# MCBO: Mammalian Cell Bioprocessing Ontology

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**MCBO** is a hub-and-spoke, IOF-anchored application ontology for mammalian cell bioprocessing
and RNA-seq data curation. It builds on IOF process patterns and BFO foundations, with 
domain-specific extensions that reference OBO ontology classes for measurement, sequencing, 
and biological entities.

The ontology is designed to support:

- RNA-seq analysis and gene expression integration
- Culture condition optimization (temperature, pH, dissolved oxygen)
- Product development for CHO and HEK293 cell bioprocessing
- Integration of curated bioprocessing samples from published studies

**Repository:** https://github.com/lewiscelllabs/mcbo

**New Term Request:** Please visit the [GitHub Issues](https://github.com/lewiscelllabs/mcbo/issues) 
and select "MCBO Term Request" to submit your request.

## Citation

Please cite:

> Robasky, K., Morrissey, J., Riedl, M., Dräger, A., Borth, N., Betenbaugh, M. J., & Lewis, N. E. (2025). 
> MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology.
> *ICBO-EAST 2025*.

**Authors:**

- Kimberly Robasky <sup>1,*</sup> - University of Georgia
- James Morrissey <sup>2</sup> - Johns Hopkins University
- Markus Riedl <sup>3</sup> - BOKU University, Vienna
- Andreas Dräger <sup>4</sup> - Martin Luther University Halle-Wittenberg
- Nicole Borth <sup>3</sup> - BOKU University, Vienna
- Michael J. Betenbaugh <sup>2</sup> - Johns Hopkins University
- Nathan E. Lewis <sup>1</sup> - University of Georgia

<sup>*</sup> Corresponding author: kimberly.robasky@uga.edu

## Evaluation Summary

MCBO has been evaluated with real curated bioprocessing data:

- **724 cell culture process instances** curated from published studies
- **326 unique bioprocess samples** across culture runs
- **Process breakdown:** Batch (518), Fed-batch (135), Perfusion (49), Unknown (22)
- **100% competency question coverage** with sub-second query times; synthetic sample data provided for demonstration; real data curation in progress.

## Competency Questions

MCBO is evaluated against 8 competency questions (CQs):

1. **CQ1**: Under what culture conditions (pH, dissolved oxygen, temperature) do the cells reach peak recombinant protein productivity?
2. **CQ2**: Which cell lines have been engineered to overexpress gene Y?
3. **CQ3**: Which nutrient concentrations in cell line K are most associated with viable cell density above Z at day 6 of culture?
4. **CQ4**: How does the expression of gene X vary between clone A and clone B?
5. **CQ5**: What pathways are differentially expressed under Fed-batch vs Perfusion in cell line K?
6. **CQ6**: Which are the top genes correlated with recombinant protein productivity in the stationary phase of all experiments?
7. **CQ7**: Which genes have the highest fold change between cells with viability (>90%) and those without (<50%)?
8. **CQ8**: Which cell lines or subclones are best suited for glycosylation profiles required for therapeutic protein X?

All 8 CQs have SPARQL query implementations in `eval/queries/`.

## License

MCBO is released under the **MIT License**. See the [LICENSE](https://github.com/lewiscelllabs/mcbo/blob/main/LICENSE) file for details.

```{toctree}
:maxdepth: 2
:caption: User Guide

installation
quickstart
workflows
cli
agent
```

```{toctree}
:maxdepth: 2
:caption: Ontology

ontology
```

```{toctree}
:maxdepth: 2
:caption: API Reference

api
```

```{toctree}
:maxdepth: 2
:caption: Development

development
```

## Indices and tables

- {ref}`genindex`
- {ref}`modindex`
- {ref}`search`