Samples

Biological and digital materials that flow through your research processes.

What is a sample?

A sample represents any material tracked through the research workflow — biological specimens, extracted nucleic acids, sequencing libraries, or digital data objects. Samples flow between processes as inputs and outputs, forming the provenance chain.

Creating samples

Samples are created as outputs of a process:

1. Navigate to a process page
2. Go to the Samples tab
3. Under Output Samples, click Add Sample
4. Fill in:
   • Name — A unique identifier (e.g., "HaFB_RNA_01")
   • Material type — What the sample is (RNA, DNA, library, tissue, etc.)
   • Characteristics — Key-value metadata (species, tissue, treatment, etc.)
5. Click Create

Sample page

Each sample's page shows:

• Basic info — Name, material type, characteristics
• Source process — The process that created this sample
• Downstream processes — Processes that use this sample as input
• Storage location — Where the sample is physically stored (if recorded)
• Assays — Measurements and QC results linked to this sample
• Analysis runs — Computational analyses that processed this sample
• Ontology annotations — Structured metadata terms
• Provenance view — Visual lineage diagram showing the complete chain

Sample characteristics

Characteristics are key-value pairs that describe sample properties. They are included in ISA exports and can use ontology terms for machine readability.

Common characteristics:

Key	Example value	Ontology
Organism	Helicoverpa armigera	NCBI Taxonomy
Tissue	Fat body	UBERON
Sex	Female	PATO
Developmental stage	5th instar larva	UBERON
Treatment	Control	EFO

Provenance and lineage

The provenance view shows the complete history of a sample — every process it has passed through, from the original source material to the current state. This is visualised as a directed graph.

To view a sample's lineage:

1. Navigate to the sample page
2. The provenance diagram is displayed automatically, showing upstream and downstream connections

Linking samples to processes

To use an existing sample as input to a new process:

1. Navigate to the process page
2. Go to the Samples tab
3. Under Input Samples, click Link Sample
4. Search for the sample by name
5. Select and confirm

This creates the provenance link between the two processes.

Sample access control

Sample visibility follows the access rules of the process and investigation they belong to. Additionally, sample-level access checking ensures that users can only see samples from processes they have permission to view.

For sequencing QC dashboards, sample-run links connect ISA samples to platform-specific run data. Admin users can see all samples; non-admin users see only samples linked to their group's projects.

Bulk sample import

For processes with many output samples, you can import samples in bulk:

1. Prepare a CSV file with columns: name, material_type, and any characteristic columns
2. On the process page, use the Bulk Import option
3. Upload the CSV file
4. Map columns to fields
5. Review and confirm the import