The biomedical ontology landscape offers a choice between open-access resources — maintained by academic consortia, standards bodies, and publicly funded research programmes — and proprietary commercial ontologies maintained by specialist vendors. Both options have legitimate places in pharmaceutical knowledge infrastructure, and the choice between them should be based on the specific requirements of each application domain rather than on a blanket preference for either openness or proprietary depth.
The Case for Open Ontologies
The open biomedical ontology ecosystem — anchored by the OBO Foundry and including SNOMED CT (for countries with national licences), MedDRA (for licensing organisations), Gene Ontology, Disease Ontology, ChEBI, and hundreds of domain-specific resources — is extraordinarily rich. These resources represent decades of collaborative expert curation and are updated regularly by communities that include the world's leading domain experts. Their open licensing (for the OBO Foundry resources specifically) means that they can be incorporated into commercial knowledge products without royalty concerns. Their use by multiple organisations creates network effects: mappings, annotations, and tools developed by one organisation are reusable by others, and community-reported errors are corrected faster than in single-organisation proprietary systems.
Where Proprietary Ontologies Add Value
Proprietary commercial ontologies — such as those offered by clinical data analytics vendors, drug information database providers, and knowledge graph platform companies — provide value in specific use cases where depth, update frequency, or coverage of commercially important concepts exceeds what open resources offer. Drug interaction ontologies that are updated daily against curated literature, clinical trial eligibility ontologies tuned to current regulatory language, or competitive intelligence ontologies that include coverage of late-stage pipeline compounds may justify commercial licensing for pharmaceutical organisations where these capabilities are operationally critical.
The Hybrid Architecture
The most robust pharmaceutical knowledge infrastructure uses a hybrid architecture: open ontologies for the foundational layers (disease biology, molecular entities, anatomical structures, clinical procedures) where community curation provides better coverage and stability than any single vendor can offer, supplemented by proprietary ontologies for specific application domains where commercial depth and update frequency provide operational advantages. The key design principle is that the proprietary layer should be an extension of, not a replacement for, the open foundation — using the same concept identifier patterns, the same property types, and the same modelling conventions, so that reasoning can cross the open-proprietary boundary without architectural complexity. This hybrid approach maximises both coverage and control while avoiding the strategic risk of deep dependency on a single commercial knowledge provider.
