iwis review sdd november 2003 iwis international wheat information system

IWIS Review SDD November 2003

IWISIWISInternational Wheat Information International Wheat Information

SystemSystem


IWIS OverviewIWIS Overview

Introduction

IWIS Architecture

IWIS Components

IWIS and the wheat breeding process


IntroductionIntroduction

“ The International Wheat Information System (IWIS) manages and integrates diverse information pertaining to bread wheat, durum wheat, triticale, and barley. IWIS provides each germplasm used in the wheat breeding process with a unique identifier. Using the IWIS identifier, users can pinpoint a particular wheat despite its many names, trace its family tree, and then explore what is known about the wheat line.”


IntroductionIntroduction

IWIS allows researchers to: Trace the ancestry of individual wheat lines and estimate the degree of

relatedness among them

Update family trees as additional data on ancestry become available

Generate field books for germplasm evaluation

Gather genetic, environmental, and phenotypic information to be used in germplasm improvement


IWIS ArchitectureIWIS Architecture

Function/Task 1

Function/Task 2

Update Tools Report Tools Query Tools

Operating System (Windows NT)

Database System(SQL Server)

Network System

Application 1 Application 2 Application n. . . . . . . . . . . . . .

. . . . . . . . . . . . . . Function/Task n

Infrastructure Perspective

SystemPerspective

UsersPerspective

uses

supports


IWIS ComponentsIWIS Components

Pedigree Management(WPMS)

Data Management (WDMS)

Field BooksManagement(WPFBS)

Germplasm Bank (WGBS)

International Nurseries(WINS)



IWIS Tools for:

Germplasm Data Curators



IWIS Tools for:

Research Assistants



IWIS Tools for:

Researchers



IWIS Tools for:

Database Administrators



IWIS Tools for:

International Nursery Testing


IWIS Components - PMS FunctionsIWIS Components - PMS Functions

Unique identification of crosses and selections - Cross Id, Selection Id (CID, SID)

Female CID

Female SID

Male CID

Male SID

BOBWHITE, CM 33203

CM33203-K-10M-7Y-3M-2Y-1M-0Y

GARA , CM33203-K-9M-19Y-3M-3Y-0M-0ETH[ETH]



Semantic interpretation of crosses and selections Generic/Specific names

Synonyms

Sister lines

BOBWHITE, CM 33203

CM33203-K-10M-7Y-3M-2Y-1M-0Y

GARA , CM33203-K-9M-19Y-3M-3Y-0M-0ETH[ETH]

PAI MISTOL , CM33203-K-9M-19Y-3M-3Y-0M-0ETH[ETH]



Syntactical analysis of crosses and selections

Pedigree

CID,SID



Genealogy tree generation



Purdy notation expansion


IWIS Components - PMS FunctionsIWIS Components - PMS Functions Foreign material introduction

Pedigree

Origin



Genetic relationships quantification


IWIS Components - FBS FunctionsIWIS Components - FBS Functions

Crossing block

New cross

Female parent

Male parent



Trial Data

Entry

Progenitors

Selection History

F1 fieldbooks


IWIS Components - FBS FunctionsIWIS Components - FBS Functions Selection of segregating material

New selection

Source material



Trial data

Entry

Pedigree

Origin

Segregating material fieldbooks



Trial data

Design

Pedigree

Origin

International nurseries fieldbooks


IWIS Components - DMS FunctionsIWIS Components - DMS Functions Electronic data input and validation


IWIS Components - DMS FunctionsIWIS Components - DMS Functions Environmental data management


IWIS Components - DMS FunctionsIWIS Components - DMS Functions Genetic data management


IWIS Components - DMS FunctionsIWIS Components - DMS Functions Phenotypic data management


IWIS Components - DMS FunctionsIWIS Components - DMS Functions Alpha lattice statistical analysis (REML)


IWIS Components - WINS FunctionsIWIS Components - WINS Functions International nurseries distribution and shipment


