Building a Pharmacogenomic Relationship Ontology
Author Information
Author(s): Adrien Coulet, Yael Garten, Michel Dumontier, Russ B. Altman, Mark A. Musen, Nigam H. Shah
Primary Institution: LORIA – INRIA Nancy – Grand-Est
Hypothesis
Can a relationship ontology be constructed to integrate heterogeneous text-mined relationships in pharmacogenomics?
Conclusion
The PHARE ontology provides a framework for integrating over 40,000 pharmacogenomic relationships into a knowledge base that can be queried and visualized.
Supporting Evidence
- The PHARE ontology integrates over 40,000 relationships extracted from biomedical literature.
- The ontology allows for querying and visualization of pharmacogenomic relationships.
- Manual curation improves the identification of similar relationships expressed differently.
Takeaway
This study created a system to organize and connect information about how genes and drugs interact, making it easier to find and use this information.
Methodology
The study involved extracting relationships from MEDLINE abstracts and organizing them into a structured ontology.
Limitations
The manual curation process is slow and may not capture all relationships due to the vast amount of literature.
Digital Object Identifier (DOI)
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