Presentation Title Goes Here …presentation subtitle. Information Management - Phenotype Arllet M....

Presentation Title Goes Here …presentation subtitle.

Information Management - Phenotype

Arllet M. Portugal

Crop Informatics Specialist

CIMMYT

:: color, composition, and layout

Outline

• Rationale• ICIS Workbook • Workbook template• Trait Dictionaries• ICIS Workbook Functionalities• Field books• Handheld integration


Rationale

Efficient management of phenotypic data is important for easy integration with pedigree data and molecular data. This includes fast recording of voluminous phenotypic data through the aid of electronic data capture and handheld computers

It also involves sufficient and proper documentation of the traits being measured including measurement units and methods.

Data from experiments that are repeated should be standardized through templates.


ICIS Workbook

• A macro in Excel that facilitates creation of data template, field books and loading and retrieval of studies to and from the database.

• It reads the content of the spreadsheet and uploads it to a local database designed to contain phenotyping, genotyping and environmental data.


Workbook template


Workbook Template

A STUDYis the basic, reportable unit of research. It is synonymous with the notions of experiment, trial or nursery

A classifying variable whose value is already known before the study is conducted is called a FACTOR. A common example would be an entry number or id. which identifies each individual entry on a given list. It consists of discrete values. A factor that has a single level throughout the study is called a CONDITION

A variable that is being measured or observed in the study is called a VARIATE. A variable that is measured only once in the study is called a CONSTANT. Typical examples are the characteristics of the soil used in a particular study that is conducted in one location.


Trait Dictionaries

PROPERTY or TRAIT is a measurable characteristic of an experimental unit or experimental material that is manipulated or measured in a study.

SCALE is a unit of measurement used in expressing a property.

METHOD is the manner a property is measured, observed or applied.

The Trait Dictionary or Ontology enables different studies using different variable names but pertaining to similar concepts to be compared and summarized.

Trait Template


Trait Dictionaries


ICIS Workbook Functionalities

• Creating a template

• Creating a field book

• Handheld Integration

• Retrieving/Loading Study


Creating a template

• Create a new Workbook file

• Specify the variables

• Describe the variables in terms of its trait, scale and method


• Set-up the Observation sheet

Creating a template …

Template


Creating a field book

• A germplasm list created in SetGen

• A Workbook template

• A layout design in Excel file


Creating a layout file


Generate field book for several trials

Multi-trial field books


Generate field book for replicated trial

RYT field book


Handheld Integration


Handheld Integration

• Run IWIS FieldLog• Open a template• Retrieve a list• Click Fieldlog->Create New

Characteristics/Traits to generate the csv file for the list of traits to measure

• Click Fieldlog-> Get Germplasm to Score to generate the csv file for the list of entries

• Transfer the csv files to handheld machine

Fieldlog


Loading of a Study


Retrieval of Study Data


CIMMYT-CRIL

Presentation Title Goes Here …presentation subtitle. Information Management - Phenotype Arllet M....

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