The Ionomics Atlas
Progress Report
Mourad Ouzzani
David Salt
Nabeel Mohamed
Goal of the project
Develop a Google Map based intuitive graphical user interface
that allows to access, analyze, interpret and find correlations
among the following three properties in plant populations.
1. Ionomic information
2. Genetic information
3. Environmental information
Tasks
• Requirement analysis [DONE]
o Understand the project proposal
o Decide the functional requirements
• Understand Piims and related data sources [DONE]
• Understand and gather input data [DONE - ionomic and
genetic info; TODO - environmental info]
• Database design [DONE]
• System design [DONE]
• Front-end design [IN PROGRESS]
• Query mode [IN PROGRESS]
• Browsing mode [IN PROGRESS]
• Populate database [DONE - ionomic/genetic, TODO environmental]
• Implementation [IN PROGRESS]
Input Data
• Ionomic information: The project utilizes 360 different
populations of the plant Arabidopsis thaliana. Each
accession has the corresponding GIS information and
ionomics information available through PiiMS database.
• Genetic information: For each accession, genotype
information available in a compact representation containing
250,000 sub-sequences.
• Environmental information: The project utilizes the
environmental information such as geographic location,
altitude, climate (rainfall, temperature), soil properties, etc.
Such environmental information are retrieved from public
European databases.
Ionomic/Genetic/Environmental data
• There were some data quality issues with the input data we
received.
• Following are the main inconstancies:
o Encoding errors
o Formatting errors
o Missing data
• Cleaned the data programmatically as well as manually
Arabidopsis thaliana data
• 360 accessions in total, we currently have
o ionomic information for 350 accessions
o genetic information for 337 accessions
o GIS information for all 360 accessions
Technologies
• Database - Postgresql
• Application server - Tomcat (back-end in Java)
• Web technologies - GWT - Google Web Toolkit which
supports AJAX based web pages (javascripts), JSP
• Map - Google Maps along with free libraries to create
overlays
Database design
Simple system architecture
Initial front-end layout
• The web page consists of two frames
o Filters and output options
o Google map overlaying accessions
A screen shot of work-in-progress front
end
• Initially, all the 360 accessions are displayed
• Depending on the filters, only the relevant accessions
are shown (back-end functionality for filtering is inprogress)