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Published on: October 13, 2023
OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding
Lawrence Hunter1, Zhiyong Lu, James Firby
1Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Larry.Hunter@uchsc.edu
OpenDMAP, an ontology-driven system, improves biomedical information extraction (IE) for protein transport, interactions, and gene expression. Evaluations show its effectiveness in handling complex biological data.
Area of Science:
- Biomedical Informatics
- Computational Biology
- Natural Language Processing
Background:
- Biomedical knowledge extraction is crucial due to vast literature.
- Existing information extraction (IE) systems face challenges with diverse data.
- OpenDMAP is introduced as an advanced ontology-driven IE system.
Purpose of the Study:
- To design and implement OpenDMAP, an integrated concept analysis system.
- To leverage ontological resources and advanced pattern language for IE.
- To evaluate the performance of OpenDMAP for specific biomedical extraction tasks.
Main Methods:
- Developed OpenDMAP, an ontology-driven IE system.
- Integrated diverse text processing applications.
- Utilized an expanded pattern language combining syntactic and semantic elements.
- Created specialized systems for protein transport, protein-protein interactions, and gene expression.
Main Results:
- Achieved F-scores ranging from .26 to .72 across different extraction tasks.
- Extracted substantial numbers of biological assertions: 72,460 transport, 265,795 interaction, and 176,153 expression instances from MEDLINE abstracts.
- Demonstrated high precision (.39-.85) and recall (.16-.85) in evaluations.
Conclusions:
- OpenDMAP sets new performance standards for extracting protein-protein interactions.
- The system's performance generalizes to other IE tasks, including multi-argument predicates.
- Ensures grounded knowledge representation using ontological elements, aiding manual curation and integrated information systems.
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