http://caisis.org/wiki/index.php?title=Special:Contributions&feed=atom&target=FearnpCaisisWiki - User contributions [en]2024-03-29T07:24:49ZFrom CaisisWikiMediaWiki 1.15.1http://caisis.org/wiki/index.php?title=Main_PageMain Page2008-09-24T22:39:34Z<p>Fearnp: Added data dictionary link and mentioned user manual</p>
<hr />
<div>Welcome to the Caisis Wiki. We welcome contributions from the Caisis community. <br />
<br />
10.25.2007 Caisis 4.0 is now available! <br />
<br />
Previous Caisis documents, such as the User Manual, are here [http://caisis.org/documentation.aspx here].<br />
<br />
== Data Dictionary ==<br />
Here is an Excel file of the data dictionary for version 4.1. It may be easier to just view this one than to extract the dictionary from the Downloads, Data Model package using SQL.<br />
<br />
== Technical & Administrator Information ==<br />
<br />
* v4.1 [[Installation]] documentation.<br />
* [[Known Issues]]<br />
* [[Change Log]]<br />
* [[Frequently Asked Questions]]<br />
* Caisis 4.0 [[Export Analysis Utility]]<br />
* Caisis 4.0 [[Data Warehouse]]<br />
<br />
== Application Configuration ==<br />
* Managing [[Meta Data]]<br />
<br />
== Development ==<br />
Common Customization Tasks<br />
* Creating [[Eforms]] in Caisis<br />
* [[Adding Tables to Caisis]]<br />
Design and Coding<br />
*[[Caisis Input Controls]]<br />
<br />
== User Information ==<br />
<br />
* [[Longitudinal Followup]]<br />
* [[How to use the biobank module]]<br />
<br />
== Presentations ==<br />
* 05.2007 Presentation at the ISBER conference: Biobanking with CAISIS[http://biobank-suisse.ch/e/SBBS_Download/08-05-18_ISBER_2008_final.pdf]<br />
* 11.2007 Presentation at Indian Association for Medical Informatic [http://openmed.nic.in/2490/]<br />
* 10.2007 Presentation (with audio) from APIII, Pittsburg[http://apiii.upmc.edu/breakout/archive/2007/Fearn/APIII_Caisis4_DataSupplyChainx.ppt]<br />
* 11.2006 Presentation from Caisis Face-To-Face Meeting in New York[http://caisis.org/downloads/CaisisPresentation2006.ppt]</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2008-09-08T16:15:14Z<p>Fearnp: added writeDB fields source code for Chiragh</p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a Windows security group with permissions to read data on your Caisis SQL Server warehouse<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
* Localization Issues<br />
** For Longitudinal Followup will need to modify WHERE clause in the following queries to remove IN() statement or modify to your own OpCaseSurgeon and OpInstitution values: qryFU_NeedLetter_Kidney, qrptFU_LastNephrectomy, qrptFU_LastRPLND, qryFU_NeedLetter_Testis, qryFU_NeedLetter_Prostate, qryFU_NeedLetter_Bladder, qryFU_NeedLetter_LapProstateIMM, qryFU_NeedLetter_Survivorship, qryFU_NeedLetter_Survivorship_Jul08_2005<br />
<br />
== Features ==<br />
* Splash Screen. This form opens automatically when you open the Export Analysis Utility. It displays the location of the MDB file and the database your tables are linked to, and it provides buttons to launch each of the following features.<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through Metadata tables) The recode feature is exclusively available through the Caisis system admin tool.<br />
* [[Nomograms]]. Links to [http://nomograms.org web nomograms] on [http://www.mskcc.org MSKCC web site]. Also includes functions for calling nomogram library to calculate nomogram predictions for sets of patients in a tables or spreadsheet.<br />
* [[Longitudinal Followup]]. Wizards and partially automated tools to help manage the process of mailouts to patients to find out how they are doing after treatment if they are not coming back regularly to your practice. NOTE: You will need to keep your own local copy of the Signatures table after you have started using the Longitudinal Followup process to maintain custom letters to patients from your local physicians. <br />
<br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
== SAMPLE CODE ==<br />
<br />
