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Track normalization and averaging of epigenetic features across various cell and tissue types derived from Roadmap Epigenomic datasets

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65050 | GEO | 2015/01/20

SECONDARY ACCESSION(S): PRJNA272798

REPOSITORIES: GEO

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Project description:ObjectivesNormalizing mentions of medical concepts to standardized vocabularies is a fundamental component of clinical text analysis. Ambiguity-words or phrases that may refer to different concepts-has been extensively researched as part of information extraction from biomedical literature, but less is known about the types and frequency of ambiguity in clinical text. This study characterizes the distribution and distinct types of ambiguity exhibited by benchmark clinical concept normalization datasets, in order to identify directions for advancing medical concept normalization research.Materials and methodsWe identified ambiguous strings in datasets derived from the 2 available clinical corpora for concept normalization and categorized the distinct types of ambiguity they exhibited. We then compared observed string ambiguity in the datasets with potential ambiguity in the Unified Medical Language System (UMLS) to assess how representative available datasets are of ambiguity in clinical language.ResultsWe found that <15% of strings were ambiguous within the datasets, while over 50% were ambiguous in the UMLS, indicating only partial coverage of clinical ambiguity. The percentage of strings in common between any pair of datasets ranged from 2% to only 36%; of these, 40% were annotated with different sets of concepts, severely limiting generalization. Finally, we observed 12 distinct types of ambiguity, distributed unequally across the available datasets, reflecting diverse linguistic and medical phenomena.DiscussionExisting datasets are not sufficient to cover the diversity of clinical concept ambiguity, limiting both training and evaluation of normalization methods for clinical text. Additionally, the UMLS offers important semantic information for building and evaluating normalization methods.ConclusionsOur findings identify 3 opportunities for concept normalization research, including a need for ambiguity-specific clinical datasets and leveraging the rich semantics of the UMLS in new methods and evaluation measures for normalization.

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Track normalization and averaging of epigenetic features across various cell and tissue types derived from Roadmap Epigenomic datasets

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