Ontology Design

MCBO (Mammalian Cell Bioprocessing Ontology) uses a hub-and-spoke architecture with the Industrial Ontology Foundry (IOF) Core as the central hub, building on BFO foundations with domain-specific extensions.

Hub-and-Spoke Architecture

MCBO reuses terms from multiple OBO Foundry ontologies:

Ontology

Scope / Coverage

Example Terms Used

Role in MCBO

IOF Core

Industrial processes

ProductProductionProcess, hasOutput

Hub anchor for all processes/outputs

CLO

Cell lines

CHO-K1

Standardized cell line IDs

CL

Cell types

Chinese hamster ovary cell

Biological cell type grounding

OBI

Assays

RNA-seq assay, has specified input/output

Experimental processes

EFO/ENVO

Conditions, environments

Hypoxia, culture pH

Capture experimental context

ChEBI

Chemicals

Glucose, L-glutamine

Media components

UO

Units

gram per liter

Normalize quantitative values

PATO

Phenotypes

Cell viability

Describe traits

SO/GO/PRO

Molecular entities

Transcript, gene ontology term, IgG protein

Link outputs to biology

Core Modeling Patterns

MCBO follows BFO-compliant semantic patterns to ensure interoperability with OBO Foundry ontologies.

Process–Participant–Quality Chain

The core pattern for culture conditions:

Process (BFO:process)
  └─ RO:0000057 (has participant) → CellCultureSystem (BFO:material entity)
      └─ RO:0000086 (has quality) → CultureConditionQuality (BFO:quality)
          ├─ hasTemperature (xsd:decimal)
          ├─ hasPH (xsd:decimal)
          └─ hasDissolvedOxygen (xsd:decimal)

How it works:

  1. A bioprocess (e.g., BatchCultureProcess, FedBatchCultureProcess) is a BFO:process instance

  2. The process RO:0000057 (has participant) a CellCultureSystem (a BFO:material entity)

  3. The CellCultureSystem RO:0000086 (has quality) a CultureConditionQuality instance (a BFO:quality)

  4. Temperature, pH, and dissolved oxygen values are attached as datatype properties to the CultureConditionQuality instance

This pattern preserves BFO semantics: processes have material entity participants, which bear qualities. It avoids direct process-to-quality links that would conflict with BFO’s occurrent–continuant distinction.

Cell Line Engineering

CellLine (material entity)
  └─ mcbo:overexpressesGene → Gene (information entity)

  • Cell lines can mcbo:overexpressesGene gene individuals

  • Inferred from Producer (boolean) + ProductType fields when explicit gene columns not present

  • Antibody products (mAb/BsAb) use shared placeholder gene mcbo:AntibodyProductGene

Sample Outputs

CellCultureProcess (process)
  └─ mcbo:hasProcessOutput → BioprocessSample (material entity)
      └─ mcbo:inCulturePhase → CulturePhase (StationaryPhase, ExponentialPhase)

  • Runs produce samples via mcbo:hasProcessOutput

  • Samples can be in specific culture phases

  • Productivity measurements are attached to runs

Key Data Structures

Structure

Location

Description

TBox (Ontology)

ontology/mcbo.owl.ttl

Ontology schema - class definitions, properties

ABox (Instances)

<data-dir>/mcbo-instances.ttl

Instance data generated from CSV

Evaluation Graphs

<data-dir>/graph.ttl

Union of TBox + ABox for SPARQL queries

Scope and Boundaries

In Scope

  • Mammalian cell bioprocessing (CHO, HEK293)

  • Culture process types: Batch, Fed-batch, Perfusion, Continuous

  • RNA-seq data integration

  • Culture conditions (temperature, pH, dissolved oxygen)

  • Productivity measurements

  • Cell line engineering (gene overexpression)

Out of Scope

  • Non-mammalian cell culture (yeast, bacterial)

  • Downstream purification processes (future work)

  • Proteomics data (future work)

Dataset Classification

All dataset classes are subclasses of IAO:dataset (IAO_0000100), which is an information content entity (ICE) in the BFO/IAO hierarchy:

  • RNASeqDataset

  • RawReadsDataset

  • AlignedReadsDataset

This ensures proper classification: datasets are ICEs, not material entities or processes.

CSV to RDF Conversion

The mcbo.csv_to_rdf module transforms tabular metadata into RDF:

  • Maps process types (Batch, FedBatch, Perfusion, etc.) to ontology classes

  • Creates material entities (CellCultureSystem, cell lines, culture media)

  • Attaches culture conditions (temperature, pH, dissolved oxygen) as qualities

  • Handles productivity categorization (VeryHigh, High, Medium, LowMedium, Low)

  • Infers gene overexpression from Producer + ProductType columns

  • Generates IRI-safe identifiers from run/sample accessions

SPARQL Query Architecture

Competency questions in eval/queries/*.rq leverage:

  • rdfs:subClassOf* property paths for class hierarchies

  • OBO relation IRIs (RO_0000057, RO_0000086) for standard relationships

  • Filters on productivity types for optimization queries

  • Cross-table relationship traversals via the RDF graph structure

IOF Alignment

MCBO process classes (e.g., CellCultureProcess, MammalianCellCultureProcess) are direct subclasses of BFO:process to maintain strict BFO alignment and interoperability with OBO Foundry ontologies.

We use rdfs:seeAlso annotations to iof:ManufacturingProcess and iof:ProductProductionProcess to indicate conceptual alignment with IOF manufacturing concepts, while preserving direct BFO classification.

This approach ensures compatibility with both BFO-based biomedical ontologies and IOF-based industrial ontologies.