Cropfinder
From ICISWiki
Contents |
Assessment from IRRI Developers and Users
Comments from Users
- Genebank Staff (GRC)
- Attendees of CropFinder demonstration (Jan 11, 2007 2-3pm), CRIL Conference Room, IRRI
- Nigel Ruaraidh Sackville Hamilton (Head, T.T. Chang Genetic Resources Center), Adelaida Alcantara (Data Management, GRC), Flora de Guzman (International Rice Genebank Manager), Nelia Resurreccion (Data Management, GRC), Digna Salisi (Admin support to Dr. Hamilton, GRC), Ma. Celeste Banaticla (Wild Rice taxonomist, GRC), Ma. Socorro Almazan (Wild Rice species curator, GRC), Juan Carlos Alarcon (CRIL, CIMMYT), Maria Corina Habito (CRIL, IRRI), Arllet Portugal (CRIL, IRRI).
- OVERVIEW/GENERAL FEEDBACK: CropFinder would be a suitable new web interface for querying passport, characterization and evaluation data of germplasms in the International Rice Genebank Collection (IRGCIS). Certain features would have to be implemented to cater to the needs of GRC staff, and those who request for data from GRC. Current IRGCIS web interface at http://www.irgcis.irri.org:81/grc/irgcisHome.html
- Suggestions:
- Sequence of field/column names as they appear in the report: accession number should be first, also allow flexibility in sequencing.
- Allow query of evaluation data (reaction of germplasms to biotic/abiotic stress. i.e. disease/insect resistance)
- Need outer join in linking of tables. e.g. some germplasms have passport data but no characterization data
- Store/show descriptions of field names, descriptor codes (e.g. in tree view of ExperimentResult table fields include "Apiculus color at reproductive" instead of just the column name (APCO_REV_REPRO); for country of origin: "MALAYSIA" instead of just "MYS")
- Allow query using SMTA number, query by study
- One "entry point" for CropFinder but separate sections/portals for different crops (i.e. one for rice, one for wheat, one for maize)
- Perhaps adopt querying approach of SINGER: set initial criteria, view results of initial criteria then set further criteria to refine the query results
- Allow query by specifying list of GIDS/accession numbers (e.g. import a text file?)
- Allow for "OR" operation in WHERE clause of SQL statement (maybe allow editing of SQL before running the query)
- Allow for "IN" operation, and also "NOT IN" and "<>" (not equal to)
- Have option to display all queried germplasm info on the same page
- Display total number of records retrieved along with queried germplasm info
- Have some sort of indicator field to distinguish GIDs in IRIS that are available for distribution, and those not available
- Have summary type/tabulation reports/collection statistics: e.g. number of germplasms grouped by country of origin. See collection statistics section in current IRGCIS web interface: http://www.irgcis.irri.org:81/grc/CollStat.htm
- Attendees of CropFinder demonstration (Jan 11, 2007 2-3pm), CRIL Conference Room, IRRI
- Plant Breeding and INGER
- Attendees of CropFinder demonstration (Jan 16, 2007 3:30-4:30pm), CRIL Conference Room, IRRI
- Grace Lee S. Capilit (Plant Breeding, Genetics and Biotechnology-Database Administration), Ma. Concepcion U. Toledo (Plant Breeding, Genetics and Biotechnology-Associate Scientist), Janice Bautista (Seed Health Unit, IRRI), Juan Carlos Alarcon (CRIL, CIMMYT), Arllet Portugal (CRIL, IRRI), Veritas Morena Salazar (CRIL, IRRI)
- Suggestion/Comments:
- INGER requires query for Environment X Germplasm interaction; Passport to be replaced by Environment Profile
- The possibility to limit the variables to show based on the selected Nursery/Ecosystem/Study (e.g. Heat Tolerance related variables, rainfed related variables). This is because not all variables that will be in the data warehouse are measured for a particular nursery or breeding program)
- Attendees of CropFinder demonstration (Jan 16, 2007 3:30-4:30pm), CRIL Conference Room, IRRI
Suggestions/Comments from Developers
- To split the tree box that shows the tables and variables into 2 controls. The first control shows the list of tables and the other control will show the variables of the selected table
- Softcode the Joins of the tables by storing them in a table
- For the conditions of the query, have a fixed number of variables but provide a button to add extend the number of condition
- Alternative way of specifying the condition is a step-by-step or one condition at a time where the number of records is returned after each condition
- For the Operators, add Not Equal, In the set of values, Not in the set of Values
- The Unique ID of the table is too Microsoft-dependent. Alternative and more meaningful and simple Unique ID is suggested like the LSID.
Issues in Integrating with ICIS
- The possibility of using Views or stored queries because of so many IDs that need to be link to another table
(e.g. GERMPLSM table to link with LOCATION for descriptive value of GLOCN)
- NAMES and ATRIBUTS table have types. The ability to show information from this kind of table (e.g. ATRIBUTS -> Species -> O. Glaberima)
- The ability to store in a GMS List the germplasms included in a query. This list can be useful to Seed Stock manager to know the seeds of interest for a particular requestor. Or this list can used as condition to suceeding query
Comparison with the IRRI Recommended Lines Web Page
Similarities
| CropFinder | Recommended Lines http://iris.irri.org/nursery/ | |
|---|---|---|
| Web-based | yes | yes |
| Both use AND in Query in between Traits | yes | yes |
| Issue of integration with other tables like SeedStock | Both need to change the code to extend the tables |
Differences
| CropFinder | Recommended Lines http://iris.irri.org/nursery/ | |
|---|---|---|
| Browser compatibility | IE (could find a solution to display well in Firefox) | Firefox (can work in IE if a different AJAX library is used) |
| Dev’t used | ASP.Net | AJAX, Java |
| Database backend | Microsoft SQL server | MySQL |
| Cross-platform applicability | Runs in Windows only (IIS) | Runs in any environment – Windows and Linux (Tomcat) |
| Feature | No histogram yet | Has histogram feature |
| Displaying of field names | Actual database column names are displayed | Logical names are displayed so it is more readable |
| In choosing Traits… | Allowed to choose one value only in the combo box with discrete values | Can choose one or more in list of discrete values. OR is used to generate this query. (Ex. any germplasm is selected having yellow OR blue color) |
| Showing of Traits/trait values | Displays trait values with corresponding data in other tables | Display all trait values even if there’s no recorded data for that trait |
| Showing of Traits/trait values | Can show/hide Traits that can be displayed to the user | Shows all Traits |
| Record / Frequency computation | Records are counted on-the-fly for every trait selected | Pre-computed frequency values from the database are displayed |
| For Trait values with continuous scale | No min or max values specified | Has min & max values |
| Report generation | Shows traits with values | Does not show any values for traits |
| Report generation | Users can select which column(s) to include in the report | Fixed number of columns |
