KGG: a fully automated workflow for creating disease-specific knowledge graphs

Knowledge graphs (KGs) in life sciences have become an important application of systems biology as they delineate complex biological and pathophysiological phenomena. They are composed of biological and chemical entities represented with standard ontologies to comply with Findable, Accessible, Interoperable and Reusable (FAIR) principles. Alongside serving as a graph database, KGs hold the potential to address complex scientific queries and facilitate downstream analyses. However, the process of constructing KGs is expensive and time consuming as it primarily relies on manual curation from published literature and experimental data. The existing text-mining workflows are still in their infancy and fail to achieve the accuracy and reliability of manual curation.

Knowledge graph generator (KGG) is an automated workflow for representing chemotype and phenotype of diseases and medical conditions. It embeds the underlying schema of curated databases such as OpenTargets, Uniprot, ChEMBL, Integrated Interactions Database and GWAS Central resembling a clockwork-esque mechanism. The resultant KG is a comprehensive and rational assembly of disease-associated entities such as proteins, protein-related pathways, biological processes and functions, genetic variants, chemicals, mechanism of actions, assays and adverse effects. As use cases, we have used KGs to identify shared entities for possible link of comorbidity and compared them with KGs from other sources. We have also demonstrated a use case of identifying putative new targets and repurposing drug candidates in Parkinson's Disease. Lastly, we have developed reusable workflows to explore drug-likeness of chemicals and identify structures of proteins.

The resources and codes for KGG are publicly available at: https://github.com/Fraunhofer-ITMP/kgg.