Tomato Phenomics WEB Project
Raskind, A.1, Gur, A.2, Sobolev, V.1,
Zamir, D.2 and Edelman, M.1
1Department of Plant Sciences, Weizmann Institute of Science
2Department of Field Crops, Vegetables and Genetics, Faculty
of Agriculture, Hebrew University of Jerusalem
Phenomics may be described as the integrated informatics study of phenotypic
and genotypic information to better understand the complex relationship
between the two. This relationship often involves a complex network of gene
interactions and quantitative trait loci that considerably hinders the use of
classical genetic approaches. Integration of phenotypic and genomic analyses
may provide important clues for understanding the flow of information from
genome to phenotype. During the last few years, the Israeli Tomato Genome
Project has generated a significant amount of data concerning different
aspects of tomato biology. The current bioinformatics project aims at
introducing the phenomics concept into tomato genomic research. Our goal is a
public web-based tool that will facilitate data mining and experimental design
by combining genetic, phenotypic, biochemical and physiological data in a
single relational database.
Our work concentrates on analysis and presentation of phenotypic data and
linking them to the existing genomic resources. This includes web-based
tools for statistical analysis of experimental data and mapping of
Quantitative Trait Loci. Currently, the system works with a dataset from
tomato introgression lines and allows performance of the following operations:
comparison of different genotypes for a given quantitative trait; analysis of
quantitative trait variation within the whole population; quantitative trait
profiling of genotype (comparison of all measured quantitative traits to the
parental cultivar); analysis of correlation between the traits.in different
years and environments.
Selection of input data and form of output are highly customisable.
The user may create a custom sub-list of genotypes to work on. Analysis of
results can be viewed in graphic and tabular formats. Publication quality
graphics (PDF) and printer-friendly versions of the tables are built into
the system. The system is founded on high-quality public-domain software.
The combination of an Apache web server, PHP server scripting language and
MySQL relational database server provides the means for building a dynamic
database-driven interactive web site. It also readily allows inclusion of
additional modules as the need develops (discussion forums, message boards,
protocol books, etc). Statistical analysis is performed by R-package
(www.r-project.org), an extensive and
expanding set of analysis tools in combination with elaborate graphic
capabilities.
We are currently developing the following capabilities for the system:
mapping of QTLs to chromosomes; data submission system; integration of
data from mutagenesis experiments; additional options for statistical
analysis; repository of relevant methods and protocols.
The URL for the Tomato Phenomics Web Site is:
http://bioinfo2.weizmann.ac.il:8080/tomato/PHP/index.php