* How do I find out which fields are most/least populated?<br />
<br />
<pre><br />
Function WriteDBFields()<br />
On Error GoTo Error_Handler<br />
<br />
Dim db As DAO.Database<br />
Dim tbl As DAO.TableDef<br />
Dim fld As DAO.Field<br />
Dim fldType As String<br />
Dim outfilename As String<br />
Dim strTableDescription As String<br />
Dim strFieldDescription As String<br />
<br />
Dim rs As DAO.Recordset<br />
Dim lngTableRecords As Long<br />
Dim lngFieldRecords As Long<br />
Dim lngZLS As Long<br />
Dim strCount As String<br />
<br />
Set db = CurrentDb()<br />
outfilename = Left(CurrentDb.Name, Len(CurrentDb.Name) - 4) & " Data Dictionary.txt"<br />
<br />
Debug.Print outfilename<br />
<br />
Open outfilename For Output As #1<br />
<br />
Write #1, "TableName", "TableDesc", "FieldName", "DataType", "FieldDesc", "TableRecords", "FieldRecords", "ZeroLengthStrings"<br />
Debug.Print """TableName"",""TableDesc"",""FieldName"",""DataType"",""FieldDesc"",""TableRecords"",""FieldRecords"",""ZeroLengthStrings"""<br />
<br />
For Each tbl In db.TableDefs<br />
<br />
'To prevent system tables from printing, include: Left(tbl.Name, 4) <> "MSys" - or for specific tbls only: Left(tbl.Name, 6) = "CSMM_S"<br />
If Left(tbl.Name, 4) <> "MSys" And tbl.Connect = vbNullString Then<br />
Set rs = tbl.OpenRecordset(dbOpenSnapshot)<br />
If rs.EOF Then<br />
lngTableRecords = 0<br />
Else<br />
rs.MoveLast<br />
lngTableRecords = rs.RecordCount<br />
End If<br />
rs.Close<br />
For Each fld In tbl.Fields<br />
strCount = "SELECT [" & tbl.Name & "].[" & fld.Name & "] " _<br />
& "FROM [" & tbl.Name & "] " _<br />
& "WHERE (([" & tbl.Name & "].[" & fld.Name & "]) Is Not Null);"<br />
Set rs = db.OpenRecordset(strCount, dbOpenSnapshot)<br />
If rs.EOF Then<br />
lngFieldRecords = 0<br />
Else<br />
rs.MoveLast<br />
lngFieldRecords = rs.RecordCount<br />
End If<br />
rs.Close<br />
If fld.Type = 10 Or fld.Type = 12 Then<br />
strCount = "SELECT [" & tbl.Name & "].[" & fld.Name & "] " _<br />
& "FROM [" & tbl.Name & "] " _<br />
& "WHERE (([" & tbl.Name & "].[" & fld.Name & "]) = """");"<br />
Set rs = db.OpenRecordset(strCount, dbOpenSnapshot)<br />
If rs.EOF Then<br />
lngZLS = 0<br />
Else<br />
rs.MoveLast<br />
lngZLS = rs.RecordCount<br />
End If<br />
rs.Close<br />
Else<br />
lngZLS = 0<br />
End If<br />
Debug.Print """" & tbl.Name & """,";<br />
strTableDescription = vbNullString<br />
strTableDescription = tbl.Properties("Description")<br />
Debug.Print """" & strTableDescription & """"<br />
Debug.Print """" & fld.Name & """,";<br />
Select Case fld.Type<br />
Case 1<br />
fldType = "Yes/No"<br />
Case 10<br />
fldType = "Text:" & fld.Size<br />
Case 12<br />
fldType = "Memo"<br />
Case 8, 22, 23<br />
fldType = "Date/Time"<br />
Case 2<br />
fldType = "Number:Byte"<br />
Case 3<br />
fldType = "Number:Integer"<br />
Case 4<br />
fldType = "Number:Long"<br />
Case 5<br />
fldType = "Number:Currency"<br />
Case 6<br />
fldType = "Number:Single"<br />
Case 7<br />
fldType = "Number:Double"<br />
Case Else ' 9, 11, 15, 17, 19, 20, 21<br />
fldType = "Numeric"<br />
End Select<br />
Debug.Print """" & fldType & """,";<br />
<br />
strFieldDescription = vbNullString<br />
strFieldDescription = fld.Properties("Description")<br />
Debug.Print """" & strFieldDescription & """,";<br />
Debug.Print lngTableRecords & ",";<br />
Debug.Print lngFieldRecords & ",";<br />
Debug.Print lngZLS<br />
<br />
Write #1, tbl.Name, strTableDescription, fld.Name, fldType, strFieldDescription, lngTableRecords, lngFieldRecords, lngZLS<br />
<br />
Next<br />
End If<br />
Next<br />
<br />
Debug.Print "***************** END OF RUN ********************"<br />
Close #1<br />
<br />
Exit_Procedure:<br />
Set fld = Nothing<br />
Set tbl = Nothing<br />
Set db = Nothing<br />
Exit Function<br />
Error_Handler:<br />
If Err.Number = 3270 Then<br />
Resume Next<br />
Else<br />
MsgBox Err.Number & Err.Description<br />
Resume Exit_Procedure<br />
End If<br />
Resume<br />
End Function<br />
