ExportXLS v3.3 User`s Manual
Contents
1. column display when the valuetype_cd N the qualifier gt lt gt lt or l for the numerical Observation Value e g gt means the Observation ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 13 Value is greater than the one shown refer to the i2b2 Data Repository CRC Cell Design Document for further details Warning About The i2b2 Hive Paging When a user specifies very complex Concepts against very large Patient Set the i2b2 hive may attempt to page that large query or separate it into smaller sub groups of queries and then combine the results of these smaller queries into one set of data to be returned However sometimes it may lose track of its pages and cause an error resulting in an apparent hang in this plugin i e this plugin appeared to be never finishing When it is detected that the i2b2 hive has paged the request this plugin will display a warning along with its estimates message to urge the user to try options that would avoid future pagings from occurring like the following ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 14 ExportxLs Specify Data Output Options View Results Plugin Help Retrieving data from the server i2b2 hive to create the table Cur2. Acute but ill defined cerebrovascular disease Intracerebral hemorrhage Click a Concept to remove it from the list Notice that the instruction Click a Concept to remove it from the list is displayed as soon as a concept is dropped into the box Also a warning pop up dialog will be displayed if a repeated concept is dropped in similar to the following from a Chrome browser that was used note IP address blotched out ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 5 The page atL___ says This concept has already been selected duplicate concept would not be accepted The Output Options Tab Navigate to the Output Options tab to select the output format and options There are four sections in this tab the Formatting section the Patient Demographic Data section the Options that can cause long running time section and the CSV Export Option section ExportxLs specify Data Output Options View Results Plugin Help Formatting 1 row per observation duplicates removed 1 column per observation se Y C Replace Patient IDs with Ascending Numbers starting at 1 _ Birth Year Vital Status L Language L Race L Religion L Income O Locality Marital Status ns that can cause long running time L Resolve Concept Modifier Codes L Include Ontology Path of Concepts CSV rt Op
3. Please consider the numbers count for the current view of the table and are not related to real patient IDs If the queried concepts are changed in a way that the resulting patient set is changed as well the ascending numbers used to designate the patients of a previous query may not be the same in a new query The Patient Demographic Data Section A number of demographic data items can be tabulated as well Check the respective boxes to include these data items Always selected only those data that are germane to the investigation at hand to reduce cluttering in the resulting table as well as faster turn around time Please note that the list of demographic data options in your institution may differ from those shown in the illustration above as there are built in flexibilities to allow the administrator of each establishment to make available only those options that are relevant or compliant to its missions The Options that can cause long running time Section There are two such resource intensive options Resolve Concept Modifier Codes and Include Ontology Path of Concepts The Resolve Concept Modifier Codes Option If you want to resolve the concept and modifier codes e g ICD codes to see their denotation check the box Resolve Concept Modifier Codes Warning this will also require massive database querying and can therefore cause a very long running time or crash It is a good idea to select t
4. appropriate Observation BLOBs when valuetype_cd is B and the user has the appropriate access right DATA_DEID e Optionally replaces patient IDs with ascending numbers e Minor enhancements amp bug fixes in certain demographic patient details This document outlines the usage of this plugin Please refer to its complimentary document the ExportXLS v3 3 Installation Guide for installation details Instructions As with any i2b2 Webclient plugins this plugin is listed under the Plugins panel under the Analysis Tools tab Detailed List View Categon ALL ExportaLs This plugin tabulates unidentified patient date of selectable concepts cbservations and provides options to download the result to specified file type ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 1 The Plugin Help Tab The first thing a user should do if this document is not readily available is to click its Plugin Help tab which contains a summary of the contents in this document Specify Data Output Options View Results Plugin Help Introduction This plugin provides the following functions labulates 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 t
