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ExportXLS Web Client Plugin

Introduction

This As of v.3.3, this plugin provides the following functions:

• Tabulates any selected concepts (ontology terms) relevant to (observed on) a set of selected patients.
• Optionally uses smaller queries of patient subgroups (from the large patient set) iteratively, in place of one single large query of that huge patient set, to reduce risk of overwhelming the server.
• Optionally uses selected subset of patients from a large patient set, to further reduce risk of overwhelming the server.
• Provides feedbacks on current progress, elapsed time, and estimated remaining run time.
• Provides notification & suggestion in cases of paging (query-subgrouping) by the server.
• Provides termination, indication & suggestion (for recovery) when the server failed.
• Provides detailed 'HELP' and 'HINT' dialogs in response to corresponding hotlinks strategically placed next to input fields that may need explanations or suggestion.
• Offers different formats and levels of detail.
  • Optionally returns appropriate 'Observation BLOBs' when 'valuetype_cd' is 'B' and the user has the appropraite access right ("DATA_DEID").
• 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.

It can be downloaded from the Download Page (at codeplex).

 Instructions

Refer to this Installation Guide and this User's manual for details.

Please refer to the built-in help ("Plugin Help" tab) for detailsconcise information after installation.

A PDF is available here.

 Usage Case Suggestions

• Resolving concept/modifier codesis 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).

 Browser Compatibilities

• 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), Chrome (v24.0) and Safari (v5.1.7) and Opera (v18.0, v20.0).
• The i2b2 web client itself does not work with Opera (v12.11, v12.16).

 i2b2 version compatibilities

This version (v3.03) is compatible with i2b2 v.1.3-1.67.

 Version History of this Plugin

Release Notes

Version 3.0

• Added export of CSV files.
• Improved tabulating of observations: all observations of a patient are now tabulated (not only the first one).
• Added flexible formatting of the output table.
• Added resolving of concept (and modifier) codes to export their denotation.
• Added inclusion of ontology path of concepts.
• Added replacing patient IDs by numbers (independently from i2b2 features)
• Added more flexible selection of demographic data.
• Added activity feedback for long running queries.
• Added re-querying of automatically paged results.
• Added possibility to page queries manually.

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