Experiment Sample Templates

Experiment Sample Templates act as blueprints to create Sample Types within ISA Studies and ISA Assays and ensure that the metadata collected conforms to community standards. The same Experiment Sample Template can be applied multiple times to create Sample Types in different ISA Studies or ISA Assays.

The ISA Study Sources, Samples and ISA Assay Samples tables are Sample Types associated with the ISA Study or ISA Assay and can only be accessed through the ISA Study or ISA Assay interface. The tables can only be created starting from an existing Experiment Sample Template.

An Experiment Sample Template must have the following specifications.

1. One ISA Level
   • Study Source
   • Study Sample
   • Assay material
   • Assay data file
2. One Repository name or SEEK Project
   • Repository or data archive (e.g. EBI databases)
   • SEEK Project (Project specific templates)
3. Organism: optional free text

Types of Experiment Sample Templates

There are two types of Experiment Sample Templates: platform-wide and project-specific.

Platform-wide Experiment Sample Templates

Platform-wide Experiment Sample Templates

• must be provided by the platform administrator by uploading a json file via the Server admin panel
• are platform-wide (or instance-wide) and visible to every registered user
• are not subjected to sharing permission nor associated to any project

Project-specific Experiment Sample Templates

Project-specific Experiment Sample Templates

• can be created by project members
• must be associated to specific project(s)
• are subjected to sharing permissions

Creating Experiment Sample Templates as a project member

Project members have the capability to create Experiment Sample Templates for their laboratory or research project, called “Project specific Experiment Sample Templates”. These templates can be shared among Projects and Programmes on the platform via granular sharing permissions, allowing other project members to utilize them for designing their experiments.

1. From the header menu bar, select “Create” and then “Experiment Sample Templates” under the Experiments section.
2. Fill out the mandatory and optional fields.
3. Under “Template Information”, click on the “Choose from existing templates” button.
4. Choose the template to start from: after selecting the parameters listed below, choose the templates you wish to use as a basis, and then click “Apply”.
   • The repository you want your template to comply to (e.g. ENA, ArrayExpress or your institutional repository). Select “Project specific templates” if you want to use a template made for or by a specific Project.
   • The ISA Level you want your template to be applicable for.
   • The Organism.
5. Customise the template by usig the Attributes table. However, be aware that applying changes may compromise the compliance to the original template.
   • If you want to add new attributes of your choice to your new template, select “Add new attribute” button.
   • Fill out the mandatory and optional fields. Note that for ISA-JSON compliant Experiments, the ISA Tag is a mandatory field.
   • For ISA tag, note that the following tags can only be present once in a template: source, sample, other_material, data_file, protocol. One of these tags is already present in existing templates, so select one of the following as ISA tags: source_characteristic, parameter_value, sample_characteristic, other_material_characteristic, data_file_comment.
6. Select “Create”.

ISA minimal starter templates

Project members have the option to create project-specific Experiment Sample Templates using the “ISA minimal starter templates”. These basic templates, which are not associated with any repository, contain only the minimal attributes necessary to comply with the ISA-JSON model, identified by ISA-tags. One ISA minimal starter template for each ISA Level is provided. When utilizing the ISA minimal starter templates, project members should edit and customize attributes such as name, description, PID, data type, and unit.

Creating Experiment Sample Templates as system administrator

JSON upload via Server admin panel

If ISA-JSON compliance feature is enabled, an option appears in the Server admin panel to upload instance-wide Experiment Sample Templates, compliant to ISA-JSON schemas.

The Experiment Sample Templates must be in .json format and comply to the expected specification. JSON definitions of Experiment Sample Templates tailored for submission towards EBI repositories can be found in this GitHub repository.