File formats

The submission files in SHiNeMaS are « tabulated » files and must fit with the following rules :

• Text file

• Column separator : tabulation

• Text delimiter : “

For example, a file open with a simple text editor, that will be submitted into SHiNeMaS must look like this :

"project" "location" "id_seed_lot" "etiquette" "event_year" "split" "quantity"
"PPB"  "FLM"  "Rouge-du-Roc_JFB_2004_0001"  2004 1 250
"PPB"  "FLM"  "Clomone_JFB_2004_0001"  2004 1 122

Each file type is described by mandatory fields (headers). It is possible to add additional columns regarding the method file (section Methods file ). With this feature a user can customize variables definition.

Methods file

The method file contains the description of measures and the methods used to make these measures. Four fields described this file :

• variable : the name of the measured variable

• type : the type of the variable (described in this section)

• method_name : the name of the method used to measure this variable.

• correlation_group : correlation groups used for this variable. Correlation groups usage is described in this section.

Events types

Cross-breeding

A cross-breeding event occur between different varieties, as shown on the figure below. A cross-breeding creates a new variety.

Cross breeding event

File headers :

The breeding file describes the information necessary to create a cross-breeding event in the database. The fields needed to create a breeding are the following :

• project: Project in which the event has occurred

• sown_year: Parents seeds lots’ sown year.

• harvested_year: Harvest year of the seed lot descended from the cross-breeding

• quantity_harvested: Quantity harvested after the cross-breeding. It is the initial quantity of the harvested seeds lot.

• cross_year: Year of the cross-breeding

• cross_germplasm: Name of the new created variety

• number_crosses: Number of cross-breeding done

• kernel_number_F1: Number of seeds obtained from the cross-breeding and used for the F1

• male_seed_lot: ID of the seeds lot used as a male

• male_etiquette: Label used for the male seed lot

• male_split: Indicates if the entire seed lot was used at cross-breeding: 0 for all and 1 otherwise

• male_quantity: Quantity of seeds from the seed lot used

• male_block: Block in which the seed lot has been sown

• male_X: X coordinate of the male seed lot

• male_Y: Y coordinate of the male seed lot

• female_seed_lot: Identifier of the seed lot used as female

• female_etiquette: Label used for the female seed lot

• female_split: Indicates if the entire female seed lot was used for the cross-breeding: 0 for all and 1 otherwise

• female_quantity: Quantity of the female seed lot used

• female_block: Block in which the female seed lot has been sown

• female_X: X coordinate of the female seed lot

• female_Y: Y coordinate of the female seed lot

Diffusion

This file is used to create diffusion events. A diffusion makes possible to send a seeds lot, entirely or partly, from a place A to a place B, as represented on Figure 11.

File headers:

The diffusion file describes the information needed to create a diffusion event in the database. The fields required to create a diffusion are:

• project: Project in which the diffusion takes place

• location: Place where the seed lot is diffused

• id_seed_lot: Identifier of the “parent” sent seed lot

• etiquette: Label used for the parent seed lot

• event_year: Year of the diffusion

• split: Indicates if the entire “parent” seed lot has been diffused: 0 for all and 1 otherwise

• quantity: Quantity of seed lot released (“child” seed lot)

Mixture

This file is used to create mixture events as shown in Mixture event. A mixture consists in using at least two seeds lots and grouping them into a single seeds lot. There is no limit on the number of seed lots that can be mixed. However, all seed lots must come from the same place. A mixture leads to the creation of a new variety.

