Synergy between Allotrope’s taxonomies & Pistoia Alliance’s Ontologies Mapping work

What’s in a ‘word’, or a collection of them? The answer depends on how much you invest in that collection of words. Standardizing the vocabularies and knowledge collections of experimental data and biomedical concepts has emerged as an important and fundamental activity to allow our industry to fully leverage data and extract the greatest value from it. Several industry collaborations are driving complimentary efforts in this area including Allotrope Foundation ( and The Pistoia Alliance (

The taxonomies Allotrope Foundation are developing to describe the materials, processes, equipment and results for analytical chemistry provide the content for the metadata repository that is one of the three core components of the Allotrope Framework. Even in the early stages of identifying sources of terms and concepts from which to construct these taxonomies it became clear that publically available taxonomies and ontologies could be modeled in very different ways and therefore be challenging to relate to one another or integrate.

This common issue which hinders the integrated use of complimentary ontologies and just reinforces data silos is the focus of a recently initiated project at the Pistoia Alliance. Pistoia’s Ontologies Mapping project has been set up to create better tools and establish best practices for ontology management in life sciences R&D. The project will see the Pistoia Alliance develop a set of standardized guidelines, tools and services to enable the universal application of ontologies, but not develop entirely new ontologies. (for more information:

With common interests and adjacent activities the two organizations will be collaborating and sharing experience to ensure that Allotrope Taxonomies are mapped in the context of the other ontologies in scope for Pistoia. The complementary nature of these Pistoia and Allotrope efforts could lead to the long term benefit of straight forward semantic integration of the analytical process and measurement with the biological context of the entity in the vial!

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