IWIS Components - WINS FunctionsIWIS Components - WINS Functions Cooperator data management


IWIS Components - WINS FunctionsIWIS Components - WINS Functions Phytosanitary certificates


IWIS and the wheat breeding processIWIS and the wheat breeding processDiagram of Germplasm Flow

Cd. Obregon A x B

Toluca F1 x C or A or B

Cd. Obregon (Individual plants)1 F2

Toluca (Bulk of 10 spikes) F3

Cd. Obregon (Bulk of 10 spikes) F4

Toluca (Bulk of 10 spikes) F5

Cd. Obregon (10 individual spike) F6

Toluca (Bulk of whole plot) F7

F1T

F2 (Individual plants)

F3 (Bulk of 10 spikes)



F6 (10 individual spikes)

Cd. Obregon PYT AL F7 (Bulk of whole plot) (ME1, ME4, ME5) (ME2, ME3, ME6)

Toluca EAL PYT AL (ME1, ME4, ME5) (ME2, ME3, ME6) (ME1, ME4, ME5)

Cd. Obregon YT EAL PYT

(ME1, ME4, ME5) (ME2, ME3, ME6) (ME1, ME4, E5)

Toluca YT EAL

(ME2, ME3, ME6) (ME1, ME4, ME5)

Cd. Obregon YT

(ME1, ME4, ME5)

El Batan Candidates, International Nurseries and Yield Trials (Small Increase)

Mexicali Candidate, International Nurseries and Yield Trials (Large Multiplication)

WORLD International Nurseries and Yield Trials

Crossing

Selection of segregatingmaterial

Germplasm evaluation

Germplasm multiplication

Replicated yield testing


IWIS and the wheat breeding processIWIS and the wheat breeding process

Crossing



Selection ofsegregating material



Germplasm evaluation and multiplication



Replicated yield testing


IWIS Recent improvementsIWIS Recent improvements WPMS

Any reports

Standard reports

Parser functionality 100%

WFBS New fonts and field book layouts

Conversion of IN field books to laser printer format

Randomized field books in Excel format

WDMS (PGD) Phenotypic data queries on multiple traits

Direct access at Obregon (soon at Toluca)


WPMS Update Tools - WPMS UpdateWPMS Update Tools - WPMS Update

Type in the pedigree or paste it from another application (for instance Excel). Then click the Parse button to get Unknown Elements. Now you can create the crosses with the “Next” button.



Insert new cross from the “Next” button of Pedigree, or Update/Delete of existing crosses.

Make a Standard BCID using the fields Program, Year, Free, Organization and Location.



Manage names for both crosses and selections.

Search by Name

Search by Abbreviation

Search by CID

List of names for this CID (7691)



Type in the selection history or paste it from another application (for instance Excel). Then click the Parse button to get Unknown Elements. Now you can create the selections with the “Next” button.

Search by CID+SID



Insert new selection from the “Next” button of Selection History, or Update/Delete of existing selections.

Search by CID+SID



Search by Name

Search by Abbreviation

Search by CID+SID

Manage Selection Names

List of names for this CID (7691) and SID (0).



Manage parts of a selection history that doesn’t consist of standard selection elements.

Search by CID+SID


WPIDWPID

Results list of CID and BCID related to Name or Cross that we are looking for.

Input field for Name or Cross

WPIDWPID


WPSELWPSEL

Input field for Selection history

Resultant Cross

CID ,SID

Aditional description about results

WPSELWPSEL


WPMS Query Tools- DendrogramWPMS Query Tools- Dendrogram

Search by name, BCID or CID/SID



Expansion level

Genealogy tree display options

Name and selection history



Mendelgram: Theoretical percentage contribution of ancestors to a pedigree assuming equal contribution from both parents in a cross


Wheat Coefficient of Parentage Wheat Coefficient of Parentage

Capture information for: Cross Name

Cross Identification (CID) and Selection Identification (SID)

Breeder Cross Identification (BCID)

List Target Genotypes

Generate and Display Coefficients of Parentage Matrix


Wheat Coefficient of ParentageWheat Coefficient of Parentage Creating Genealogical Dendrogram

creates the fully expanded genealogical tree for each target genotype.

