TY - JOUR
T1 - The Plant Ontology Database
T2 - A community resource for plant structure and developmental stages controlled vocabulary and annotations
AU - Avraham, Shulamit
AU - Tung, Chih Wei
AU - Ilic, Katica
AU - Jaiswal, Pankaj
AU - Kellogg, Elizabeth A.
AU - Mccouch, Susan
AU - Pujar, Anuradha
AU - Reiser, Leonore
AU - Rhee, Seung Y.
AU - Sachs, Martin M.
AU - Schaeffer, Mary
AU - Stein, Lincoln
AU - Stevens, Peter
AU - Vincent, Leszek
AU - Zapata, Felipe
AU - Ware, Doreen
N1 - Funding Information:
The Plant Ontology Consortium gratefully acknowledges the Gene Ontology Consortium for the contributed infrastructure, software and kind support. Special thanks to Chris Mungall and John Day-Richter from the GOC, to Peter Van-Buren, our system administrator at Cold Spring Harbor Laboratory and Ken Youens-Clark for critical review of the manuscript. We also thank all database groups, annotation contributors, researchers, curators, reviewers, collaborators, specifically Alice Clare Augustine from Monsanto and David Selinger and Arthur Lane from Pioneer Hi-Bred International companies, and users who have participated in the effort. Full list of collaborators and contributors is available at http:// www.plantontology.org/docs/otherdocs/collab.html and http://www.plantontology.org/docs/otherdocs/acknowledgment_list.html. This project is supported by the National Science Foundation (Grant No. 0321666) to the Plant Ontology Consortium and the U.S. Department of Agriculture-Agricultural Research Service. Funding to pay the Open Access publication charges for this article was provided by National Science Foundation (Grant No. 0321666).
PY - 2008/1
Y1 - 2008/1
N2 - The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.
AB - The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.
UR - http://www.scopus.com/inward/record.url?scp=38549134393&partnerID=8YFLogxK
U2 - 10.1093/nar/gkm908
DO - 10.1093/nar/gkm908
M3 - Article
C2 - 18194960
AN - SCOPUS:38549134393
SN - 0305-1048
VL - 36
SP - D449-D454
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -