Pedigree Import

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Nov 17, 2013 (3 years and 11 months ago)

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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


21
st

selection from IR 88888 F2 population


IR 88888
-
21
-
2 is an F4.


2
nd

selection from the IR 88888
-
21 (F3)


IR 88888
-
21
-
2
-
2 is an F5.


2
nd

selection from the IR 88888
-
21
-
2 (F4)


IR 88888
-
21
-
2
-
2
-
2 is an F6.


2
nd

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!