Multi-modal Protein Knowledge Graph Construction and Applications

• URL: http://arxiv.org/abs/2207.10080v3
• Date: Mon, 14 Nov 2022 16:26:52 GMT
• Title: Multi-modal Protein Knowledge Graph Construction and Applications
• Authors: Siyuan Cheng, Xiaozhuan Liang, Zhen Bi, Huajun Chen, Ningyu Zhang
• Abstract summary: We create ProteinKG65, a knowledge graph for protein science. Using gene ontology and Uniprot knowledge base as a basis, we transform various kinds of knowledge with aligned descriptions and protein sequences. ProteinKG65 is mainly dedicated to providing a specialized protein knowledge graph, bringing the knowledge of Gene Ontology to protein function and structure prediction.
• Score: 30.500520131560112
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: 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.

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