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About the ExportXLS Web Client Plugin
Introduction
This plugin provides the following functions:
- Tabulates any selected concepts (ontology terms) relevant to (observed on) a set of selected patients.
- Offers different formats and levels of detail.
- Optionally replaces patient IDs with ascending numbers.
- Optionally adds a selection of demographic patient details.
- Optionally resolves concept codes and displays their denotation.
- Optionally includes ontology path of concept codes.
- Exports tabulated data into a CSV file that can easily be used by Excel, SPSS and other statistics software.
Instructions
Please refer to the built-in help ("Plugin Help" tab) for details.
A PDF is available here.
Usage Case Suggestion
Currently the resulting table will only include the first observation from the selected concept (among the many possible if a selected concept is very broad) associated with each patient. In other words, if a selected concept contains multiple subconcepts (e.g. Circulatory system), the resulting row, for a patient, will contain only the first observation (e.g. Hypertensive disease), and ignore other observations (e.g. Ischemic heart disease, arterial vascular disease, etc.) that happen to be also observed in a particular patient.
Note that including all possible observations corresponding to a selected concept for a patient may result in rather complicated and confusing data, and may not be too useful.
It's therefore important to exercise prudence, and select finer-grained concepts that may not be related to multiple non-exclusive observations in patients. For example, while a patient set may be for Circulatory system, selecting several concepts like Hypertensive disease, Ischemic heart disease, and arterial vascular disease, etc. would result in more meaningful results than simply specifying a single concept of Circulatory system.
Browser Compatibilities
- This plugin has been successfully tested with the following browsers: Firefox (v18.0.2), Internet Explorer 32/64 (v9.0.13 - there seems to be a problem with scrolling bars in small windows, though), Chrome (v24.0) and Safari (v5.1.7)
- The i2b2 web client itself does not work with Opera (v12.11).
i2b2 version compatibilities
This version (v3.0) is compatible with i2b2 v.1.3-1.6.
Version History of this Plugin
1.0 |
Initial release, for i2b2 v1.5. |
June 2011 |
1.6 |
Updated for i2b2 v1.6. |
Jan. 2012 |
2.0 |
Updated for i2b2 v1.3-1.6, Internet Explorer compatibilities; added flexible column exclusion, table title & caption, leading row count column, and other enhancements. |
Feb. 2012 |
3.0 |
Major upgrade; many new features (CSV export, detailed tabulating of all observations, formatting options, paged queries...), heavily re-engineered. |
Feb. 2013 |
Feature Summary of v2.0
Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:
- Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).
- Added table title and caption to the resulting output table.
- Added new 1st column for patient row counts (no column title).
- Renamed the "StateCity" column title to "State/City".
- Removed any leading and trailing redundant "Zip codes" values from each state value string.
- Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.
- Improved efficiencies.
- Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.
- Fixed the Internet Explorer (IE) hang problem.
- Fixed the missing "concept" columns on IE problem.
- Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.
- Fixed table content getting cutoff on IE problem.
- Centered content in each table cell of the resulting output table.
- Added unique time-stamp to name of exported XLS file.
- Updated the description of this plugin displayed (in the available plugin list).
- Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.
- Updated plugin category from "text" to "standard".
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.
About Us
- 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 (S. Wayne Chan, Rajani Sadasivam, Thomas Houston, & the rest of the BMI-Core), and the Universita' di Pavia, Italy (Mauro Bucalo).
- The latest version (v3.0) 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).
Please don't hesitate to contact us concerning any questions or problems. Thanks.
Copyright 2011-2013 University of Massachusetts Medical School, Universita' di Pavia & Friedrich-Alexander-University Erlangen-Nuremberg.
Terms of Use
This plugin is published under the GNU GPL v3 license.
This software is distributed as a plugin to the i2b2 v1.3-1.6 webclient framework, and may be used free of charge. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.