Mixture event

File headers:

The mixture file describes the information needed to create a mixture event in the database. The mixture file has the particularity of describing a mixture event on several lines of the file. Each line describes a lot of seeds used in the mixture. The germplasm field, repeated on several lines, makes possible to group the seeds lots that are used in the same mixture. The fields needed to create a mixture are:

• project: Project in which the mixture has been done

• id_seed_lot: Identifier of the « parent » seeds lot mixed

• etiquette: Label used for the « parent » seeds lot

• split: Indicates if the entire seeds lot has been used for the mixture : 0 for all and 1 otherwise

• quantity: Quantity of the « parent » seeds lot mixed

• germplasm: Name of the created new variety

• event_year: Year of the mixture

Reproduction

This file makes it possible to create reproduction events as described on Figure 15. A reproduction takes place on a given place, at a given position, defined by its block and its X and Y coordinates. A reproduction consists in sowing a seed lot at one or more plots and then harvesting the seed lot(s).

File headers:

This file makes it possible to create reproduction events. A reproduction takes place on a given place, at a given position, defined by its block and its X and Y coordinates:

• project: Project in which the reproduction takes place

• sown_year: Sowing year of the parent seed lot

• harvested_year: Harvest year of seed lot “child”

• id_seed_lot_sown: ID of the « parent » sown seed lot

• intra_selection_name: Name of the selection

• etiquette: Label used for the « parent » seed lot

• split: Indicates if the entire « parent » seed lot has been sown : 0 for all, 1 otherwise

• quantity_sown: Quantity of the « parent » seed lot used

• quantity_harvested: quantity harvested for the « child » seed lot

• block: location block of the reproduction

• X: coordinate X

• Y: coordinate Y

Selection

This file is used to create selection events. A selection event is always associated with a reproduction. A selection can be made by an actor of the network.

File headers: The selection file describes the information needed to create a selection event in the database. The fields required to create a selection are :

• project: Project in which the selection takes place

• sown_year: Sowing year of the « parent » seed lot

• harvested_year: Harvest year of seed lot « child »

• id_seed_lot_sown: Identifier of « parent » seed lots

• etiquette: Label used for the « parent » seed lot

• block: block where the reproduction take place

• X: X coordinate

• Y: Y coordinate

• selection_person: Short name informing the person who made the selection

• selection_quantity_ini: Quantity selected

• selection_name: Name given to this selection

Note that the selection_name can be used only one time for a specific germplasm. To help you to respect this rules you can use the selection table.

Individual data

This file is used to enter individual data concerning reproductions or selections. Individual data is associated with numbered individuals.

File headers:

The individual data file describes the information needed to insert individual data into the database. The fields required to insert this data are as follows:

• project: Project in which the selection takes place

• sown_year: Sowing year of the « parent » seed lot

• harvested_year: Harvest year of seed lot « child »

• id_seed_lot_sown: Identifier of « parent » seed lots

• intra_selection_name: Name of selection if applicable

• sown_etiquette:Label used for the « parent » seed lot

• id_seed_lot_harvested: Identifier of the « child » seed lot harvested

• harvested_etiquette: Label used for the «child» seed lot

• block: block where the reproduction take place

• X: X coordinate

• Y: Y coordinate

• individuals: Number of the individual

Correlation groups

Correlation groups are used for individual data. Let’s consider a data series (at a same date for example) on numerated individuals. For the next series (at another date) the user collect data on the same number of individuals. But two scenarios can occur :

• The numerated individuals are not the same (You lost the numeration between the two series of data). In that case the data of the first series and the second series can’t be correlated as it’s haven’t be done on the same individuals. Example : In figure A, on a single line, data in green, blue and orange aren’t correlated and belongs to 3 different groups B, C, and D

• The numerated individuals are the same. In that case all data can belong to the same correlation group. Example : In figure A, the lines in yellow. The data belongs to the group A.

A : Reproduction file with correlation groups

In the method file you should report in the correlation_group column all the correlation groups in which a variable is implied (figure B). For example, the variable ‘plant_height’ is implied in the correlation groups A (yellow) and B (green).

B : Method file with correlation groups

Particular cases

It is possible to measure a same variable with two different method. To do the variable must be tagged with a prefix in the data file and in the method file. The following syntax is used (Figure below)  : prefix%variable_name

Variable using 2 differents methods