CINCALLI Database
Tables of the database
Table Name
Description
Site
Informations that describe the sites of experimentation
Genotype
Genetic informations about the genotypes
Trial
Who, where, when and how the trials? Measure
Descriptions of all the variables used (environmental and phenotypic)
Plot
Characterization of the experimental plots (design informations)
DailyEnvironment
Environmental daily data HourlyEnvironment Environmental hourly data
PlotMeasure
Phenotypic data at the plot scale
PlantMeasure
Phenotypic data at the plant scale
TrialAssoMeasure
Which measures performed in which trials?
Description of the fields of the tables
Site Field Name
Description
SiteName [primary key] Name of the place where experimental site is located country
Country where experimental site is located
longitude
Longitude of the experimental site (°)
latitude
Latitude of the experimental site (°)
altitude
Altitude of the experimental site (meters above sea level)
soilType
Informations about the soil of the experimental site
Genotype Field Name
Description
genotypeName [primary key]
Registered name of the genotype
precocity
Precocity group of the genotype
pedigree
Genealogy, genetic origin of the genotype
genotypeSource
Seeds source
markerLink
Attachment to files with allelic frequencies of markers
genotypeInfo
Attachment to files with various informations about the genotype
Trial Field Name
Description
idTrial [primary key]
Unique trial identifier (2 letters from the siteName with year and sample group if necessary)
projectName
Name of the program with which trial is in line siteName [foreign key]
Site identifier in which trial takes place
startDate
Start date of the trial
endDate
End date of the trial
trialResp
Trial responsible (institutes or persons names)
scenariiNumber
Number of treatments applied for the trial
stressType
Types of hydric stress applied (NONE or SS or DH­PRE and DH­POST)
entriesNumber
Number of genotypes tested in the trial
referentNumber
Number of referent genotypes (témoins) in the trial
sampleGroup
Which sample group of genotypes used for the trial ?
repNumber
Number of repetitions
sblockNumber
Number of sublocks
plotLength
Length of each experimental plot
plotWidth
Width of each experimental plot
trialPictures
Attachment to files that illustrate the trial
protocolLink
Attachment to files that describe protocols and modes of operation
documentLink
Attachment to files with various informations about the trial (reports, articles ...)
Measure
Field Name
Description
idMeasure [primary key]
Unique measure/variable identifier (abbreviation) measureNature
Nature of the variable (to be completed)
measureDefinition
Description of the variable
measureType
Type of values of the variable (integer, score, date...)
measureUnit
Unit of the values of the variable measureMinimum
Minimum value of the variable if it exists
measureMaximum
Maximum value of the variable if it exists
measureFormula
Formula to obtain the measure if it's adjusted
frenchDescription
French description of the variable
Remark : The main interests of this table are the fact that a new measure can be easily added to the database, since a new entry in this table is enough instead of creating new fields in the data tables. Beyond, this Measure Table linked to the structure of the data tables avoid empty fields or missing data when a measure hasn't been observed for a trial. Plot Experimental plot corresponds to a repetition (many plants) of a fixed genotype under a fixed treatment for a fixed trial. Field Name
Description
idPlot [primary key]
Unique plot identifier (idTrial_plotNumber) genotypeName [foreign key]
Genotype of the plants in the plot
idTrial [foreign key]
Trial in which is the plot treatment
Treatment applied for the plot (IRRIG, SS, PRE­DH or POST­DH)
rep
Repetition identifier of the plot
sBlock
Sblock identifier of the plot
xplot
X­coordinate of the plot in the design of the trial
yplot
Y­coordinate of the plot in the design of the trial
sowingGroup
Sowing group of the plot if it exists
totalPlantNumber
Total number of plants in the plot
samplePlantNumber
Number of sampled plants of the plot for plant­ observations
cancelPlot
If plot observation suspended and if desired the reason
The Data
Each data table has its specifics, the data type that can be environmental or phenotypic, the scale time for the environmental ones or the observation level fot the phenotypic ones. Yet, a common structure is present in all the tables. An observation is defined by the fields described below.
The following table doesn't exist as such but it introduces a set of fields present in the tables of data :
− DailyEnvironment
− HourlyEnvironment
− PlotMeasure
− PlantMeasure
DataTable
Field Name
Description
idMeasure [foreign key]
Measure identifier of the data
tableNameValue
Data value
tableNameConfidence
Confidence level for the value (between 0 et 1)
tableNameData
Data type : « observed », « average », or « adjusted »
tableNameObs
Any observation about the data
The specific fields of every data table are presented below :
DailyEnvironment
Field Name
Description
idDailyEnvironment [primary key]
Unique data identifier idTrial [foreign key]
Trial to which data are linked
dateD
Date of the data observation stationName
Meteo station name from which data are come
treatmentSite
Treatment to which data are linked (example of irrigation as data)
scale
Observation scale : “General Meteo” or “Trial device”
DataTable
Fields defined above
HourlyEnvironment
Field Name
Description
idHourlyEnvironment [primary key]
Unique data identifier idTrial [foreign key]
Trial to which data are linked
dateH
Date of the data observation timeH
Date and hour of the data observation (special format)
stationName
Meteo station name from which data are come
treatmentSiteH
Treatment to which data are linked (example of irrigation as data)
DataTable
Fields defined above
Remark : HourlyEnvironment data can be averaged by day to get the same information in the DailyEnvironment table.
PlotMeasure
Field Name
Description
idPlotMeasure [primary key]
Unique data identifier idPlot [foreign key]
Plot to which data is linked plotMeasureDate
Date of the data if specified
plotTemporal
Indicates if the data is a temporal observation or not
DataTable
Fields defined above
PlantMeasure
Field Name
Description
idPlantMeasure [primary key]
Unique data identifier idPlot [foreign key] Plot to which data is linked plantEntry
Unique plant identifier in a fixed plot plantMeasureDate
Date of the data if specified
plantTemporal
Indicates if the data is a temporal observation or not
DataTable
Fields defined above
Remark : PlantMeasure data can be averaged by plot to get the same information in the PlotMeasure table.
Files Format and Structure for Data Recording
The file format most appropriate for the recording of data in the database, is the extension CSV (comma­separated values) with semicolon as cell separator.
1. – Informations Tables
The tables Site, Genotype, Trial, Measure and Plot need to be populated by CSV files that have the same framework.
2. ­ Data Tables
As regards with the data tables, even if they have a row­structure (values of different nature in the same field), input files can present a column­structure i.e a variable by field. For this, it's important to
•
fill the fields reported as specific to each table.
•
respect the nomenclature of the table Measure for the names of the variables.
firm up details for each variable about its type (« observed », « average » or « adjusted ») and its date of measurement. These details can be stored in another CSV file named « measureInformation » with a field by information.
•
•
Add if necessary field with observations related to a variable in input files, an observation related to a data could help to ascribe a confidence level to the value.