</pre><br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Longitudinal follow-up process<br />
** Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T22:16:36Z<p>Fearnp: longitudinal f/u description</p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a Windows security group with permissions to read data on your Caisis SQL Server warehouse<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Splash Screen. This form opens automatically when you open the Export Analysis Utility. It displays the location of the MDB file and the database your tables are linked to, and it provides buttons to launch each of the following features.<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through Metadata tables) The recode feature is exclusively available through the Caisis system admin tool.<br />
* [[Nomograms]]. Links to [http://nomograms.org web nomograms] on [http://www.mskcc.org MSKCC web site]. Also includes functions for calling nomogram library to calculate nomogram predictions for sets of patients in a tables or spreadsheet.<br />
* [[Longitudinal Followup]]. Wizards and partially automated tools to help manage the process of mailouts to patients to find out how they are doing after treatment if they are not coming back regularly to your practice. <br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Longitudinal_FollowupLongitudinal Followup2007-12-20T21:52:05Z<p>Fearnp: New page: Category:Data Management Category:Policies and Procedures == Introduction == The purpose of this project is to continually update our databases with current medical information a...</p>
<hr />
<div>[[Category:Data Management]]<br />
[[Category:Policies and Procedures]]<br />
<br />
== Introduction ==<br />
<br />
The purpose of this project is to continually update our databases with current medical information and vital status on all patients. This is an ongoing process that will be maintained on a daily basis whereby we can account for each patient’s follow-up status in our system. <br />
<br />
The following flow-diagram summarizes the whole process.<br />
<br />
== II. Selecting patients that need follow-up ==<br />
[http://caisis.org Caisis] is a web-based database in the Department of Surgery that stores information on the patients that are seen by the attendings. Each patient has a contact status that can be viewed in Caisis as seen below. Choosing a contact status from this list will bring up a list of patients who are in that category. Each patient’s contact status also can be seen in the Patient Info Tab when clicking on the Patient Data Tab after selecting the patient.<br />
<br />
[[Image:PatientLists_ContactStatus.jpg]]<br />
<br />
[[Image:PatientData_ContactStatus.JPG]]<br />
<br />
'''**NOTE: THIS IS NOT REAL DATA'''<br />
<br />
=== A. Patients that do not need any follow-up: ===<br />
<br />
• '''DoNotContactPerPt''' - The patient or family has requested that they not be contacted.<br />
<br />
• '''DoNotContactPerMD''' - The physician has requested that we not contact the patient (ie: VIPs).<br />
<br />
• '''Current''' - Medical information on the patient is within the last 14 months. Deceased patients are in this category as well, unless their family has specified that they wish to not be contacted. Each night, Caisis takes patients who have no data record within the past 14 months, and places them in the NeedTumReg category, while filtering out patients who are deceased or did not have their primary surgery at your site.<br />
<br />
• '''LTF''' -Lost to Followup. The patient has not responded after 3 tries at mailing a questionnaire to them, or we cannot find updated contact information on them.<br />
<br />
=== B. Patients that require a series of 2 steps to determine if they need a follow-up letter: ===<br />
<br />
• '''NeedTumReg''' - patients who have no data record within the past 14 months, are not deceased, are not in '''DoNotContactPerMD''' or '''DoNotContactPerPt''', the primary surgery was performed at your site, are not '''LTF''', and have not had vital status checked by the tumor registry in the last 60 days.<br />
