Trait Management System 5.4

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Contents 1 DMS PROPERTIES, TRAIT AND SCALES 1.1 INTRODUCTION 1.2 THE TRAIT MANAGEMENT MODULE 1.2.1 TRAITS 1.2.1.1 The TRAIT table (List of all traits) 1.2.2 Scales 1.2.2.1 Scale Table 1.2.2.2 The SCALEDIS Table (For all traits measured in binary/discrete scales) 1.2.2.3 The SCALECON table 1.2.3 METHODS 1.2.3.1 The TMETHOD Table (Information on the method being used to measure a trait)

DMS PROPERTIES, TRAIT AND SCALES

INTRODUCTION

This chapter describes the Trait Management Module (TMM) and the Data Control and Validation Module (DCVM) of the ICIS.

The functions of the DCVM are:

a) To link all measurement variates and factors into distinct classes, each representing a single property or trait of the experimental material. These traits are the basis of linking information across studies.

b) To manage and relate all the scales in which a trait can be measured or expressed as well as conversion between scales. DMS stores data in measurement units whenever possible but the DCVM may convert it to standard units for display or analysis.

c) To record details of all the measurement or manipulation methods for traits.

d) To manage and control quality of data recorded into the DMS.

THE TRAIT MANAGEMENT MODULE

TRAITS

A trait is a measurable characteristic or property of an experimental unit or experimental material (e.g., of a variety or environment), which is manipulated or measured in a study. Traits are defined in the TRAITS table. All theoretically convertible variables belong to the same trait. For example: Urea, artificial NPK-fertilizer and mulch can all be converted for their amount of Nitrogen and therefore all belong to the same trait: N-application. Traits can either serve as experimental factors in one study or as experimental variates in another study (water can either be irrigation or rainfall). Traits are the key to integration of different studies in the database because all variates linked to the same trait are, in some sense, comparable. Similarly, all factors representing the same trait define comparable conditions. Because of the diversity of research thousands of traits exist. To make it easier to view, query or update traits in ICIS, traits are grouped in the TRAIT_GROUPS table. Logical groups are, e.g., genetic traits and environmental traits, but the system supports additional grouping by discipline (e.g. breeding, economics, natural resources management, industrial quality laboratory), or other criteria. People are used to name the same trait in a different way, e.g., Germplasm, Entry, Variety. This is also handled in the TRAIT table with a TNSTAT field to tag the status of the name.

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The TRAIT table (List of all traits)

Field name	Description	Type	Length
TID	A unique number that identifies a trait name	Long
TRAITID	A number that identifies a trait.	Long	4
SCALEID	The standard scale for the trait	Long	4
TMETHID	The standard Method for the trait	Longr	4
TNSTAT	The status of the trait name. 1 – Preferred name, 2 – Preferred abbreviation	Long	2
TRABBR	The abbreviation of the trait name	Char	6
TRDESC	Description of the trait.	Memo	-

Scales

Each scale is described in the SCALE table, while the actual scale values are defined in the SCALEDIS and SCALECON tables. The first handles discrete scales, binary scales (yes, no), classification scales (seed color scales) and ordinal scale (disease score). The second handles continuous scales (length).

Scale Table

Table 3.2.4.

The SCALE Tabl'e (The scale in which a trait is measured)

Field name	Description	Type	Length
SCALEID	A unique number that identifies a scale	Integer	4
SCTYPE	Identifies the used scale (C)ontinuous or (D)iscrete.	Char	1
SCNAME	The name of the used scale	Char	30
TRAITID	The Trait using this scale	Integer	4

The SCALEDIS Table (For all traits measured in binary/discrete scales)

Field name	Description	Type	Length
SCALEID	Link to the SCALE table	Integer	4
VALUE	The used value	Char	10
VALDESC	The meaning of the value	Char	255

The SCALECON table

Field name	Description	Type	Length
SCALEID	Link to the SCALE table	Integer	4
SLEVEL	Definition of where a scale starts	Real	4
ELEVEL	Definition of where a scale ends	Real	4

METHODS

The method of measuring or applying a trait should be recorded for complete documentation. Every method for measuring the same trait can lead to a different result. For example, you can measure color with a Minolta chromometer or with color cards. Preferably all methods should be defined and recorded as Standard Operating Procedures.

For every trait, we can describe one or more methods in the TMETHOD table. This includes information on how factors are applied or how variates are measured or derived and information on equipment, calibration, possible values, accuracy and precision as well as the method of conversion to the standard representation for the property (Appendix 3.2).

Bibliographic references may describe methods in detail and are linked to the METHOD table through the REFLINKS table and the UDFLDS table (user defined fields).

The TMETHOD Table (Information on the method being used to measure a trait)

Field name	Description	Type	Length
TMETHID	A unique number that identifies a method	Integer	4
TMNAME	The name of a method	Char	50
TMABBR	The abbreviated name of a method	Char	6
TMDESC	The description of a method	Memo	--
TRAITID	The Trait using this Method	Integer	4