5. many new features CSV export detailed tabulating of all observations formatting options paged queries heavily re engineered By Axel Newe Friedrich Alexander University Erlangen Nuremberg Germany ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 18 3 2 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 amp hint added server failure termination amp notification By Wayne Chan University of Massachusetts Medical School Worcester USA 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 etc By Wayne Chan University of Massachusetts Medical School Worcester USA and PARIS Nicolas H pital Ambroise Par Boulogne France 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 7 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 ExportXLS v3 3 User s Manual University of Massachusetts Medical
6. note the following e Since it is possible for the server i2b2 hive to take a long time to provide all the data requested this plugin has been enhanced with occasional updates of Elapsed time and estimated remaining run time etc displays These displayed values are best rough estimates based on occasional data coming back from the server In the case of zero Query Subgroup Size selected i e no query subgrouping then there would be no data coming back from the server until either of the following situations o The whole single query is done o The server itself started paging i e query subgrouping and the result of the 1 of such paged subqueries just arrived o The server got overwhelmed by all the excessive data and failed returning an error ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 17 In any of these cases the updates of Elapsed time and estimated remaining run time will be quite infrequent as updates from the server i2b2 hive will most likely take a long time and far and few in between if any e This plugin also tries to provide updates on the current subgroup the server i2b2 hive is fetching However in the cases when the server i2b2 hive itself started paging i e query subgrouping then the current subgroup being fetched may exceed the original stated total number of subgroups e The
7. to the option above but timestamps of the observations are tabulated as well Therefore duplicates are not possible and nothing is removed e 1 row per observation detailed 1 column per observation detail This is the most detailed option A new row is created for each observation and all observation details concept code value unit etc are written to dedicated columns o The Observation Value column will contain the appropriate Observation BLOBs provided that the valuetype_cd is B and the user has the appropraite access right DATA_DEID e 1row per patient 1 column per observation set A new row is created for each patient One column is created for each concept that has been dragged onto the input box All observations of a patient are then written into one cell with respect to the concept column Note This is the only output option where the first column starting number will match the specified value of Starting Patient ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 7 The Replace Patient IDs with Ascending Numbers starting at 1 checkbox If you want to replace the patient IDs with an ascending numbers starting with 1 check the Replace Patient IDs with Ascending Numbers starting at 1 box This works independently from other i2b2 anonymization pseudonymization features and always replaces the patient IDs
8. 1 row per patient 1 column per observation set option of tabulation is the only output option where the first column starting number will match the specified value of Starting Patient e 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 e This plugin has been successfully tested with the following browsers Firefox v18 0 2 v28 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 v33 0 Safari v5 1 7 and Opera v18 0 v20 0 e The i2b2 web client itself does not work with Opera v12 11 v12 16 i2b2 version compatibilities This current version is compatible with i2b2 v 1 3 1 7 Version History 1 0 Initial release for i2b2 v1 5 By Mauro Bucalo Universita di Pavia Italy 1 6 Updated for i2b2 v1 6 By Mauro Bucalo Universita di Pavia Italy 2 0 Updated for i2b2 v1 3 1 6 Internet Explorer compatibilities added flexible column exclusion table title amp caption leading row count column and other enhancements By Wayne Chan University of Massachusetts Medical School Worcester USA and Mauro Bucalo Universita di Pavia Italy 3 0 Major upgrade
