Improved characterisation of clinical text through ontology-based vocabulary expansion
Type
PreprintKAUST Department
Bio-Ontology Research Group (BORG)Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Date
2020-07-11Permanent link to this record
http://hdl.handle.net/10754/664429
Metadata
Show full item recordAbstract
AbstractBackgroundBiomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same concepts being described by several terms in the same or similar contexts across several ontologies. While these terms describe the same concepts, they contain different sets of complementary metadata. Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks.ResultsWe develop and present an algorithm that expands the set of labels associated with an ontology class using a combination of strict lexical matching and cross-ontology reasoner-enabled equivalency queries. Across all disease terms in the Disease Ontology, the approach found 51,362 additional labels, more than tripling the number defined by the ontology itself. Manual validation by a clinical expert on a random sampling of expanded synonyms over the Human Phenotype Ontology yielded a precision of 0.912. Furthermore, we found that annotating patient visits in MIMIC-III with an extended set of Disease Ontology labels led to semantic similarity score derived from those labels being a significantly better predictor of matching first diagnosis, with a mean average precision of 0.88 for the unexpanded set of annotations, and 0.913 for the expanded set.ConclusionsInter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. While the accuracy of the extended vocabulary is not perfect, it nevertheless led to a significantly improved ontology-based characterisation of patients from text in one setting. Furthermore, where run-on error is not acceptable, the technique can be used to provide candidate synonyms which can be checked by a domain expert.Citation
Slater, L. T., Bradlow, W., Ball, S., Hoehndorf, R., & Gkoutos, G. V. (2020). Improved characterisation of clinical text through ontology-based vocabulary expansion. doi:10.1101/2020.07.10.197541Publisher
Cold Spring Harbor LaboratoryAdditional Links
http://biorxiv.org/lookup/doi/10.1101/2020.07.10.197541https://www.biorxiv.org/content/biorxiv/early/2020/07/10/2020.07.10.197541.full.pdf
ae974a485f413a2113503eed53cd6c53
10.1101/2020.07.10.197541