Transcript Pedigree Import

Pedigree Import
IBP Activity 2.2.2, Subactivity 2:
Develop Genealogy Manager Application
Principal Investigator:
Mylah Anacleto, IRRI
Presentor: Alex Cañeda, IRRI
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
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 88888 is an F2 plant.
• IR 88888-21 is an F3
21st selection from IR 88888 F2 population
• IR 88888-21-2 is an F4.
2nd selection from the IR 88888-21 (F3)
• IR 88888-21-2-2 is an F5.
2nd selection from the IR 88888-21-2 (F4)
• IR 88888 -21-2-2-2 is an F6.
2nd selection from the IR 88888-21-2-2 (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.
• Create GID’s.
GUI
• 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 string(s) to process
Restful Web Services
Standardized name(s)
Filename
(where result was stored)
Pedigree Import GUI
Pedigree string(s) to process
Apache Web Server
Matching germplasm,
Created GIDS
Filename
(where result was stored)
Pedigree Import Web
Services Component
(Pedigree string parsers)
IBP middleware
(.jar file)
-create germplasm
-search germplasm
IRIS GMS
With availability of IBP Web services
Restful Web Services
Pedigree
Import GUI
Apache Web Server
Pedigree Import Web
Services Component
(Pedigree string parsers)
Pedigree Import
Restful Web Services
IBP middleware
-create germplasm
-search germplasm
IRIS GMS
*Only 1 deployment in
IRRI
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
Thank you!