9. 81 Patient VYaital ee Marital pee pa Year Status Status TCDS 414 00 7925084 E HA RTA TCDS 4314 02 TCDS 414 01 TCDS 401 1 PRIMARY TCDS 414 00 2 1561206 H T7 HORTHERIDGEMA IcD9 414 00 PRIMARY TCDS 411 1 TCDS 414 05 th Note that for the figure above the formatting option was selected 1 row per patient 1 column per observation set ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 10 If you want to export the table into a CSV file click the So Salt button This initiates the download of a file onto your desktop The file is named _ i2b2 export_patient observations _ timestamp csv If you want to export the table into an HTML encoded Excel file click the HTML XLS Export button This initiates the download of a file named i2b2 export_patient observations timestamp html xls The file is HTML but due to the suffix it can directly be opened with Excel If you want to open it in a web browser simply remove the xls suffix Note Excel may launch a warning message if the file is loaded This message can be ignored confirmed click Yes Displaying Observation BLOBs The Observation BLOBs are only available when the following conditions are met 1 User has been grant the DATA_DEID access by the i2b2 Administrator izb2 Query amp Analysis Tool Help Log
10. 82694 LC5 I282 0000109060 2009 06 01 7009 06 01 a 4 1000000001 482694 LCS 1282 p000109060 2009 06 01 2009 06 01 476659 LCS I2B2 0000109050 2004 06 03 2004 06 03 Reports LCS I2B2 CT_RPT 476659 LC5 I282 D000109060 2004 06 03 2004 06 03 7 1000000005 475950 LCS 1282 D000109062 2003 09 05 2003 09 09 Reports LCS 1282 MRI_RPT 475950 LCS 1282 0000109062 2003 03 09 2003 09 09 1 ports Se roteeees 10 1000000006 473265 LCS 1282 D000109061 2000 08 10 2000 08 10 1 LES I2B2 XR_RPT_DID 11 1000000009 473136 LCS 1282 1000109061 2000 06 14 2000 06 14 1 rts LCS 1282 XR_RPT 17 1nnnnnnnna 473136 l a1 annn nn ta annneniata 1 CSV Export HTML XLS Export Patient Information for patierts i 100 of Patient Set Isochemi Male 13 25 22 11 21 2013 demo PATIENTSET 281 O TT Patient Provider Timestamp are ID ID Start End 5705s J lei l ae eres as 088 OL 07 18 system Aa a e e a a Pe e AA 7 18 system 7 o eaa e a a ee Ee ee 0 18 system E a ea Circulatory 07 18 system sl asa zaszans Lndetineny 2006 08 zosa sa A _ fcsmcoracory rene ant a The Observation Type column indicate whether Observation Value entries are numeric text or BLOB for the user The Confidence Number column will provide the measure of the confidence of the observation The Observation Operator
11. ExportXLS v3 3 User s Manual Introduction This i2b2 Webclient plugin enables the user to obtain the specified concepts for a set of patient The user can then further capture those data in a XLS Excel spreadsheet Workbook or CSV comma separated values file This plugin has been quite popular and has undergone several revisions by several institutions each contributing to its robustness usability and user friendliness The following are some of the key functions in this version of this plugin e Tabulates any selected concepts ontology terms relevant to observed on a set of selected patients e 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 i2b2 hive e Optionally uses selected subset of patients from a large patient set to further reduce risk of overwhelming the server e Provides feedbacks on current progress elapsed time and estimated remaining run time e Provides notification amp suggestion in cases of paging query subgrouping by the server e Provides termination indication amp suggestion for recovery when the server failed e Provides detailed HELP and HINT dialogs in response to corresponding hotlinks strategically placed next to input fields that may need explanations or suggestion e Offers different formats and levels of detail o Optionally returns
12. School Worcester amp H pital Ambroise Par Boulogne swc Page 19
13. ed to specify the subset of the patient set to use and the smaller queries of subgroups of patients to use to facilitate reducing the risks of overwhelming the server i2b2 hive Click on the corresponding HELP hotlinks next to the Starting Patient and Number of Patients fields and the HELP hotlink next to the Query Subgroup Size field for detailed The Specify Data Tab Navigate to the Specify Data tab Drag and drop a Patient Set and one or more concepts ontology terms onto the appropriate input box es I ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 2 ExportxLs Specify Data Output Options Plugin Help Drop a patient set and atleast one concept ontology term onto the approriate input boxes below then click the Output Options tab to specify layout of the resulting data before clicking on the View Results tab to retrieve the respective observations in the selected patient set For more information refer to the Plugin Help tab Patient Set Drop a Patient Set here Concept s Drop one or more Concepts here As soon as a Patient Set is specified i e dropped in then more fields will be displayed for additional input ExportxLs Specify Data Output Options Plugin Help Drop a patient set and atleast one concept ontology term onto the approriate input boxes below t