Fusing Common Elements of Genealogical Dendrograms

combines the genealogical trees of target genotypes into a kind of "multiple genealogical tree" where common ancestors are "shared" by their offspring.

Creating Matrix

the matrix of Coefficients of Parentage is generated based on the Rodgers & Cox algorithm.

Loading Matrix the matrix is constructed and displayed

with the HTC (highest theoretical genetic contribution at maximum expansion) values for each target genotype.


Wheat Coefficient of ParentageWheat Coefficient of Parentage

The generated COP Matrix is displayed in the Matrix

window.

You can print the matrix by clicking the "Print COP Matrix" icon.

Gen (a sequential genotype number for each target genotype assigned for the COP analysis)

Cross ID and Selection ID.

Name.

Abbreviation.

HTC (highest theoretical genetic contribution).


WPMS ReportsWPMS Reports Use this command to define the

format used to display or print WPMS records.

Query Builder. This command will display the Query Builder screen, which permits searching the WPMS database and retrieving subsets of records, which can be displayed or printed.

Fast Query Report. This command will display the Fast Query Builder, which permits to search with a single search criteria.


WPMS ReportsWPMS Reports

Select Crosses Fields and Names Fields. This box shows the list of data fields, associated with genotypes, that can be included as a search criteria in the query expression:

Operator. This box is displayed after selecting one field (Cross or Names) and shows the list of logical operators that can be used to associate Cross or Names fields with specific data field values:

Verify. Check the correct syntax of the query expression. If the query expression is correct, the Execute button becomes active and the search can be performed. Otherwise, the application will ask you to correct the expression.

Execute. Execute the query expression and retrieve the records matching the search criteria.


WPMS ReportsWPMS Reports Sort retrieved data. You may select one

of the displayed fields for sorting. Then proceed, browsing or printing the retrieved and sorted records.

Print. This command has two options:

Print All-Fields. Choose this option to print all the fields defined for the active format.

Print Selected_Fields. Choose this option to print a subset of the fields defined for the active format. If you choose this option, the application displays a screen showing all the fields defined for the active format. You may select one field at the time, select all the fields or cancel the operation clicking on the corresponding buttons included on this screen.


WFB PCWFB PC

Search CID, SID information by Name

for the checks.


WFB PCWFB PC


WFB Trial From OriginsWFB Trial From Origins

The program Trial From Origins offers an interactive method for entering all related information for the entries of a given trial, and to evaluate if this information is correct. This is done by keeping a list of origins for each trial.

There are 5 types of Trials:

1. Crosses Trial

2. Selections Trial

3. Movements Trial

4. CIDs with no origin Trial

5. Mixed Trial



An example of a Mixed Trial. In this example, some records are Crosses origins (CRS), some records are Female Movement origins (FMOV). Only columns that are relevant for that type of record are filled out.



An example of a Crosses Trial.



An example of a Selections Trial with checks in entries 401 and 402.



An example of a CIDs with no origin Trial.



An example of a Movements Trial.



Buttons:

1. Fill a column with a number or a range of numbers.

2. Verify that the origins are correct.

3. Save the trial.

4. Insert an Entry.

5. Delete an Entry.

6. Make selections automatically.

7. Generate a report of which BCIDs will be generated based on the origins (only enabled for Crosses Trials).

8. Import Clipboard from Excel (or a text file).



When verifying the trial, all origins will be checked for errors. All errors are reported in the error file shown here. If no errors are found, only Trial ID (here 99054), type of trial and number of entries and number of checks are mentioned.



