TY - JOUR
T1 - GSD
T2 - A genetic screen database
AU - Henrich, Thorsten
AU - Ramialison, Mirana
AU - Segerdell, Erik
AU - Westerfield, Monte
AU - Furutani-Seiki, Makoto
AU - Wittbrodt, Joachim
AU - Kondoh, Hisato
PY - 2004/7
Y1 - 2004/7
N2 - The systematic assignment of gene function to a sequenced genome is one of the outstanding challenges in the post-genomic era. Large-scale systematic mutagenesis screens are important tools for reaching this goal. Here we describe GSD, a software package that allows storage and integration of data from genetic screens. GSD was initially developed for a large-scale F3 mutagenesis screen for developmental mutants of medaka (Oryzias latipes). The version presented here supports a wide range of different screens (mutagenesis, RNAi, morpholinos, transgenesis and others) using different organisms. Data are stored in a relational database and can be made accessible through web interfaces. Researchers can enter data describing their screened embryos: They can track statistics, submit images and describe the resulting phenotypes using a phenotype classification ontology. We developed a fish phenotype classification ontology of medaka and zebrafish for this software package and made it available to the public. In addition, a list of genetic lines resulting from each screen can be generated. These lines (mutant alleles, transgenic lines) can be described and categorized in the same ways as the screened individuals. Raw data from the screen can be integrated to describe these lines. A query module that searches this list can be used to publish the screen results on the Internet. A test version is available at http://www.embl.de/wittbrodt/gsd and the software can be downloaded from this site.
AB - The systematic assignment of gene function to a sequenced genome is one of the outstanding challenges in the post-genomic era. Large-scale systematic mutagenesis screens are important tools for reaching this goal. Here we describe GSD, a software package that allows storage and integration of data from genetic screens. GSD was initially developed for a large-scale F3 mutagenesis screen for developmental mutants of medaka (Oryzias latipes). The version presented here supports a wide range of different screens (mutagenesis, RNAi, morpholinos, transgenesis and others) using different organisms. Data are stored in a relational database and can be made accessible through web interfaces. Researchers can enter data describing their screened embryos: They can track statistics, submit images and describe the resulting phenotypes using a phenotype classification ontology. We developed a fish phenotype classification ontology of medaka and zebrafish for this software package and made it available to the public. In addition, a list of genetic lines resulting from each screen can be generated. These lines (mutant alleles, transgenic lines) can be described and categorized in the same ways as the screened individuals. Raw data from the screen can be integrated to describe these lines. A query module that searches this list can be used to publish the screen results on the Internet. A test version is available at http://www.embl.de/wittbrodt/gsd and the software can be downloaded from this site.
KW - Medaka
KW - Mutant screen
KW - Ontology
KW - Phenotype
KW - Zebrafish
UR - http://www.scopus.com/inward/record.url?scp=3042569516&partnerID=8YFLogxK
U2 - 10.1016/j.mod.2004.02.006
DO - 10.1016/j.mod.2004.02.006
M3 - Article
C2 - 15210199
AN - SCOPUS:3042569516
SN - 0925-4773
VL - 121
SP - 959
EP - 963
JO - Mechanisms of Development
JF - Mechanisms of Development
IS - 7-8
ER -