A framework for integrating biomedical knowledge in Wikidata with open biological and biomedical ontologies and MeSH keywords.

ABSTRACT: This study presents a comprehensive framework to enhance Wikidata as an open and collaborative knowledge graph by integrating Open Biological and Biomedical Ontologies (OBO) and Medical Subject Headings (MeSH) keywords from PubMed publications. The primary data sources include OBO ontologies and MeSH keywords, which were collected and classified using SPARQL queries for RDF knowledge graphs. The semantic alignment between OBO ontologies and Wikidata was evaluated, revealing significant gaps and distorted representations that necessitate both automated and manual interventions for improvement. We employed pointwise mutual information to extract biomedical relations among the 5000 most common MeSH keywords in PubMed, achieving an accuracy of 89.40 % for superclass-based classification and 75

SUBMITTER: Turki H 

PROVIDER: S-EPMC11471508 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature