Submitted by sook on Thu, 09/02/2021 - 14:12

To import data into BIMS, the data needs to be in the BIMS templates. Phenotype data can also be imported to BIMS using exported files from Field Book or BrAPI, but data other than phenotype, such as contact, dataset, site, cross, progeny, and accession, need to be loaded using templates. 

Data templates are available for download in the Template list under the Data Import section on the left-hand accordion menu. In the Data Templates tab, users can view the description of each template and download the templates. Data templates are Excel files that contain metadata types as headings where users can enter data to be loaded into the database. In the current version of BIMS, templates are available for each of the following data types: property, contact, dataset, trait descriptor, site, accession, cross, progeny, marker, haplotype block, phenotype, genotype, haplotype, and image. There can be multiple templates for some data types. 

As explained in Creating a New Breeding Program section of the BIMS manual, users can choose to change the names of the required column names for Field Book App and the phenotype templates (phenotype_long_form_bims or phenotype_bims) of the template. This can be done when users create a new breeding program or in the BIMS/Field Book section of the configuration panel shown below. The change made here will be reflected in the template that the user downloads.

BIMS Template Overview Figure 1

The same names of the four required columns should be used when preparing an input file for Field Book App. The figure below shows matching column names in the Field Book App input file and phenotype_bims template.

BIMS Template Overview Figure 2

Different types of columns

In each template, the required columns have * as a prefix as shown above. Other columns can be used to enter data or left empty. Columns that are not specified in the templates will be ignored when loading data. Users can, however, make custom columns in some of the templates which should be specified in the property_bims and have ## as a prefix of the column name as shown above. In phenotype_bims, trait descriptor names are entered as column headings, and they need to have # as a prefix as shown above. The trait descriptor names need to match an entry in the  descriptor_name column in the descriptor_bims if they have not been loaded to BIMS already. In the genotype_snp_wide_form_bims, marker names are entered as column headings, and they need to have $ as a prefix. The marker names need to match marker_name in the marker_bims if they have not been loaded to BIMS already. For some columns, only one of the specified terms can be entered as valid data. For example, valid entries for the type column in contact_bims are person, company, database, institution, lab, and organization. Those columns and their valid entries will be described in each data template section.