14. gress and the resulting table of the observations specify Data Output Options View Results Plugin Help Retrieving data from the server i262 hive to create the table Currently busy retrieving patient data for subgroup 1 tout of some 25 subgroups of roughly 20 each or a total of Some 500 patients Elapsed time as ofthe last completed subgroup 0 sec estimated remaining runtime 9 min 55 sec Please wait ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 9 Depending on the size of the Patient Set the number and complexities of the concepts and the various options specified it could take quite a while for the i2b2 hive to complete the chore requested However while the data are being fetched there will be constantly updated feedback displays to provide estimations as to how much data have been retrieved how much are yet to be fetched elapsed time and remaining run time etc Successful Run At the end of a successful run after all the requested data have been returned by the server i2b2 hive the resulting table will be displayed specify Data Output Options View Results Plugin Help Click on one ofthe buttons on the right to download the CSV Export HTML JX LS Export following table in the appropriate format Patiert Information for patiert 1 gt 00 of Patient Jet Isohemi Male la 25 22 11 21 2013 demo PATISNTSST 2
15. hat huge patient set to reduce risk of overwhelming the server i2b2 hive 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 amp suggestion in cases of paging query subgrouping by the server Provides termination indication amp 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 BD and the user has the appropraite access right DATA _DEID Optionally replaces patient Ds 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 or XLS file that can easily be used by Excel SPSS and other statistics software Instructions 1 Navigate to the Specify Data tab Drag and drop a Patient Set and one or more concepts ontology terms onto the appropriate input box es Select the appropriate Starting Patient Number of Patients and Query Subgroup Size fields that are then present
16. hen click the Output Options tab to specify layout of the resulting data before clicking on the View Results tab to retrieve the respective observations in the selected patient set For more information refer to the Plugin Help tab Patient Set Ischemi Male 13 25 22 11 21 2013 demo PATIENTS contains some 2000 patients using patients 1 500 or just 500 of the set starting Patient 1 Number of Patients 500 HELF Query Subgroup Size z 0 HELF Concept s Drop one or more Concepts here Select the appropriate Starting Patient defaulted to 1 Number of Patients defaulted to 500 and Query Subgroup Size defaulted to 20 fields that are then presented to specify the subset of the patient set to use and the smaller queries of subgroups of patients to use to facilitate reducing the risks of overwhelming the server i2b2 hive ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page3 Click on the corresponding HELP hotlink next to the Starting Patient and Number of Patients fields and the HELP hotlink next to the Query Subgroup Size field for detailed information in corresponding pop up dialogs and enter corresponding appropriate values About Starting Patient and Number of Patients lf your patient set contains thousands of patients you may want to use just a subset ofthat By so doing
17. his option only right before you are sure your dataset is complete and ready to be exported As long as you are still varying your query this option should be left unchecked The Include Ontology Path of Concepts Option If you want to include the ontology path of the concept codes check the box Include Ontology Path of Concepts ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 8 Warning this also requires massive database querying and can therefore cause a very long running time or crash However if you check both Resolve Concept Modifier Codes and Include Ontology Path of Concepts options the running time will not double since both options require the same ontology querying The CSV Export Option Section 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 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 The View results Tab Finally select the View Results tab to view the pro
18. me resulting in hang i e this plugin appeared to be never finishing The cause of such situation has traced to the i2b2 hive somehow losing track of its pages when it attempted to page the large query or separate it into smaller sub groups of queries and then combine the results of these smaller queries into one set of data to be returned Despite of all the additional options introduced it is still possible for one to have selected options that sensitize this problem of the i2b2 hive s When that occurs then the following display will result ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 16 ExportxLl specify Data Output Options View Results Plugin Help Elapsed time 1 min 56 sec Warning The server i2b hive has returned an error apparently it has been overwhelmed by the amount of data requested of it and had failed Unfortunately this server failure has also left this current webclient session in a bad state Please logout of this webclient session to allow the flushing of remnants of this server failure in certain occasions it may even be necessary to close the current web browser and login to a new webclient session Then start this webclient plugin again and reduce either the Number of Patients or Query Subgroup Size to a smaller non zero value or both in the Specify Data tab Caveats Please
