Key Concepts

Understand the data model, FAIR principles, and access control that underpin the platform.

The ISA framework

Libre Biotech organises research data using the ISA (Investigation–Study–Assay) framework, an internationally recognised standard for structuring experimental metadata. ISA is maintained by the ISA Tools community and is widely adopted in life sciences.

Hierarchy

Investigation          (research project)
  └── Study            (experimental campaign)
       └── Process     (a specific activity)
            ├── Input Samples
            ├── Output Samples
            ├── Files
            ├── People
            └── Assays / Measurements

Level	What it represents	Example
Investigation	A research project or programme	"Moth transcriptome characterisation"
Study	An experimental campaign within the investigation	"Larval tissue RNA-Seq"
Process	A specific activity that transforms inputs to outputs	"RNA extraction from fat body tissue"
Sample	A biological or digital material	"HaFB_RNA_01" (extracted RNA sample)

Process categories

Processes are classified by category, which determines the metadata fields available and how they connect in the workflow:

Category	Purpose	Examples
Extraction	Isolating material from a source	DNA extraction, RNA extraction, tissue dissection
Sample Preparation	Preparing samples for analysis	Library preparation, bead selection, pooling
Sequencing	Generating sequence data	Nanopore sequencing run, Illumina run submission
Measurement	Quantitative assessment	Fragment Analyzer QC, Qubit quantification
Data Transformation	Computational analysis of data	Alignment, assembly, annotation pipeline

Process chains

Processes link together through their input and output samples to form process chains — a complete provenance trail from raw material to final result.

Dissection → RNA Extraction → Library Prep → Sequencing → Analysis
  (tissue)    (RNA sample)     (library)     (FASTQ)      (GFF3, BAM)

Each step in the chain records who performed it, which protocol was followed, what equipment was used, and what files were produced. This gives you full reproducibility and audit capability.

FAIR principles

Libre Biotech is built on the FAIR principles — guidelines to make research data Findable, Accessible, Interoperable, and Reusable.

Principle	How Libre Biotech implements it
Findable	Rich metadata with ISA structure, ontology annotations from 3M+ OBO terms, searchable public API, public discovery pages
Accessible	Open access to public content without login, REST API with CORS, share links for controlled access
Interoperable	ISA-JSON and ISA-Tab export, CWL workflow definitions, RO-Crate packaging, standard file formats (FASTQ, BAM, VCF, GFF3)
Reusable	Sample provenance chains, protocol versioning with changelogs, per-entity licensing, community review

FAIR score: Each investigation displays a FAIR self-assessment score showing how well it meets each principle (Findable, Accessible, Interoperable, Reusable), with actionable suggestions for improvement.

Ontology annotations

Libre Biotech includes over 3 million ontology terms from the OBO Foundry, enabling precise, machine-readable annotations on any entity. Common ontologies include:

NCBI Taxonomy — Species and organism classification
EFO — Experimental Factor Ontology
OBI — Ontology for Biomedical Investigations
UBERON — Anatomical structures
ENVO — Environmental conditions
SO — Sequence Ontology

The term picker (available on process, sample, and investigation pages) provides type-ahead search across all loaded ontologies. Terms are stored with their CURIE identifiers (e.g., NCBI:7529) for machine readability.

Access control

Access control operates at three levels:

Visibility levels

Level	Who can see it
Private	Members of the owning group only
Group	Members of associated groups (e.g., a research group + the core facility)
Public	Anyone, including non-logged-in visitors and search engines

Group roles

Within a group, each member has a role that determines what they can do:

Leader — Full control: create/delete investigations, manage members, change visibility settings
Manager — Create and edit content, manage processes, invite members
Member — View content, create processes and samples, upload files

Admin role

Platform administrators have visibility across all groups and can manage users, instruments, and system-wide settings. Admin status is separate from group roles.

Data ownership

You own your data. Libre Biotech has a licence to host and display it — nothing more. Key guarantees:

Full export at any time in standard formats
No proprietary schemas — ISA, CWL, and RO-Crate throughout
Account deletion removes your personal data
90-day notice before any service changes

See the Data Sovereignty Statement for the complete commitment.