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With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. We present novel methods that annotate the unstructured clinical notes and transform them into a deidentified patient-feature matrix encoded using medical terminologies. We demonstrate the use of the resulting(More)
Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to complex disease risk. We detect thousands of associations(More)
Ontology evaluation has proven to be one of the more difficult problems in ontology engineering. Researchers proposed numerous methods to evaluate logical correctness of an ontology, its structure, or coverage of a domain represented by a corpus. However, evaluating whether or not ontology assertions correspond to the real world remains a manual and(More)
Ontology Design Patterns (ODPs) provide a means to capture best practice, to prevent modeling errors, and to encode formally common modeling situations for use during ontology development. Despite the popularity of ODPs and supposed positive effects from their use, there is scant empirical evidence of their level of adoption in real world ontologies or on(More)
Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive(More)
Biomedical ontologies are becoming increasingly large and complex. A single user cannot easily develop or maintain them. Researchers have developed various automated techniques to assist with ontology development and engineering at scale. However, these solutions are not always complete. Microtask crowdsourcing, wherein workers are paid small amounts to(More)
OBJECTIVES The verification of biomedical ontologies is an arduous process that typically involves peer review by subject-matter experts. This work evaluated the ability of crowdsourcing methods to detect errors in SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms) and to address the challenges of scalable ontology verification. METHODS We(More)
STUDY OBJECTIVES Although gonorrhea may infect the cervix, rectum, or pharynx of women, culturing non-cervical sites is rare outside of sexually transmitted disease (STD) clinics. This study aims to compare rectal and pharyngeal gonorrhea prevalence in adolescent and adult women and to calculate the percentage of cases that would be missed with cervical(More)
In recent years there has been a large amount of research into capturing, publishing and analysing Ontology Design Patterns (ODPs). However, there has not been any analysis into the typical language ex-pressivity required to represent ODPs and how these requirements sit with lightweight fragments of the widely used ontology language OWL. In this paper we(More)
Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP(More)