Abstract
BackgroundBiomedical 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 entities being described by several concepts in the same or similar contexts across several ontologies. While these concepts describe the same entities, 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.
Highlights
Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining
Open Biomedical Ontologies (OBO) [3] and the Information Artifact Ontology (IAO) [4] define a series of conventional annotation properties that can be used for the expression of labels and synonyms
The synonym expansion algorithm is available as part of the Komenti text mining framework, which is available under an open source licence at https://github. com/reality/komenti, while the files used for validation are available at https://github.com/reality/synonym_expansion_validation
Summary
Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. Redundancies exist in the ontology ecosystem, which lead to the same entities being described by several concepts in the same or similar contexts across several ontologies While these concepts describe the same entities, they contain different sets of complementary metadata. Open Biomedical Ontologies (OBO) [3] and the Information Artifact Ontology (IAO) [4] define a series of conventional annotation properties that can be used for the expression of labels and synonyms. These features are widely used: an investigation of ontologies in BioPortal found that 90% of classes had a label associated with them [5]. The labels associated with ontology terms constitute a controlled domain vocabulary [1]
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