Elias' Research Stay: Semantic Biological & Health Data in Switzerland
This spring, I had the opportunity to embark on a two-month-long research stay in Switzerland,
hosted by the Swiss Institute of Bioinformatics (SIB).
The visit was split across multiple SIB sites and partner institutions,
each offering a unique environment to dive into different aspects of semantic technologies,
their applications in genomic and clinical data, and ways to extract information from the complex datasets.
My overarching goal was to to communicate my work on using personal data pods (i.e. Solid Pods) for
the storage of sensitive genomic and health data, explore conversion and querying strategies for
complex genomic data represented in semantically rich formats, and
collaborate with experts in the Swiss Personalized Health Network (SPHN)
about how usage of these semantic data can be applied to clinical settings in the context of
their work on similar semantic technologies within the Swiss Health system.
I spent most of my stay in Lausanne, I was embedded with the SIB
Knowledge Representation Unit,
where I focused on the representation of genomic data -
specifically, the semantic modeling of
Variant Call Format files, and
the federated querying of these data along with large biological SPARQL Endpoint databases hosted by SIB.
Working closely with ontology and knowledge representation experts,
I reviewed existing standards, extended them to fit the nuances of genomic variants, and
discussed RDF conversion pipelines that align with both technical and domain-specific requirements.
This work laid the foundation for enabling more structured and interoperable genomic data
in clinical and research contexts, a crucial component of my PhD.
During my visit, I was also able to visit
SwissProt in Geneva,
where I turned my attention to the challenge of querying large, distributed RDF datasets.
I conducted hands-on experiments with federated SPARQL queries, tested performance across synthetic and
real-world scenarios, and explored strategies for optimizing and
executing semantic queries across disparate endpoints.
These activities not only deepened my technical skill set but also produced insights that will support
upcoming publications about surveying SIB’s large public SPARQL endpoints
using real-world federated queries over real-world SPARQL endpoints.
Finally, I concluded my stay with a visit to Basel, where I presented my PhD findings and
aims to colleagues at SPHN and engaged in discussions
around the clinical applications of semantic data infrastructures.
The feedback I received was invaluable and highlighted
how semantic technologies could be pragmatically aligned with ongoing healthcare data initiatives.
Throughout the stay, I gained not only technical expertise but
also a better understanding of how semantic interoperability can be woven into real-world health systems.
Overall, the research stay was an inspiring experience -
one that strengthened international collaborations, sparked new ideas, and
pushed the boundaries of what's possible when semantic technologies meet complex biomedical data.