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Application 2.2.1 Trait Dictionary Schema

Extension of ICIS schema to Convert SCALES

ENTITIES
TRAIT
Data Group
{@TRAITID + TRNAME + TRABBR + TRDESC + TMETHID + TNSTAT + TRAITGROUP + ONTOLOGY}
Comment
E, G, OR GE variable to be measured in an experiment
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@TRAITID
Data Element
Number
Comment
A number that identifies a trait
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@TRNAME
Data Element
Text
Comment
Name of a an E, G or GE trait measured by a breeding program
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TRABBR
Data Element
Number
Comment
Abbreviation of a trait
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TRDESC
Data Element
Text
Comment
Description of a trait
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TMETHID
Data Element
Number
Comment
Method identifier for a trait
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TNSTAT
Data Element
Number
Comment
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TRAITGROUP
Data Element
Text
Comment
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ONTOLOGY
Data Element
Text
Comment
The name of ontology along with its CO_ prefix to define class or domain. For example: CO_322: prefix represents the domain or class "maize_trait ontology".
Number: Automatically generated identifier for each trait or term such as CO_322:0000032 for "days to maturity".
Indentifies identifiers generated by OBO-Edit formatted file. For example: CO_322:0000032. Last seven numbers represent the identifier for the TRAITID "2096" or/and TRNAME "days to maturity".
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SCALE
Data Group
{@SCALEID + SCNAME + SCTYPE + ONTOLOGY}
Comment
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SCALEID
Data Element
Number
Comment
A number that identifies a scale
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SCNAME
Data Element
Text
Comment
Name of a scale used by a breeding program
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SCTYPE
Data Element
Text
Comment
Type of a scale (Numeric, Text)
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ONTOLOGY
Data Element
Text
Comment
The name of ontology along with its CO_ prefix to define class or domain. For example: the CO_042: prefix represents the domain or class "ICIS scale ontology".
Number: Automatically generated identifier for each scale or term such as CO_042:0000139 for "percentage".
Indentifies identifiers generated by OBO-Edit formatted file. For example: In the case of CO_042:0000139, last seven numbers represent the identifier for the scale "percentage".
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CONSISTENCY-CHECKS
Data GROUP
{@IMPLICATIONID + LOGICALOPERATOR + TRAITID + SCALEID + VALUE + LINK}
Comment
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IMPLICATIONID
Data Element
Number
Comment
Number that identifies an implication
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LOGICALOPERATOR
Data Group
[IMPLIES | AND]
Comment
Operator used to build a rule
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IMPLIES
Data Element
Text
Comment
Reserved word that uses the logical operator
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AND
Data Element
Text
Comment
The logical AND operator
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VALUE
Data Group
[VALUE + OPERATOR + VALUE | LETTERS]
Comment
Definition of operation(s) in form of rules to check data
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LINK
Data Group
{TRAITID + SCALEID}
Comment
A pointer to an IMPLICATION or CONSISTENCY-CHECK
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IMPLICATION
Data Group
[LINK + LOGICALOPERATOR + @TRAITID + @SCALEID + VALUE + IMPLICATIONID]
Comment
Definition of relations between attributes in form of rules, i.e.
If PlotSize(X,m2) and GrainYield(Y,kg/plot) then GrainYield(10000/X)*Y,kg/ha)
LOGICALOPERATOR = implication means that the record is a right hand side of an implication. LOGICALOPERATOR = and means that the record is a left hand side of an implication.
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MEASUREDIN
Data Group
{TRAITID + SCALEID + STANDARDSCALE + REPORT + FORMULA}
Comment
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STANDARDSCALE
Data Element
[TRUE | FALSE]
Comment
Identifies the scale that will be used to convert values when is TRUE
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REPORT
Data Element
[TRUE | FALSE]
Comment
Used for reporting purposes when FALSE it will not appear in reports
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FORMULA
Data Element
Text
Comment
Used to execute analyses one per Trait + Scale combination
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TRANSFORMATIONS
Data Group
[TRANSFORMATION]
Comment
Entity used to transform among different scale/units
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TRANSFORMATION
Data Group
{[DISCRETE-CONVERSION | CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION] + TRANSID + FROMSCALEID + TOSCALEID + TRANSTYPE}
Comment
Convert among different scale FROM/TO
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TRANSID
Data Element
Number
Comment
Transformation Key
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FROMSCALEID
Data Element
Number
Comment
Identifies the SCALEID that one SCALE is going to be transformed from
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TOSCALEID
Data Element
Number
Comment
Identifies the SCALEID that one SCALE is going to be transformed to
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TRANSTYPE
Data Element
Text
Comment
Indicates the type of transformation to be used to convert to other scale (a standard scale is used)
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CONTINUOUS-CONVERSION
Data Group
{TRANSID + OPERATOR + FACTOR}
Comment
The factor is used to convert between scales
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OPERATOR
Data Element
[PLUS | MINUS | MULT | DIV]
Comment
Used as a conversion factor
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FACTOR
Data Element
[INTEGER | REAL]
Comment
A number used to convert between different scales
