Analytical Methods are often authored and published in free-text formats that lack both structural and semantic consistency.
Given the widespread adoption of software and systems (LIMS, ELNs, LES, etc. systems) that must accurately represent methods in ways that machines can store, export, import, and compare what was specified in the method against executed results, the current paradigm presents problems for Data Entry, Reproducibility and Results Analysis.
Methods that are authored in free text are often entered into electronic systems in 2 ways:
- Humans (e.g. analytical chemists) transcribing the method into electronic systems
- Software programs using NLP, of various degrees of sophistication and quality, “screen scraping” the content to avoid the need for manual transcription
Both of these approaches introduce the possibility for error as well as interpretation of the method, depending on the subject matter expert or even the Natural Language Processing algorithm’s interpretation. This can impact reproducibility as well as introduce unintended errors.
The key objective of the Methods Hub project is to simplify the transferring of method information between two parties. This will involve the creation of a cloud-based database that will allow downloading and sharing of analytical methods in machine-readable formats. This will:
- Increase reproducibility of methods as deviations are reduced
- Reduce variance in the execution of the method
- Reduce time for method transfer
- Automate quality standards live within workflows
- Increase consistency of information between different sources on a Method Marketplace
- Scientific Literature, Publishers
- Pharmacopeia USP
- Commercial Method Information sources
Methods Hub could lead to commercially available repositories of methods where digital as well as text-based method information with appropriate metadata, in a machine-readable format, would be shared and exchanged. The platform would allow for both free and paid downloads of monographs or manuscripts, the interchange between CRO/CMO and Pharma, and also free access of methods that are currently open source.
To date, Pistoia Alliance has, in collaboration with Allotrope Foundation, developed a Methods database based on Zontal Space with a public API specification and human-readable representation of a limited number of chromatography instruction sets. This will provide a good entry point for the Methods Hub Project.
All available sources for Analytical Method information will be evaluated in terms of their information structure from free-text, via semi-structured to fully digital information e.g. based on the Allotrope Foundation Ontology (AFO) and other available ontology providers.
For free-text and semi-structured methods, the extraction of key metadata would be considered.
Natural Language processing tools could be used to pre-populate a standard format for a fully digital representation of the method. Alternatively, well-implemented methods can be exported from a Chromatography Data System (CDS) and just validated by comparison to the text-based description.