The aim of the Unified Data Model (UDM) project is to create and publish an open and freely available data format for storage and exchange of experimental information about compound synthesis and biological testing.

Project deliverables

We don’t start from scratch.  Elsevier has transferred to the Pistoia Alliance ownership of their UDM file format used to upload chemical reaction data into the Reaxys system. We are working on making it more generic and vendor-neutral as well as extending it to cover various screening and compound testing experiments.

The lack of a common standard to exchange data creates unnecessary barriers in drug discovery:

  • Collaboration and data exchange with partners and CROs using different systems is difficult.
  • Integration, comparison and analysis of research data from various sources is very laborious.
  • It is problematic to develop and share business rules and protocols, for consistent representation of experiments and IP capture.

The UDM file format will help to address those issues and enable a seamless data integration between various systems, in particular, Electronic Laboratory Notebooks.

 

UDM Releases

The first public UDM XML schema release 4.0.0 is available here. This is a milestone that everybody can use the same openly available and improved UDM schema and so the exchange of chemical experimental information just became easier !

A larger package, containing additionally sample UDM datasets, as well as source code demonstrating conversion to the UDM file format and its validation, can be found here.

FAQ

1. Why would I want to start using this new version?

Its open and publically available and as more people start to use it, the storage and exchange of chemical experimental data becomes easier and more effective

2.  What else has changed in version 4.0.0 ?

It’s a cleaner version with less ambiguity, now has explicit support for units of measure, documented key entities, contains sample UDM files and example Python script.

3. Are there any more changes planned to the open version?

Yes, requirements are already gathering for the next major release, they include enhanced support for reaction conditions, molecular properties, formatting of the preparation section  etc

How to get involved

If you would like to participate or have any further questions, please contact our project manager Jarek Tomczak (jarek.tomczak@pistoiaalliance.org) or Gabrielle Whittick (Gabrielle.whittick@pistoiaalliance.org).

Project Funders