Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

Abstract

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

“…One example is NeuroML [38], a language to represent neuronal models. Another example is PharmML [39], which is used in pharmacometrics to encode models, associated tasks and their annotations. PharmlML is also a project of the European Innovative Medicines Initiative (IMI, http://www.imi.europa.eu/).…”

The Standard Output: A Tool‐Agnostic Modeling Storage Format

“…The DDMoRe project has addressed these shortcomings through the definition, implementation and integration of a set of standards into the so-called IOF. [6][7][8][9] Among these, the SO has been proposed as the tool-independent format for storing output typically produced from pharmacometric M&S tasks and workflows to guide the model building through assessment of the goodness-of-fit between the model and the dataset and the appropriateness of the underlying model assumptions, as well as to allow the reproducibility of the results. Developing a standardized output format across M&S tools allows better sharing of information, reusable code, and better integration of a wide variety of tools within a single pharmacometric workflow.…”

Harnessing Big Data for Systems Pharmacology

“…Several modeling formats have been proposed to encode systems biology models (36). Notably, the Pharmacometric Markup Language PharmML for the representation and exchange of pharmacometric models is under development (42). A recent development of the YAML metabolic modeling format enables version tracking and provides a flexible infrastructure for the distribution tracking and collaborative annotation of metabolic models (37).…”