Related Experiment Video
Updated: May 17, 2026

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
Published on: October 13, 2023
SemMedDB: a PubMed-scale repository of biomedical semantic predications
Halil Kilicoglu1, Dongwook Shin, Marcelo Fiszman
1Lister Hill National Center for Biomedical Communications, National Library of Medicine, Bethesda, MD 20894, USA. kilicogluh@mail.nih.gov
Summary:
Effective access to the vast biomedical knowledge present in the scientific literature is challenging. Semantic relations are increasingly used in knowledge management applications supporting biomedical research to help address this challenge. We describe SemMedDB, a repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations. We propose the repository as a knowledge resource that can assist in hypothesis generation and literature-based discovery in biomedicine as well as in clinical decision-making support.
Availability And Implementation:
The SemMedDB repository is available as a MySQL database for non-commercial use at http://skr3.nlm.nih.gov/SemMedDB. An UMLS Metathesaurus license is required.
Contact:
kilicogluh@mail.nih.gov.
More Related Videos
09:20Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
Published on: February 23, 2019
05:47Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Related Concept Videos
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Anatomical Terminology
Nonsense-mediated mRNA Decay
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Genomics
Signal Sequences and Sorting Receptors