19. out PM Navigation n Project gt undefined gt U wers gt demo gt Roles A Manage Hive Manage Cells Manage Projects 5 i2b2 Demo E User H Parama Users 4 AGG_SERVIG chemo i Roles H Params i2b2 H SUREA B Manage Users i262 Admin 7 AGS SERVICE_ACI H i b2 User E Manage Approvals E Project Requests 2 User has selected the 1 row per observation detailed 1 column per observation detail Formatting option ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 11 Output Options View Results Plugin Help Formatting 1 row per observation detailed 1 column per observation detail 1 row per observation duplicates removed 1 column per observation set Birth Year Vital Status Language Race Religion nad i E E E i Income Locality Marital Status et Resolve Concept Modifier Codes Include Ontology Path of Concepts CSV Export Option C Exclude CSV Cell Delimiter Where Possible 3 The corresponding observation valuetypce_cd is B 4 Observation BLOBs are actually available in the database The following is an example of Observation BLOBs displayed in the Observation Value column of the resulting table Expor L Glick on one of the butions on the right to download the following table in the appropria
20. r amp H pital Ambroise Par Boulogne swc Page 4 Concept hint suggestion For best results select finer qrained 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 finer concepts like Hypertensive disease Ischemic heart disease and arterial vascular disease etc that are pertinent to the interest at hand would result in more meaningful results than simply specifying a single concept of Circulatory system which contains other concepts that may be irrelevent to the present study Furthermore keep in mind that far reaching concepts that contains many branches and sub branches of concepts coupled with a As implied in the pop up dialog above one can drop in many concepts View Results Plugin Help Drop a patient set and at least one concept ontology term onto the approriate input boxes below then click the Output Options tab to specify layout of the resulting data before clicking on the View Results tab to retrieve the respective observations in the selected patient set For more information refer to the Plugin Help tab Patient Set General Cardiov 14 08 57 11 19 2013 demo PA contains some 1986 patients using patients 1 500 or just 500 of the set Starting Patient 1 Number of Patients 500 HELP Query Subgroup Size 20 HELP Concepts
21. rently busy retrieving patient data for subgroup 1 out of 1 group of 43 3 each or a total of 4373 patients Elapsed time as ofthe last completed subgroup 6 min 32 sec estimated remaining run time 1 hr 15 min 30 sec Warning the server i2b2 hive has paged this data query Le replaced it with many smaller queries that it hopes to better manage this may take longer time to finish Next time please consider reducing the Query Page Size field value non zero on the Specify Data tab to speed things up Please wait If the paging did not result in error then a similar warning would also be displayed in the all data retrieved pop up dialog similar to the following from a Chrome browser that was used to again remind the user to try to avoid this same predicament in future runs note IP address blotched out jn ____________ swc Page 15 ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne The page at C J says x Currently tabulating all data please wait Warning the query has been paged by the server i2b2 hive you can speed up future quenes by reducing the Query Page Size field value non zero on the Specify Data tab OK Unsuccessful Run In previous versions of this plugin because of its popularity user has been known to specify more and more complex Concepts against large Patient Set often ti
