CMC Process Ontology

Project Charter

The Pistoia Alliance has developed an advanced semantic architecture for a Pharmaceutical CMC Process Ontology. The objective is to create a domain lexicon and taxonomy that extend the ISA‑88 framework, enabling standardized laboratory and plant production process recipes.

The CMC Process Ontology is explicitly focused on process and process development, while providing defined integration points to related domains such as analytics, materials, equipment, and quality.

The CMC Process Ontology Version 1.0 is now released (Dated June 1, 2026)

We are pleased to announce the release of Version 1.0 of the Pistoia Alliance Pharmaceutical CMC Process Ontology. This release is a major milestone in our effort to create a standardized, machine-readable representation of pharmaceutical CMC processes.

Version 1.0 establishes the core process framework, aligned to ISA-88 principles, and provides a shared semantic foundation for representing process structure, recipes, execution context, parameters, sampling, and key process linkages. It has been tested and refined against real laboratory and process scenarios, and is structurally compatible with leading complementary ontologies, including through collaboration with the Allotrope Foundation and the IOF. This marks the point at which the ontology is sufficiently mature for broader adoption and deployment.

The CMC Process Ontology Version 1.0 is available for Pistoia Alliance members in the new Release Repo.

Development is ongoing to expand ontology coverage and facilitate its practical application. Funding members of this project have access to the latest development version via a private GitHub repository.

If you are interested in accessing the CMC Process Ontology Version 1.0 and providing feedback, please contact birthe.nielsen@pistoiaalliance.org.

Project background

The standardization achieved via the CMC Process Ontology establishes consistent definitions for processes and their development, supports digital technology transfer, and enables integration with execution systems to capture structured process data. As a result, the CMC Process Ontology improves material lot genealogy tracking, streamlines technology transfer, and enables advanced process analytics, enhancing efficiency and transparency across the pharmaceutical production lifecycle.

During the initial project phase (2024), the team delivered significant gains in addressing inefficiencies in technology transfer and data integration across stages and scales, as well as integration across production systems. We showed how an ontology‑driven approach can improve efficiency and transparency throughout the pharmaceutical production lifecycle. In the second phase (2025), we expanded the ontology scope to facilitate optimal process scale-up. The ontology now captures and defines process steps at the development stage of chemical, monoclonal antibody (mAb), and CAR‑T manufacturing, including key process parameters in the P-S-O-A (process, stage, operation, action) model.

Current Project Phase

Phase 3 (2026) will focus on three complementary areas to ensure both near-term impact and long-term sustainability:

Cross-domain connectivity and interoperability
Practical implementation and real-world enablement
Expansion of the ontology coverage

We are building out integration among the CMC Process, Equipment, Material, Analytical (measurement and quality attribute), and IDMP ontologies to ensure interoperability across the value chain. The Pistoia Alliance’s CMC Process Ontology imports the IOF Biopharma Ontologies to support aspects of biopharmaceutical CMC, and is aligned with the Basic Formal Ontology to facilitate broad interoperability.