The BCID report will show which BCIDs the different new crosses will get if the trial were to be frozen at this very moment. The actual BCIDs depend on which numbers have already been used when freezing the trial.


WFB Freeze TrialWFB Freeze Trial

When the trial has no more errors in Trial From Origins, Freeze Trial can create the entries in Wfb_Entrylist based on the origins. You enter the Trial ID and click “Send” to launch a batch process.


WFB Freeze TrialWFB Freeze Trial

The next tab shows the jobs that have been launched, whether they are pending, are currently processing or have already finished.


WPMS Report Tools - AnyReportWPMS Report Tools - AnyReport

Report Name

Parameters

There are currently 12 reports included in the combo box.


WPMS Report Tools - AnyReportWPMS Report Tools - AnyReport

The result is a report in a text file:


WFB/WPMS Standard ReportsWFB/WPMS Standard Reports

Create a report with all the selection histories of a given CID



The text file with all the selection histories of a given CID. The list contains Cross Identifier (CID), Previous Selection Identifier (PSID), Selection Identifier(SID) and Selection History.



The CID,SID report will show you all entries from Wfb_Entrylist of a given CID or CID+SID pair.



The CID,SID report will show you all entries from Wfb_Entrylist of a given CID or CID+SID pair. This is the output text file.



The CID descendants report will show you all entries from Wfb_Entrylist which has a CID which is a descendant of a given CID or CID+SID pair.



The CID descendants report will show you all entries from Wfb_Entrylist which has a CID which is a descendant of a given CID or CID+SID pair. This is the output text file.



You can get reports from many different tables based on a number of commonly used text fields, like Cross Name, Pedigree, Selection History, Trial Name etc. etc. All fields of the used table will be shown, with the records that corresponds to the search string.

Specify which fields you want to have the records ordered by.



The report text file of the Trial Names that have the string INV somewhere in the Trial Name. We ordered by Cycle and Trial Abbreviation, which can be appreciated in the example report.


RANDOMIZATIONSRANDOMIZATIONS

Options :

- Add randomizations.

Format types :

- Free design

- Alphagen

- Delete randomizations.



Range of Trials



Range of occurrences



Format type


Field Books (IWISFBS)Field Books (IWISFBS)

Tid

Ocurrences

Field Book Type

Print Field Books (on Block)



Tid

Occurrence

Field Book Type

Print Field Book (one by one)



General Trial Data

Entry

Name and Selection History of Parents

Area to take notes

Field Book Type 23, F1 Historic, with 2 columns to take notes.

Selection History



General Trial Data

Entry

Name and Selection History

Area to take notes

Field Book Type 24, National Basic Material, with 14 columns to take notes.

Origin



General Trial Data

Entry


Origin

Field Book Type 25, National Segregating without columns to take notes.



General Trial Data

Entry


Area to take notes

Field Book Type 26, National Basic Material with 5 columns to take notes.

Origin



General Trial Data

Plot


Area to take notes

Field Book Type 28, National Material with a column for code, with 13 columns to take notes.

Origin

Code



General Trial Data

Entry


Repetitions

Field Book Type 29, National with no columns to take notes.

Origin



General Trial Data

Plot


Area to take notes

Field Book Type 41, National development with 13 columns to take notes.

Entry

Origin



General Trial Data

Entry


Area to take notes

Field Book Type 42, National Basic Material from the Germplasm Bank, with 14 columns to take notes.

Introduction Id

Origin



General Trial Data

Entry


Area to take notes

Field Book Type 43, National Basic and Segregating Material from the Germplasm Bank, with 5 columns.

Introduction Id

Origin


Field Books (IWISFBS)Field Books (IWISFBS)General Trial Data

Entry


Repetitions

Field Book Type 47, National combined, cross and movement, with no columns to take notes.

Origin



General Trial Data

Plot


Area to take notes

Field Book Type 48, National combined, cross and movement with design, with 13 columns to take notes.

