Accessing OMOP Common Data Model Repositories with the i2b2 Webclient - Algorithm for Automatic Query Translation

In the era of translational research, data integration and clinical data warehouses are important enabling technologies for clinical researchers. The OMOP common data model is a wide-spread choice as a target for data integration in medical informatics. It's portability of queries and analyses across different institutions and data are ideal also from the viewpoint of the FAIR principles. Yet, the OMOP CDM lacks a simple and intuitive user interface for untrained users to run simple queries for feasibility analysis. Aim of this study is to provide an algorithm to translate any given i2b2 query to an equivalent query which can then be run on the OMOP CDM database. The provided algorithm is able to convert queries created in the i2b2 webclient to SQL statements which can be executed on a standard OMOP CDM database programmatically.

HIStream-Import: A Generic ETL Framework for Processing Arbitrary Patient Data Collections or Hospital Information Systems into HL7 FHIR Bundles

Data integration is a necessary and important step to perform translational research and improve the sample size beyond single data collections. For health information, the most recent established communication standards is HL7 FHIR. To bridge the concepts of "minimal invasive" data integration and open standards, we propose a generic ETL framework to process arbitrary patient related data collections into HL7 FHIR - which in turn can then be used for loading into target data warehouses. The proposed algorithm is able to read any relational delimited text exports and produce a standard HL7 FHIR bundle collection. We evaluated an implementation of the algorithm using different lung research registries and used the resulting FHIR resources to fill our i2b2 based data warehouse as well an OMOP common data model repository.

The top 100 cited neurorehabilitation papers

BACKGROUND

Neurorehabilitation covers a large range of disorders, assessment approaches and treatment methods. There have been previous citation analyses of rehabilitation and of its subfields. However, there has never been a comprehensive citation analysis in neurorehabilitation.

OBJECTIVE

The present study reports findings from a citation analysis of the top 100 most cited neurorehabilitation papers to describe the research trends in the field.

METHODS

A de-novo keyword search of papers indexed in the Web of Science Core Collection database yielded 52,581 papers. A candidate pool of the 200 most-cited papers published between 2005 and 2016 was reviewed by the clinician authors. The papers in the top 100 deemed to be irrelevant were discarded and replaced by the most highly-cited articles in the second tier deemed to be clinically relevant.

RESULTS

The most frequently cited neurorehablitation papers appeared in Stroke, Movement Disorders, and Neurology. Papers tended to focus on treatments, especially for stroke. Authorship trends suggest that top cited papers result from group endeavors, with 90% of the papers involving a collaboration among 3 or more authors.

CONCLUSION

Treatment studies, often focused on stroke, appear to have the highest impact in the field of neurorehabilitation.

The development of the Athens Emotional States Inventory (AESI): collection, validation and automatic processing of emotionally loaded sentences

OBJECTIVES

The development of ecologically valid procedures for collecting reliable and unbiased emotional data towards computer interfaces with social and affective intelligence targeting patients with mental disorders.

METHODS

Following its development, presented with, the Athens Emotional States Inventory (AESI) proposes the design, recording and validation of an audiovisual database for five emotional states: anger, fear, joy, sadness and neutral. The items of the AESI consist of sentences each having content indicative of the corresponding emotion. Emotional content was assessed through a survey of 40 young participants with a questionnaire following the Latin square design. The emotional sentences that were correctly identified by 85% of the participants were recorded in a soundproof room with microphones and cameras. A preliminary validation of AESI is performed through automatic emotion recognition experiments from speech.

RESULTS

The resulting database contains 696 recorded utterances in Greek language by 20 native speakers and has a total duration of approximately 28 min. Speech classification results yield accuracy up to 75.15% for automatically recognizing the emotions in AESI.

CONCLUSIONS

These results indicate the usefulness of our approach for collecting emotional data with reliable content, balanced across classes and with reduced environmental variability.

An overview of the patterns of prescription opioid use, costs and related harms in Australia

AIMS

To report Australian population trends in subsidized prescribed opioid use, total costs to the Australian government to subsidize these medicines and opioid-related harms based on hospitalizations and accidental poisoning deaths.

METHODS

We utilized three national aggregated data sources including dispensing claims from the Pharmaceutical Benefits Scheme, opioid-related hospitalizations from the National Hospital Morbidity Database and accidental poisoning deaths from the Australian Bureau of Statistics.

RESULTS

Between 1992 and 2012, opioid dispensing episodes increased 15-fold (500 000 to 7.5 million) and the corresponding cost to the Australian government increased 32-fold ($8.5 million to $271 million). Opioid-related harms also increased. Opioid-related hospitalizations increased from 605 to 1464 cases (1998-2009), outnumbering hospitalizations due to heroin poisonings since 2001. Deaths due to accidental poisoning (pharmaceutical opioids and illicit substances combined) increased from 151 to 266 (2002-2011), resulting in a rise in the death rate of 0.78 to 1.19 deaths/100 000 population over 10 years. Death rates increased 1.8 fold in males and 1.4 fold in females.

CONCLUSIONS

The striking increase in opioid use and related harms in Australia is consistent with trends observed in other jurisdictions. Further, there is no evidence to suggest these increases are plateauing. There is currently limited evidence in Australia about individual patterns of opioid use and the associated risk of adverse events. Further research should focus on these important issues so as to provide important evidence supporting effective change in policy and practice.