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.

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

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

Thank you!