NDLI: Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1

Content Provider	PubMed Central
Author	Berardini, Tanya Z. Mundodi, Suparna Reiser, Leonore Eva, Huala Garcia Hernandez, Margarita Zhang, Peifen Mueller, Lukas A. Yoon, Jungwoon Doyle, Aisling Lander, Gabriel Nick, Moseyko Yoo, Danny Xu, Iris Brandon, Zoeckler Montoya, Mary Miller, Neil Weems, Dan Rhee, Seung Y.
Copyright Year	2004
Abstract	Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species.
Related Links	http://dx.doi.org/10.1104/pp.104.040071
Ending Page	755
Page Count	11
Starting Page	745
File Format	PDF
ISSN	00320889
e-ISSN	15322548
Journal	Plant Physiology
Issue Number	2
Volume Number	135
Language	English
Publisher	American Society of Plant Biologists
Publisher Date	2004-06-01
Access Restriction	Open
Rights Holder	American Society of Plant Biologists
Subject Keyword	Plant Science Genetics Physiology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Physiology Plant Science

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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