22. te format CSV Export HTMIL XLS Export Patient Information for patients 1 52 of Patient Set Female 16 36 24 3 11 2014 demo PATIENTSET_167 teal Provider Ih imestamp Observation Observation AA ameni Observation sodil errs End Set Concept Code Value Unit Wodifier Positive for 1000000001 471260 LES I2B82 0000103060 1997 03 25 1997 03 25 Reports LC5 1282 FH H aia hypertension and kidney disease Married and lives with husband and one son Patient 2 1000000001 471760 LCS I282 0000103060 1997 03 75 1997 03 25 LCS T282 5H denies tobacco alcohol or illegal substance abuse ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 12 Note that this enhancement brings the access of Observation BLOBs that was only available through the Workbench to the Webclient In the case that the user does not have the DATA_DEID access then only protected would be displayed instead svee oma ouea onone view Ress Click on one of the buttons on the right to download the following table in the appropriate format CSV Export HTML LS Export Patient Information for patients 1 52 of Patient Set Female 16 36 24 3 11 2014 demo PATIENTSET_167 Patient Visit Provider ID Timestamp Timestamp Observation Observation Observation ID ID Start End Concept Code Wodifier 3 1000000001 4
23. tinto subgroups of your specified size and then iteratively make request of relevant data for each of these resulting subgroups and then collate and render the returned data when all these smaller queries are completed Since each subgroup should be of small enough size the requests hopefully would not cause the server to fail or hang The ideal Query Subgroup Size value cannot be predicted in general and strongly depends on the number of observations related to the total numbers of concepts and their complexities returned but values of 20 to 50 may be good higher value may result in faster processing but may also carry higher risk of the server failing where no data can be rendered at all Incidentally setting a value of 0 instructs this plugin notto divide up the original query into smaller queries and carries the risk of overwhelming and failing the server as well as practivally no Elapsed time and estimated remaining run time updates Note that the sample pop up dialogs are from a Firefox browser different browsers may have different style dialogs that are similar but contain the same key contents The following pop up dialog will be displayed when the HINT hotlink below the Concept s input box is clicked to provide suggestions regarding concept specifications that may result in faster turn around time ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worceste
24. tion L Exclude CSV Cell Delimiter m Where Possible ExportXLS v3 3 User s Manual University of Massachusetts Medical School Worcester amp H pital Ambroise Par Boulogne swc Page 6 The Formatting Section The Formatting section contains the Formatting selection list and the Replace Patient IDs with Ascending Numbers starting at 1 checkbox The Formatting Selection List There are four options in the Formatting selection list live specify Data Output Options Plugin Help View Results Formatting 1 row per observation duplicates removed 1 column per observation se Y 1 row per observation duplicates removed 1 column per observation set 1 row per observation all with timestamps 1 column per observation set 1 row per observation detailed 1 column per observation detail 1 row per patient 1 column per observation set In elo dan Dia A t aa EL Their meanings are e 1 row per observation duplicates removed 1 column per observation set A new row is created for each observation All observation details concept code value unit etc are written into one cell One column is created for each concept that has been dragged onto the input box in step 1 Attention Duplicate entries are removed This format only returns a list of the different observations that were found e 1 row per observation all with timestamps 1 column per observation set Similar
25. you will speed up your query as well as reduce the likelihood of overwhelming the server i2b hive to the point of failure and no result Also ifyou already encountered a server failure overwhelmed by the combination of large number of patients times lots of concepts then you may like to rerun this plugin several times each time specifying different Starting Patient and Number of Patients For instance use 1 and 500 respectively in your first run follow with 501 and 500 respectively in your second run then 1007 and 500 respectively in your third run and so on until you get enough data The example above should also show thatthe Starting Patient and Number of Patients refer to the patient entry order in the patient set only which has no bearing on the actual patient IDs In addition ifthe sum ofthe Starting Patient and the Number of Patients values exceeds the total patient count then itll be adjusted to the remaining patient count accordingly About Query Subgroup Size Please note that a large query i e a large patient set with many concepts especially ones consisting many subfolder trees may overwhelm the server i2b2 hive which may fail where no data can be rendered at all after considerable delays and timeouts To avoid this problem you may want to set the Query Subgroup Size value Setting the Query Subgroup Size instructs this plugin to temporarily divide up your patient se
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