GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

Jennifer M Lee, Guy F Davenport, David Marshall, T H Noel Ellis, Michael J Ambrose, Jo Dicks, Theo J L van Hintum, Andrew J Flavell

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

Original languageEnglish
Pages (from-to)619-31
Number of pages13
JournalPlant Physiology
Volume139
Issue number2
DOIs
Publication statusPrint publication - Oct 2005
Externally publishedYes

Fingerprint

plant genetic resources
Databases
genomics
Genomics
Technology
geneticists
information systems
wild relatives
physiologists
bioinformatics
Information Storage and Retrieval
Licensure
germplasm
Computational Biology
Information Systems
Breeding
phenotype
Software
breeding
Phenotype

Keywords

  • Computational Biology
  • Databases, Genetic
  • Genotype
  • Phenotype
  • Plants/genetics
  • Software Design
  • User-Computer Interface

Cite this

Lee, Jennifer M ; Davenport, Guy F ; Marshall, David ; Ellis, T H Noel ; Ambrose, Michael J ; Dicks, Jo ; van Hintum, Theo J L ; Flavell, Andrew J. / GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections. In: Plant Physiology. 2005 ; Vol. 139, No. 2. pp. 619-31.
@article{d4d1551fb20f4a16921ddda9b6cf5ae9,
title = "GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections",
abstract = "The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.",
keywords = "Computational Biology, Databases, Genetic, Genotype, Phenotype, Plants/genetics, Software Design, User-Computer Interface",
author = "Lee, {Jennifer M} and Davenport, {Guy F} and David Marshall and Ellis, {T H Noel} and Ambrose, {Michael J} and Jo Dicks and {van Hintum}, {Theo J L} and Flavell, {Andrew J}",
year = "2005",
month = "10",
doi = "10.1104/pp.105.065201",
language = "English",
volume = "139",
pages = "619--31",
journal = "Plant Physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",
number = "2",

}

Lee, JM, Davenport, GF, Marshall, D, Ellis, THN, Ambrose, MJ, Dicks, J, van Hintum, TJL & Flavell, AJ 2005, 'GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections', Plant Physiology, vol. 139, no. 2, pp. 619-31. https://doi.org/10.1104/pp.105.065201

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections. / Lee, Jennifer M; Davenport, Guy F; Marshall, David; Ellis, T H Noel; Ambrose, Michael J; Dicks, Jo; van Hintum, Theo J L; Flavell, Andrew J.

In: Plant Physiology, Vol. 139, No. 2, 10.2005, p. 619-31.

Research output: Contribution to journalArticle

TY - JOUR

T1 - GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

AU - Lee, Jennifer M

AU - Davenport, Guy F

AU - Marshall, David

AU - Ellis, T H Noel

AU - Ambrose, Michael J

AU - Dicks, Jo

AU - van Hintum, Theo J L

AU - Flavell, Andrew J

PY - 2005/10

Y1 - 2005/10

N2 - The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

AB - The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

KW - Computational Biology

KW - Databases, Genetic

KW - Genotype

KW - Phenotype

KW - Plants/genetics

KW - Software Design

KW - User-Computer Interface

U2 - 10.1104/pp.105.065201

DO - 10.1104/pp.105.065201

M3 - Article

C2 - 16219922

VL - 139

SP - 619

EP - 631

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 2

ER -