Multi-modal Protein Knowledge Graph Construction and Applications
This provides a domain-specific resource for protein researchers, though it is incremental as it builds on existing knowledge bases.
The authors tackled the problem of insufficient biological knowledge capture in protein science by creating ProteinKG65, a specialized knowledge graph that integrates gene ontology and Uniprot data with protein sequences, resulting in a publicly available dataset for protein function and structure prediction.
Existing data-centric methods for protein science generally cannot sufficiently capture and leverage biology knowledge, which may be crucial for many protein tasks. To facilitate research in this field, we create ProteinKG65, a knowledge graph for protein science. Using gene ontology and Uniprot knowledge base as a basis, we transform and integrate various kinds of knowledge with aligned descriptions and protein sequences, respectively, to GO terms and protein entities. ProteinKG65 is mainly dedicated to providing a specialized protein knowledge graph, bringing the knowledge of Gene Ontology to protein function and structure prediction. We also illustrate the potential applications of ProteinKG65 with a prototype. Our dataset can be downloaded at https://w3id.org/proteinkg65.