database infrastructure was created according to the TropGene information system (http://eurigendb.cirad.fr/). A new TropGene data model (UML) was implemented to fit to the EURIGEN relational schema and to integrate new types of biological data relevant to the EURIGEN phenotyping analyses. The database module is based upon the MySQL platform and fully modelled according to the DBMS (database management System) and a web-based consultation interface was created.
A Java package for generating flexible Web query interfaces for EuriGenDB was implemented. The results of the queries were made downloadable in Excel or text formats; compatibility with all Web browsers was tested and validated.
SEARCHING FOR DATA
The search interface of the database which is enabled from the Data
option of the Eurigen database menu consists in five tabs corresponding to the different data types stored in the database.
There are five data types recorded in the database :
- Data resulting from phenotyping studies
- Data resulting from genotyping studies
- Passport Data on germplasms used for the studies realized during the Eurigen project
- Map data for a set of rice markers
- QTLs data for Agronomic traits, Blast resistance, Drought , Field plant , Insect resistance, Lab descriptors of grain quality, Phenology, Root traits, Salinity tolerance, Yield component
A query on a data type is independent from a query on another data type.
In each tab, different search criteria can be used to retrieve information in the database. They are
predefined by the database curator but the users can add or drop criteria as they need.
The search criteria are mostly mutually independent but in some case there is a hierarchical link between several criteria.
For some search criteria one or more values can be selected in lists and for other ones a value must be typed with the keyboard.
It is not required to enter value for all the displayed criteria but at least one criterion must be filled with a value otherwise an error message is displayed.
The search criteria for a data type are combined to form a request for the database.
The default rules for the combination are the followings: a logical AND is applied between the values of different criteria and a logical OR is done for the values of a single criterion when several values can be chosen. However, the users can choose to specify a logical OR between the different criteria with the OPERATOR radio button.
Once all the values for the search criteria have been chosen, a click on the SEARCH NOW button sends the request to the database.
DISPLAYING A SEARCH RESULT
If data matching the criteria are found, they are displayed below the criteria as a table with several predefined columns.
The number of matching lines found is indicated above the result table.
A pagination system allows the navigation in the result table.
A particular page can be displayed by typing a number in the Page N° box.
The number of lines displayed on a page in a query result can be set by the user by typing a number in the Number of records per page box.
In some columns of the result table, the values are in yellow indicating that a link has be found towards more details for the data in the column.
Three different links depending of the column data are possible:
- a link towards a Detailed sheet. More details about the selected value are displayed in a new window
- a link towards Cmap, a web-based tool that allows users to view comparisons of genetic and physical maps
- a link towards Golo, the Rice catalog of the Tropical Biological Resource Center of Montpellier
EXPORTING A SEARCH RESULT
The results of a search can be exported to MS Excel or text format. The results of searches on the phenotypes which involves traits and germplasms or on genotypes data which involves markers and germplasms are displayed below the criteria are in line mode i.e. one line for a combination of germplasm/trait or germplasm/marker. When exported, those results are rebuilt as a matrix with the germplasm in line and the traits or markers in column.
The results presented in line mode on screen can be exported as a matrix (Excel or Text format).
The user has to choose a kind of file in the Export result list and confirm his choice by clicking on the button on the right of the list.
After a search, the Reset form button should be used to clear the values of the search criteria.
SUBMITTING DATA TO THE DATABASE
To submit data to the EURIGEN database, download the file templates_eurigen.zip
which contains template files to fill with the data to submit.
The file templates_eurigen.zip
can also be download from the Download
database option menu.
The template files are Microsoft Excel files. One or more template files must be filled for each type of data that can be recorded in the database.
Each template consists in two or more tabs with appropiated columns to fill.