Funded project, 2024-2027 Establishing a knowledge graph community in biomedical science

This project with Dr Sebastian Lobentanzer from the Institute for Computational Biomedicine targets the software packages Pypath, OmniPath and BioCypher. The targeted software will be modified and restructured to make it more usable, scalable and extensible. One important aspect is related to the consumption of data from different sources, for this goal different Adapters will be created in order to harmonize the information that will serve for Graph data creation or maintaining a curated Knowledge Base.  Additionally, the information in the knowledge base will be converted to different formats to make it accessible and usable in a variety of use cases such as mathematical optimization, machine learning, analysis, etc. The access to the resources will be facilitated through a web portal that allows downstream use of the curated data and allow contributions and involvment of the community.

Omnipath relies on several utilities such as ID translation, orthologous gene mapping, and taxonomy, among others and integrates over 100 different resources focused on molecular knowledge, for example about genes, proteins, and diseases. BioCypher is a modular framework for the creation of knowledge graphs based on ontologies, pursuing high performance and scalability to support many new features, targeting single cell and spatial omics, microbiomics, metabolomics, and various multi-omics modelling and machine learning methods.

This project is funded through the DFG and will run for three years.

Collaborators: Sebastian Lobentanzer and Julio Saez-Rodriguez