collect Opal 2.16 Released

We are pleased to announce that Opal 2.16 is now available. Opal is OBiBa’s core database application for biobanks.

This release facilitates the documentation of the harmonization process by reading directly the variable properties from the column attributes of the R data.frame/tibble objects. Thus harmonization algorithms can be implemented along with their documentation in the metadata of the datasets. This approach has been successfully applied by the Maelstrom Research group. As a complement, the opalr R package provides some new utility functions (since version 1.3.0) for retrieving datasets from Opal into the local R session, annotating the harmonized datasets with taxonomy terms, applying data dictionary, and saving back the datasets as Opal tables.

Additional features implemented:

  • value sequence functions median and unique have been added,
  • the data summary of temporal (date/datetime), geospatial (point/linestring/polygon) and text variables has been improved to support case of continuous data with only categories describing missing values,
  • the data dictionary of an imported dataset can be optionaly merged into the existing destination table (default behavior is still override).

This release was possible thanks to the funding of the MINDMAP and the ALSPAC programs.

See Opal documentation for installation and operation instructions. Note that a Docker Image Installation section has been added.