Entry

Origins



General Trial Data

Design


Origin

Field Book Type 60, International Yield , with 9 columns to take notes.



General Trial Data

Entry


Area to take notes

Field Book Type 61, International Screening, with 13 columns to take notes.

Origin



General Trial Data

Entry


Area to take notes

Field Book Type 62, International Segregating, with 5 columns to take notes.

Origin


Field Books (IWISFBS)Field Books (IWISFBS)General Trial Data

Design


Origin

Field Book Type 63, International Barley Yield, with 9 columns to take notes.



General Trial Data

Entry


Area to take notes

Field Book Type 64, International Barley Screening, with 14 columns to take notes.

Origin



General Trial Data

Entry


Area to take notes

Field Book Type 65, International Barley Segregating, with 5 columns to take notes.

Origin



Field Book Type 6, Excel format.

Column Titles



Field Book Type 49, Information of Parents in a excel format.

Column Titles

Column Titles



Field Book Type 66, Yield Excel format.

Column Titles

Column Titles



Field Book Type 67, Screening Excel format.

Column Titles

Column Titles



Field Book Type 4, Tags.

Cross Name

Selection History

Trial name

Program

Introduction Id

Cycle



Field Book Type 5, Labels.

Trial Name

Program

Cycle

Entry

Cross Name

SelectionHistory



Field Book Type 21, Randomized labels.

Trial Name

Program

Cycle

Plot

Cross Name

Selection History



Field Book Type 22, Randomized tags.

Cross Name

Selection History

Trial name

Program

Cycle

Plot


WDMS CatalogWDMS Catalog

Allow the users to add, update,view and delete :

- Scales or Units

- Traits

- Measured In

- Transformations

- Stations



Scale types :

- Discrete

- Continue

Value types :

- Integer

- Real

- Text

- Date



Class types :

- GE . Phenotypic (G x E)

- G . Genetic.

- E . Environmental



Scales/Units that the trait can be measured in.


WDMS ReportsWDMS Reports

WDMS Traits



Scales/Units



Titles

Continuos Transformation.



Titles

Discrete Transformations.



Titles

Geographic Data, Sorted by General Number.


WINSWINS

Institution types :

- Educational

- Government

- Private

- Other

Sowing date


WINSWINS

Program :

B. Barley

BW. Bread Wheat

DW. Durum Wheat

TR. Triticale

SP. Special Project

Trial identification

Range of occurrences


WINSWINS

Continent

Cooperator id. (coopkey)

Country

Institution name

Last name


WDMS Query Tools- PGDWDMS Query Tools- PGD

Genetic, environmental, andphenotypic data queries within trials

Phenotypic data queries bygenotypes and locations



Select cycle and trial for querieswithin trials



Genetic data is linked toPMS through CID,SID


WDMS Query Tools- PGDWDMS Query Tools- PGD Genetic data queries

Trial

G Traits

G Data



Environmental data isassociated to locations


WDMS Query Tools- PGDWDMS Query Tools- PGD Environmental data queries

Trial

E Traits (name andabbreviation)

E Data


WDMS Query Tools- PGDWDMS Query Tools- PGD Phenotypic data queries

Table options

Trial

GxE Trait in standard scale

Locations

GxE Data (REML meansacross reps)

Basic statisticsacross locations


WDMS Query Tools- PGDWDMS Query Tools- PGD Phenotypic data queries on multiple traits

Grain Yield data

Other traits statistics


WDMS Query Tools- PGDWDMS Query Tools- PGD Phenotypic data queries on genotypes

Genotype

Nurseries where the genotype has been evaluated


WDMS Query Tools- PGDWDMS Query Tools- PGD Phenotypic data queries on locations

iwis review sdd november 2003 iwis international wheat information system

Documents

iwis components iwis

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iwis architecture functiontask

sid slide

wheat breeding process

y gara

durum wheat