Susan ;

Pujar, Anuradha ;

Reiser, Leonore ;

Rhee, Seung Y. ;

Sachs, Martin M. ;

Schaeffer, Mary ;

Stein, Lincoln ;

Stevens, Peter ;

Vincent, Leszek ;

Zapata, Felipe ;

Ware, Doreen .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D449-D454

[7] Functional annotation of the Arabidopsis genome using controlled vocabularies [J].

Berardini, TZ ;

Mundodi, S ;

Reiser, L ;

Huala, E ;

Garcia-Hernandez, M ;

Zhang, PF ;

Mueller, LA ;

Yoon, J ;

Doyle, A ;

Lander, G ;

Moseyko, N ;

Yoo, D ;

Xu, I ;

Zoeckler, B ;

Montoya, M ;

Miller, N ;

Weems, D ;

Rhee, SY .

PLANT PHYSIOLOGY, 2004, 135 (02) :745-755

[8] The Gene Ontology: enhancements for 2011 [J].

Blake, J. A. ;

Dolan, M. ;

Drabkin, H. ;

Hill, D. P. ;

Ni, L. ;

Sitnikov, D. ;

Burgess, S. ;

Buza, T. ;

Gresham, C. ;

McCarthy, F. ;

Pillai, L. ;

Wang, H. ;

Carbon, S. ;

Lewis, S. E. ;

Mungall, C. J. ;

Gaudet, P. ;

Chisholm, R. L. ;

Fey, P. ;

Kibbe, W. A. ;

Basu, S. ;

Siegele, D. A. ;

McIntosh, B. K. ;

Renfro, D. P. ;

Zweifel, A. E. ;

Hu, J. C. ;

Brown, N. H. ;

Tweedie, S. ;

Alam-Faruque, Y. ;

Apweiler, R. ;

Auchinchloss, A. ;

Axelsen, K. ;

Argoud-Puy, G. ;

Bely, B. ;

Blatter, M. -C. ;

Bougueleret, L. ;

Boutet, E. ;

Branconi-Quintaje, S. ;

Breuza, L. ;

Bridge, A. ;

Browne, P. ;

Chan, W. M. ;

Coudert, E. ;

Cusin, I. ;

Dimmer, E. ;

Duek-Roggli, P. ;

Eberhardt, R. ;

Estreicher, A. ;

Famiglietti, L. ;

Ferro-Rojas, S. ;

Feuermann, M. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D559-D564

[9] Beyond the data deluge: Data integration and bio-ontologies [J].

Blake, Judith A. ;

Bult, Carol J. .

JOURNAL OF BIOMEDICAL INFORMATICS, 2006, 39 (03) :314-320

[10] The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl [J].

Bombarely, Aureliano ;

Menda, Naama ;

Tecle, Isaak Y. ;

Buels, Robert M. ;

Strickler, Susan ;

Fischer-York, Thomas ;

Pujar, Anuradha ;

Leto, Jonathan ;

Gosselin, Joseph ;

Mueller, Lukas A. .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1149-D1155

← 1 2 3 4 5 6 7 8 9 10 →