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JERM v1.0

The Just Enough Results Model (JERM) is a metadata framework used by FAIRDOM-SEEK for managing systems biology data. It extends the ISA (Investigation-Study-Assay) structure with additional asset types for computational models, workflows, and collaborative project management.

JERM is designed to capture the minimum metadata required to make experimental data discoverable and interpretable. It provides a bridge between laboratory data management and FAIR (Findable, Accessible, Interoperable, Reusable) data sharing.

Overview

JERM organizes research data hierarchically:

  • Project: Top-level organizational container for collaborative research
  • Investigation: High-level research context and goals
  • Study: Series of experiments addressing a biological question
  • Assay: Individual experimental or computational analysis

Assets can be associated at various levels:

  • DataFile: Experimental data in any format
  • Model: Computational/mathematical models (SBML, CellML, etc.)
  • SOP: Standard Operating Procedures
  • Document: Reports, specifications, protocols
  • Presentation: Slides, posters
  • Workflow: Computational pipelines (Galaxy, CWL, Nextflow)

Entity Diagram

flowchart TB
    subgraph project["Project Management"]
        PRJ[Project]
        INST[Institution]
    end

    subgraph isa["ISA Structure"]
        INV[Investigation]
        STU[Study]
        ASS[Assay]
    end

    subgraph assets["Assets"]
        DF[DataFile]
        MOD[Model]
        SOP[SOP]
        DOC[Document]
        PRES[Presentation]
        WF[Workflow]
        COLL[Collection]
    end

    subgraph bio["Biological"]
        SAM[Sample]
        ORG[Organism]
        STR[Strain]
    end

    subgraph people["People & Events"]
        PER[Person]
        PUB[Publication]
        EVT[Event]
    end

    PRJ --> INST
    PRJ --> INV
    PRJ --> PER

    INV --> STU
    INV --> PUB

    STU --> ASS
    STU --> PUB

    ASS --> DF
    ASS --> MOD
    ASS --> SOP
    ASS --> DOC
    ASS --> SAM

    SAM --> ORG
    SAM --> STR
    ORG --> STR

    PRES --> EVT

    MOD --> DF
    MOD --> ORG

    COLL --> DF
    COLL --> MOD
    COLL --> DOC

    classDef proj fill:#e3f2fd,stroke:#1976d2,stroke-width:2px
    classDef isa fill:#e8f5e9,stroke:#388e3c,stroke-width:2px
    classDef asset fill:#fff3e0,stroke:#f57c00,stroke-width:2px
    classDef bio fill:#fce4ec,stroke:#c2185b,stroke-width:2px
    classDef people fill:#f3e5f5,stroke:#7b1fa2,stroke-width:2px

    class PRJ,INST proj
    class INV,STU,ASS isa
    class DF,MOD,SOP,DOC,PRES,WF,COLL asset
    class SAM,ORG,STR bio
    class PER,PUB,EVT people

Entities

Category Entities
Project Project, Institution
ISA Core Investigation, Study, Assay
Assets DataFile, Model, SOP, Document, Presentation, Workflow, Collection
Biological Sample, SampleType, Organism, Strain
People Person, Publication, Event
Annotations OntologyAnnotation, Factor

Key Differences from ISA

Aspect ISA JERM
Top-level Investigation Project
Models Not included First-class Model entity
Protocols Protocol entity SOP entity
Workflows Not included Workflow entity
Collections Not included Collection for grouping assets
Organisms Via OntologyAnnotation Dedicated Organism/Strain entities
Events Not included Event entity for conferences

Model Formats

JERM supports computational models in various formats:

Format Description
SBML Systems Biology Markup Language
CellML Cell modeling language
BioPAX Biological Pathway Exchange
MATLAB MATLAB scripts and functions
Python Python scripts
R R scripts

Sample Types

JERM uses a flexible sample type system where:

  • SampleType defines the template with attribute definitions
  • SampleAttributeDefinition specifies required/optional attributes
  • Sample instances conform to their type with SampleAttribute values

This allows custom sample types for different experimental domains.

SEEK Integration

JERM is the underlying model for FAIRDOM-SEEK. Key integration points:

  • SEEK IDs: Persistent URIs for all entities (seek_id field)
  • Versioning: Assets track version numbers
  • Licensing: Default and per-asset license information
  • Sharing policies: Project-level default policies

References

Resource URL
JERM Ontology https://jermontology.org/
FAIRDOM-SEEK https://seek4science.org/
FAIRDOMHub https://fairdomhub.org/
SEEK API https://docs.seek4science.org/help/user-guide/api.html
JERM GitHub https://github.com/FAIRdom/JERMOntology

Usage

from metaseed.specs.loader import SpecLoader

loader = SpecLoader()
jerm = loader.load_profile(version="1.0", profile="jerm")

# List all entities
print(jerm.list_entities())

# Get specific entity
project = jerm.get_entity("Project")
for field in project.fields:
    print(f"{field.name}: {field.type.value}")