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Combining clinical and genomics queries using i2b2 – Three methods

View Article: PubMed Central - PubMed

ABSTRACT

We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical “Big Data” challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package. Three different data integration approaches were developed: The first is based on Sequence Ontology, the second is based on the tranSMART engine, and the third on CouchDB. These novel methods for representing and querying complex genomic and clinical data on the i2b2 platform are available today for advancing precision medicine.

No MeSH data available.


Display of counts per population in two subgroups in i2b2/tranSMART (use case 3).
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pone.0172187.g004: Display of counts per population in two subgroups in i2b2/tranSMART (use case 3).

Mentions: The next step highlights one of the areas that differentiate i2b2/tranSMART from the other i2b2 approaches. When we wish to view the breakdown of patient counts in different populations, we can simply drag and drop the population folder from the ontology tree into the analysis tab. This action generates a bar chart with patient counts for each population (Fig 4). A Chi-squared test is automatically run as well to let us know if the distribution between the categories is statistically different across the two subsets. In other i2b2 instances, the counts would have to be derived through several successive patient count queries, where i2b2/tranSMART allows it to be generated in one drag, thus taking less time for this simple initial query with statistical tests returned.


Combining clinical and genomics queries using i2b2 – Three methods
Display of counts per population in two subgroups in i2b2/tranSMART (use case 3).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384666&req=5

pone.0172187.g004: Display of counts per population in two subgroups in i2b2/tranSMART (use case 3).
Mentions: The next step highlights one of the areas that differentiate i2b2/tranSMART from the other i2b2 approaches. When we wish to view the breakdown of patient counts in different populations, we can simply drag and drop the population folder from the ontology tree into the analysis tab. This action generates a bar chart with patient counts for each population (Fig 4). A Chi-squared test is automatically run as well to let us know if the distribution between the categories is statistically different across the two subsets. In other i2b2 instances, the counts would have to be derived through several successive patient count queries, where i2b2/tranSMART allows it to be generated in one drag, thus taking less time for this simple initial query with statistical tests returned.

View Article: PubMed Central - PubMed

ABSTRACT

We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical “Big Data” challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package. Three different data integration approaches were developed: The first is based on Sequence Ontology, the second is based on the tranSMART engine, and the third on CouchDB. These novel methods for representing and querying complex genomic and clinical data on the i2b2 platform are available today for advancing precision medicine.

No MeSH data available.