[Pitch]:

[sgtp]

Short title

Exploring the connectivity between observational data and molecular networks

Pitch

Objective of this hackathon to explore to what degree is possible to build a Knowledge Graph spanning observational data to molecular data.

From a standardised representation of a patient record (e.g.: in OMOP) we can derive observations (diagnosis, phenotypes, biomarkers). At a molecular level, we have a range of resources in terms of protein-protein interaction networks or pathways that can explain how some molecular alterations are causally connected. Linking these two levels, we have gene-to-diseases associations, but also potentially phenotype databases or more.

To what degree is it possible to formulate a holistic network such that, given a range of patient level observations, it would be possible to trace them to the alteration of connected molecular mechanisms?

To what degree it would be possible to characterise a patient in terms of overall pathways/networks affected?

Objective of this hackathon are:

• To assess what data resources are available, what is publicly available or not.
• To assess how much such data resources can be connected or not, in terms of using common ontologies
• To assess the coverage and sparsity of such connections
• To assess how much an overall graph would be informative, given the high level of abstraction (e.g.: many statements on molecular networks are de-contextualised respect to tissue or individual characteristics)

This is an explorative hackathon. The outcome is a better understanding on what is available, gaps, potential and limitations in building a KG spanning population-to-bench data.

Expertice needed

Any knowledge of:

• Databases resources available covering: patients data (incl. synthetic), diseases, phenotypes, symptoms, pathways, p-p interactions or any other relevant data source.
• Experience in developing or using integrating knowledge graphs (e.g.: Neurocommons, Dissent, Linked-Life data,...)
• Some technical expertise to quickly explore and extract patterns from datasets
• Some biomedical expertise to assess the quality/feasibility of the information found

[alabarga]

did anyone work in this project during the hackathon? I'm interested in the project

[sgtp]

Hi, We had some discussion on the topic. I should maybe post a synthesis.