As of v.3.4, this plugin provides the following functions:
Please refer to the built-in help ("Plugin Help" tab) for concise information after installation.
Usage Case Suggestions
- Resolving concept/modifier codes is a very time consuming task. It is strongly recommended to enable this function only as a last step, after you are sure that the query itself is perfect.
- The default export CSV file encloses all data cells in quotation marks ("). This is necessary to export special characters like line breaks within a cell. However, some statistics software may get confused with the quotation marks. In this case, check the 'Exclude CSV Cell Delimiter (") Where Possible' box on the "Settings" tab to permit the writing of quotation marks where possible. Cells with special characters will still be enclosed in quotation marks, though... but it will be way less work to remove them manually than if it had to be done for every cell...
- If a query would return very large result sets, the server automatically pages the result. This causes a considerable delay that sometimes will fail or hang, due to timeouts. If you encounter this problem, the query can be paged manually by setting the 'Query Page Size' value on the "Settings" tab. This is still slower than an 'at-once' query, but faster than automatic paging and it avoids server overload. The necessary value cannot be predicted in general and strongly depends on the number of observations returned, but 20 - 50 is a good idea for beginning. Higher values result in faster processing but higher risk of server overload.
- If a patient set contains thousands of patients, and you are not sure if the concepts you are specifying would result in large run time or large result set, then it is better to start with a subset of the patient set (e.g. 'Starting Patient': 1, and 'Number of Patients: 500, etc.) first, as you can always run again with subsequent subsets (e.g. 'Starting Patient': 501, and 'Number of Patients: 500, etc.).
- The '1 row per observation (detailed, 1 column per observation detail)' option of tabulation is the only output option where the 'Observation Value' column will contain the appropriate 'Observation BLOBs' (if the 'valuetype_cd' is 'B' and the user has the "DATA_DEID" access right).
- This plugin has been successfully tested with the following browsers: Firefox (v18.0.2, v28.0), Chrome (v24.0, v33.0), Internet Explorer 32/64 (v9.0.13, v10.0, v11.0 - there seems to be a problem with scrolling bars in small windows, though), Safari (v5.1.7) and Opera (v18.0, v20.0).
- The i2b2 web client itself does not work with Opera (v12.11, v12.16).
This version (v3.3) is compatible with i2b2 v.1.3-1.7, in particular v.22.214.171.124.
Version History of this Plugin
Initial release, for i2b2 v1.5.
Updated for i2b2 v1.6.
Updated for i2b2 v1.3-1.6, Internet Explorer compatibilities; added flexible column exclusion, table title & caption, leading row count column, and other enhancements.
Major upgrade; many new features (CSV export, detailed tabulating of all observations, formatting options, paged queries...), heavily re-engineered.
Added options of using a subset of a large patient set; fixed blank 'Birth year' bug; added 'locality' column per request; added more user-friendly feedback (estimated run-time, etc.), help & hint; added server failure termination & notification. (for UMass Med School internal use only)
Added support of displaying observation blobs (for users with appropriate access) and added several useful columns to the output option of '1 row per observation (detailed, 1 column per observation detail)'.
|3.4||fixed compatibility issue with the new prototype.js v.1.7.2 (ships with webclient v126.96.36.199), other minor touch-ups; fixed selected patient subset size and starting & ending patient numbers off by 1 problems; added option to select delimiter for CSV export file; & repackaged to work with the new i2b2 Automatic Webclient Plugins Installer; etc.|
By Wayne Chan, Partners HealthCare, Charlestown, MA, USA.
- Optionally specify delimiter for CSV export file.
- Repackaged to work with the new i2b2 Automatic Webclient Plugins Installer.
- Certified to be compatible with webclient v188.8.131.52.
This new release is packed with installation guide and version supplementary note, and is available from the Google Code project download page set up for it, as well as the UMass Med School MICARD Downloads page.
- The initial version of this plugin was created by Mauro Bucalo, Universita' di Pavia, Italy, June 2011; based on the ExamplePDO plugin, by Nick Benik & Griffin Weber, Sept. 2008.
- The following major revision (v2.0) was released as a collaboration between the University of Massachusetts Medical School, Worcester, USA (S. Wayne Chan), and the Universita' di Pavia, Italy (Mauro Bucalo).
- Version 3.0 underwent heavy re-engineering and optimizations, together with the introduction of many new features. It was implemented by Axel Newe, Friedrich Alexander University Erlangen-Nuremberg, Germany with strong support from Wayne Chan and Mauro Bucalo (see above).
- Version 3.2 added GUI improvements & minor bug fixes, per local requests, and for internal usages only; in the University of Massachusetts Medical School, Worcester, USA (S. Wayne Chan).
- Version 3.3 was a collaboration between the Hôpital Ambroise Paré, Boulogne, France (PARIS Nicolas), and University of Massachusetts Medical School, Worcester, USA (Wayne Chan).
- Version 3.4 updated by Wayne Chan, Partners HealthCare.
Copyright 2011-2014 Universita' di Pavia,University of Massachusetts Medical School, Friedrich-Alexander-University Erlangen-Nuremberg, & Hôpital Ambroise Paré.
This plugin is published under the GNU GPL v3 license.