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CONTINUOUS-FUNCTION
Data GROUP
{TRANSID + FUNCTION + FUNABBR}
Comment
Entity used to store functions to convert among scales
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FUNCTION
Data Element
Text
Comment
Stored function used to convert from one scale to other scale
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FUNABBR
Data Element
Text
Comment
Abbreviation of a function
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DISCRETE-CONVERSION
Data Group
{TRANSID + VALUE1 + VALUE2}
Comment
One discrete value is substituted for another discrete value
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VALUE1
Data Group
[VALUES]
Comment
Data value
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VALUE2
Data Group
[VALUES]
Comment
Data Value
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VALUES
Data Group
[LETTERS | NUMBER | REAL | TIME]
Comment
The data values associated to a trait
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PROCEDURES
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UPDATE CONSISTENCY CHECKS:
Updates an implication with SCALES, TRAITS, VALUES in permitted DISCRETE-SCALE and CONTINUOUS-SCALE
Pre-condition 1
Operation = add. Substitute implication does not match in implications
Post condition 1
Substitute implication matches in implications
Pre-condition 2
Operation = delete. Substitute implication matches in implications
Post condition 2
Substitute implication does not match in implications
Pre-condition 3
Operation = modify. Implication to be substituted matches in implications
Substitute implication does no match in implications
Post condition 3
Implication to be substituted does not match in implications
Substitute implication matches in implications
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UPDATE MEASUREDIN:
Updates measuredin with SCALEID, TRAITID, STANDARDSCALE REPORT and FORMULA in permitted SCALE and TRAIT combination
Pre-condition 1
Operation = add. measuredin does not match in MEASUREDIN
Post condition 1
measuredin matches in MEASUREDIN
Pre-condition 2
Operation = delete. measuredin matches in MEASUREDIN
Post condition 2
measuredin does not match in MEASUREDIN
Pre-condition 3
Operation = modify. measuredin to be substituted matches in MEASUREDIN
Substitute measuredin does no match in MEASUREDIN
Post condition 3
measuredin to be substituted does not match in MEASUREDIN
Substitute measuredin matches in MEASUREDIN
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UPDATE TRANSFORMATIONS:
Updates transformation with TRANSID, SCALES, and TYPE in permitted SCALE, CONTINUOUS-CONVERSION, CONTINUOUS-FUNCTION and DISCRETE-CONVERSION
Pre-condition 1
Operation = add. transformation does not match in TRANSFORMATIONS
Transformation does not match in [CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION | DISCRETE-CONVERSION]
Post condition 1
transformation matches in TRANSFORMATIONS and [CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION | DISCRETE-CONVERSION]
Pre-condition 2
Operation = delete. transformation matches TRANSFORMATIONS and [CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION | DISCRETE-CONVERSION]
Post condition 2
transformation does not match in TRANSFORMATIONS and [CONTINUOUS-CONVERSION & CONTINUOUS-FUNCTION & DISCRETE-CONVERSION]
Pre-condition 3
Operation = modify. transformation to be substituted matches in TRANSFORMATIONS and [CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION | DISCRETE-CONVERSION]
Substitute transformation does no match in TRANSFORMATIONS and [CONTINUOUS-CONVERSION & CONTINUOUS-FUNCTION & DISCRETE-CONVERSION]
Post condition 3
transformation to be substituted does not match in TRANSFORMATIONS and [CONTINUOUS-CONVERSION & CONTINUOUS-FUNCTION & DISCRETE-CONVERSION]
Substitute transformation matches in TRANSFORMATIONS and [CONTINUOUS-CONVERSION | CONTINUOUS-FUNCTION | DISCRETE-CONVERSION]
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ADD EVAL REQ:
Group
Composition
[OPERATION + STUDY TO BE PROCESSED | OPERATION + STUDY TO BE PROCESSED + SUBSTITUTE STUDY]
Comment
A trial or nursery from a program that will be added to Data Management System
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OPERATION
Group
Composition
[ADD|MODIFY|DELETE]
Comment
Basic operations applied on the data
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ADD
Data Element
Comment
Indicates that the selected operation is the add operation. The data has to be added
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MODIFY
Data Element
Comment
Indicates that the selected operation is the modify operation. The data has to be modified
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DELETE
Data Element
Comment
Indicates the selected operation is the delete operation. The data has to be deleted
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STUDY TO BE PROCESSED:
Group
Composition
{STUDYID + INSTANCE + MESURED TRAITS + USED UNITS + E VALUES + GE VALUES + G VALUES + STATION + COUNTRY + SUB DIVISION + GROUP}
Comment
EVALUATION DATA FROM SPECIFIC LOCATION TO BE PROCESSED
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STUDYID
Data Element
Study Identification. This number identifies an experiment
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INSTANCE
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MEASURED TRAITS
Data Group
{TRAIT_NAME}
Comment
Set of traits measured in an experiment
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CONVERT SCALES:
Convert measured values from MEASURED SCALE to STANDARD SCALE. It uses CONTINUOUS- CONVERSION, CONTINUOUS-FUNCTION or DISCRETE-CONVERSION to convert; check that MEASURED SCALE are within permitted ranges.
Pre-condition 1
Study ID match in Studies
Used Scales and Trait match in measuredIn
Add.Value do not match in DATA
There is a transformation in TRANSFORMATIONS that convert from used scale to standard scale
Post condition 1
SCALES used for Add.Value are in standard scale
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Examples
CONSISTENCY-CHECKS

CONTINUOUS FUNCTION

DISCRETE-CONVERSION

MEASUREDIN

TRANSFORMATIONS

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