Pedigree Import Import of germplasm entries using a predefined file format containing pedigree strings Software allows user to verify if the entries in the imported file exist in the database Software parses the pedigree strings based on selected rice nomenclature rules and name standardization If unrecognized, allows users to edit portions of the pedigree string, and then check the resulting split for correctness, and apply the changes made back to the pedigree entry.
Pedigree Import The target end users of the application are the data managers and data curators whose tasks include the bulk loading of historical pedigree entries
Timeline and milestones October 2013 – Beta version January 2014 – Release candidate 1 June 2014 – Release candidate 2
Timeline and milestones
Collection of nomenclature rules for Rice
Sample input pedigree strings ”IR” cross number designation - for all crosses made in IRRI; assigned by the database administrator of PBGB IR is an F2 plant. IR is an F3 21 st selection from IR F2 population IR is an F4. 2 nd selection from the IR (F3) IR is an F5. 2 nd selection from the IR (F4) IR is an F6. 2 nd selection from the IR (F5)
Features Loading of large volume of historical germplasm data in to the ICIS GMS database Parse cross history strings of unknown crosses and, look for parents in the database User to control the selection of parents found in the database or create a new entry for the parents Derivative names of parents are recognized by looking for a cross number followed by letters and numbers separated by dashes
Features Pedigree Importer will use the same parsing algorithm that has been developed under the Delphi based ICIS GMS parser application the GMSInput –Note: using java, developed parser based on expected output as specified in the guide on nomenclature rules, not sure if the same algorithm basic data validation (for example, the parent should not be younger than its offspring) – not yet done The other features can be viewed from IBP site
Technologies used Web-based: GUI was written using PHP programming language Java Web Services (Jersey) Web Servers: Apache Tomcat and Apache httpd Database: MySQL while testing the IBP middleware but will eventually need to use PostgreSQL
GUI Home page
GUI File is uploaded. Pedigree Strings not in standardized format are in red color.
GUI Pedigree strings are standardized after clicking the standardize button. Unrecognized patterns are in red color. Click the pedigree string to edit.
GUI Edit Germplasm Name
GUI Changes are applied after editing germplasm names with unrecognized patterns.
GUI Create GID’s. After clicking the Create GID button. The link to display the strings created with GID’s is shown
GUI Sample of Create GID’s page.
Features: string parsers Pedigree string parser Identify tokens using ‘–’ as delimiter For each token: Name standardization Use of Regex libraries Check spaces and patterns Check cross notations (Single cross, compound cross, backcross)
Interaction of application components Pedigree Import GUI Restful Web Services Pedigree Import Web Services Component (Pedigree string parsers) IBP middleware (.jar file) -create germplasm -search germplasm IRIS GMS Pedigree string(s) to process Standardized name(s) Filename (where result was stored) Matching germplasm, Created GIDS Filename (where result was stored) Apache Web Server
Pedigree Import GUI Restful Web Services IBP middleware -create germplasm -search germplasm IRIS GMS Apache Web Server Restful Web Services Pedigree Import Web Services Component (Pedigree string parsers) Pedigree Import *Only 1 deployment in IRRI With availability of IBP Web services
Next module Pedigree Editor To communicate with IBP/Efficio on middleware requirements Scope is for pedigree/genealogy editor needs (limited germplasm editing); to be able to edit the information uploaded using pedigree import tool.
Project Information Software developer: Nikki Carumba Nikki is part of Breeding Information Management group of IRRI-PBGB With user inputs from IRRI: Dr. Ruaraidh Sackville-Hamilton William Eusebio