A variety of data models have been developed to provide a standardized data interface that suppor... more A variety of data models have been developed to provide a standardized data interface that supports organizing clinical research data into a standard structure for building the integrated data repositories. HL7 Fast Healthcare Interoperability Resources (FHIR) is emerging as a next generation standards framework for facilitating health care and electronic health records-based data exchange. The objective of the study was to design and assess a consensus-based approach for harmonizing the OHDSI CDM with HL7 FHIR. We leverage a FHIR W5 (Who, What, When, Where, and Why) Classification System for designing the harmonization approaches and assess their utility in achieving the consensus among curators using a standard inter-rater agreement measure. Moderate agreement was achieved for the model-level harmonization (kappa = 0.50) whereas only fair agreement was achieved for the property-level harmonization (kappa = 0.21). FHIR W5 is a useful tool in designing the harmonization approaches b...
Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning ... more Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/...
In this paper, we show how we have applied the Clinical Narrative Temporal Relation Ontology (CNT... more In this paper, we show how we have applied the Clinical Narrative Temporal Relation Ontology (CNTRO) and its associated temporal reasoning system (the CNTRO Timeline Library) to trend temporal information within medical device adverse event report narratives. 238 narratives documenting occurrences of late stent thrombosis adverse events from the Food and Drug Administration's (FDA) Manufacturing and User Facility Device Experience (MAUDE) database were annotated and evaluated using the CNTRO Timeline Library to identify, order, and calculate the duration of temporal events. The CNTRO Timeline Library had a 95% accuracy in correctly ordering events within the 238 narratives. 41 narratives included an event in which the duration was documented, and the CNTRO Timeline Library had an 80% accuracy in correctly determining these durations. 77 narratives included documentation of a duration between events, and the CNTRO Timeline Library had a 76% accuracy in determining these durations...
A variety of data models have been developed to provide a standardized data interface that suppor... more A variety of data models have been developed to provide a standardized data interface that supports organizing clinical research data into a standard structure for building the integrated data repositories. HL7 Fast Healthcare Interoperability Resources (FHIR) is emerging as a next generation standards framework for facilitating health care and electronic health records-based data exchange. The objective of the study was to design and assess a consensus-based approach for harmonizing the OHDSI CDM with HL7 FHIR. We leverage a FHIR W5 (Who, What, When, Where, and Why) Classification System for designing the harmonization approaches and assess their utility in achieving the consensus among curators using a standard inter-rater agreement measure. Moderate agreement was achieved for the model-level harmonization (kappa = 0.50) whereas only fair agreement was achieved for the property-level harmonization (kappa = 0.21). FHIR W5 is a useful tool in designing the harmonization approaches b...
Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning ... more Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/...
In this paper, we show how we have applied the Clinical Narrative Temporal Relation Ontology (CNT... more In this paper, we show how we have applied the Clinical Narrative Temporal Relation Ontology (CNTRO) and its associated temporal reasoning system (the CNTRO Timeline Library) to trend temporal information within medical device adverse event report narratives. 238 narratives documenting occurrences of late stent thrombosis adverse events from the Food and Drug Administration's (FDA) Manufacturing and User Facility Device Experience (MAUDE) database were annotated and evaluated using the CNTRO Timeline Library to identify, order, and calculate the duration of temporal events. The CNTRO Timeline Library had a 95% accuracy in correctly ordering events within the 238 narratives. 41 narratives included an event in which the duration was documented, and the CNTRO Timeline Library had an 80% accuracy in correctly determining these durations. 77 narratives included documentation of a duration between events, and the CNTRO Timeline Library had a 76% accuracy in determining these durations...
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Papers by Deepak Sharma