Knowledge Graphs: Changing How We Think About Data

In August 2020, PHUSE’s Knowledge Graph Project Lead, Tim Williams (UCB), presented ‘Knowledge Graphs: Changing How We Think About Data’ at the FDA Division of Regulatory Science (DRSI) Technology Forum. Laura Firey, Product Manager at Stardogprovided a cross-industry perspective.

“Participation from the Center for Tobacco Products (CTP) meant the talk was outside of my usual comfort zone of late-phase pharma, so I created example instance data as Resource Description Framework (RDF), a minimal ontology in OWL, and a SHACL example. My ‘Data Has Shape’ theme was supported by visualisations using 3d-force-graph.

The ‘white board is the data model’ concept was illustrated by transforming a diagram of demographics and smoking exposure for two individuals (Fig. 1) to RDF and visualising the resulting data as a 3D network (Fig. 2, and https://bit.ly/PamAndRay for an online, interactive view). When the data was loaded into graph database, a simple query was able to determine the unique ingredient (mango flavour) that may be a contributing factor to Pam’s COPD.

Figure 1


This led to a discussion of data validation, where SHACL was used to determine that Ray’s age value was out of range. Ray’s demographics data, SHACL constraints and validation report are again illustrated with a 3D model (Fig. 3 and https://bit.ly/RaySHACLResult). [If you are unable to view the 3D graphs online, please try another browser and ensure you are not behind a company firewall.]


Figure 2 (left) and Figure 3 (right)

The follow-on discussion included how to get started with knowledge graphs, the importance of defining scope for Linked Data projects, and how to access and analyse the data using R, SAS or other analytical tools.

A big thank you to Crystal Allard (Director, DRSI) for the invitation.

­– Tim Williams
Knowledge Graph Project Lead, PHUSE
Lead Statistical Solutions Analyst, UCB Biosciences

You can access the presentation slides for Knowledge Graphs: Changing How We Think About Data by clicking the link.

If you are interested in hearing more about Tim’s work on knowledge graphs, take a look at his other recent presentations and discussions:

Modernizing FDA Data Strategy

In June Tim was a panellist for the Data Sharing discussion at the Modernizing FDA Data Strategy public meeting, where he discussed how knowledge graphs, data fabric and data-centric approaches should be integral components in the FDA roadmap.

 

How Knowledge Graphs Will Transform the Pharmaceutical Industry

Along with Stardog, in this joint webinar Tim discussed topics such as the challenges in our current data landscape (common to many industries), the necessary data-centric transformation, implementation strategies, examples from industry, and the PHUSE Knowledge Graph projects.

 

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