Pistoia-Alliance-PGO

Pistoia Alliance Pharma General Ontology:

Objective

Defining a set of agreed-upon core entities and recommendations for associating controlled terminologies to service data exchange of Research & Development (R&D) information among Pharmaceutical Industry stakeholders.

Rationale

Information exchange within and across organizations in the pharmaceutical industry is hampered by insufficient or ambiguous asset descriptions. These descriptions should ideally allow for validation, facilitation of discovery and promotion of interoperability. All of these have the potential to deliver significant gains for data exploitation and value delivery in the drug development pipeline, ultimately bringing better treatments to patients.

The remit of PGO, rather than mandate the use of a resource over another, is to enable clarity when declaring which controlled terminologies are used and why.

True to the FAIR principles of data management [1] and their use in the Pharmaceutical Industry [2], the PGO aims to reuse existing semantic resources (ontologies and controlled terminologies) as well as open source community software, rather than creating new ones.

The initial goal of PGO is to provide enough coverage to represent essential entities, most frequently used or referred to when exchanging data.

The key objectives are therefore:

• Unambiguously identifying essential entities
• Specifying, when applicable, value-sets for key attributes by relying on community-agreed controlled terminologies
• Creating machine actionable documentation.

On the issue of defining value-sets, PGO's intent is to provide clear mechanisms to enable unambiguous declaration of the resources used as well as capture the criteria used to select semantic artifacts. We will do so by following community best practices.

Technology

PGO is currently evaluating the LinkML for representing and documenting each of the types [3].

PGO list of core entities

Concept	Definition	Status
Assay (method)		under development
Assay (biological)		under development
Biomarker		under development
Biospecimen		under development
Cell line		under development
Cell type		under development
Clinical study		under development
Compound		under development
Equipment		under development
Disease		under development
Drug		under development
Device		under development
Gene		under development
Indication		under development
Molecular target		under development
Product		under development
Program		under development
Project		under development
Protein		under development
Site		under development
Gene		under development
Species		under development
Subject-Person		under development
Target		under development
Unit		under development
Vocabulary		under development

Roadmap

• 2023: scoping and use case definition
• 2024: identification formalization of core concepts, testing using LinkML
• 2025: application and field testing with real life scenarios

Participating Organizations:

• Astrazeneca
• Chiesi Farmateuci
• Glaxo Smith Kline PLC
• Merck Group
• Novo Nordisk
• Pfizer
• Pistoia Alliance
• Hoffman la Roche AG

References:

1. https://www.nature.com/articles/sdata201618
2. https://pubmed.ncbi.nlm.nih.gov/35066138/
3. https://pubmed.ncbi.nlm.nih.gov/36125173/