<br />
• '''NeedSSDI''' - patients who have had tumor registry checked in the last 60 days, but no SSDI checked in the last 60 days.<br />
<br />
==== 1. NeedTumReg ====<br />
<br />
In many cancer centers, the Tumor Registry is responsible for keeping a patient’s vital status updated. This information is stored in your site's electronic medical record (EMR.) Checking the Tumor Registry involves looking through EMR for vital status updates as well as for any recent medical information that is not already entered into Caisis.<br />
<br />
===== a. Look through the list of patient records for vital status and recent medical information. <br />
<br />
===== b. Entering medical records information into Caisis =====<br />
<br />
i. Vital Status-If the patient has died, enter the death date and cause of death under the Patient Info tab, and update the patient’s contact status to “Current”. If there is new information that indicates the patient is still alive, enter that date into the Status as “ALIVE.”<br />
<br />
ii. Medical Information-If recent medical information is found that has not been entered into Caisis, enter in under the appropriate tabs in the database, and re-assess whether or not to update the patient to “Current.”<br />
<br />
===== d. Enter under Actions tab, “TumRegChecked,” =====<br />
<br />
==== 2. NeedSSDI ====<br />
<br />
a. To access the SSDI, go to click on the links to the [http://ssdi.rootsweb.com/ SSDI]. If you haven’t done an SSDI before, you can click on the link to SSDI tips. A general search involves using the patient’s last name, social security number, and date of birth as search references. If the patient has died, enter the death date and cause of death under the Patient Info tab in Caisis.<br />
<br />
b. Enter into the Actions tab, “SSDI_Checked.”<br />
<br />
3. Notifying the Tumor Registry if a patient has died<br />
<br />
=== NeedLetter1, 2, or 3 ===<br />
<br />
NeedLetter1-patients who have had vital status checked by the tumor registry and SSDI in the last 30 days, whose last item in the chronological list is > 14 months. Once the action SSDI_Checked is entered, Caisis automatically updates the patient’s contact status to NeedLetter1. Three attempts are made at contacting the patient. If the patient hasn’t responded in 30 days (indicated by having no action entered), and the and tumor registry or SSDI hasn’t been checked again, the contact status is automatically updated to NeedTumReg (follow same instructions as before), then NeedSSDI (follow same instructions as before). Once their vital status has been checked, their contact status should be changed to NeedLetter2. The same events will occur if the patient still hasn’t responded after 30 days (NeedTumReg, then NeedSSDI, then NeedLetter3). Please do not send out letters to patients during the holiday season.<br />
<br />
==== Preparing mail out material: ====<br />
<br />
**Print out cover letter, follow-up questionnaire, and authorization and mailing labels for each patient using Microsoft Access. Explain wizard<br />
<br />
** The cover letter should have the current physician’s letterhead and correct contact information.<br />
<br />
**Include a business reply envelope with the letter and questionnaire. <br />
<br />
**All items should be stuffed in an envelope with the institutional logo.<br />
(See the Ordering Supplies section for how to order any of these items)<br />
<br />
1. The envelopes should be tied together in bunches and taken to the mailroom with the appropriate cost center attached to the bunch. If necessary, contact the department administrator for the appropriate cost center.<br />
<br />
2. Correspondence to patients residing outside of US should be by UPS to expedite correspondence<br />
<br />
3. Inform Physician Office Assistants which patients have been sent letters and questionnaires. Inform them who they should refer any calls to about this. In addition, give them a copy of the questionnaire and letter.<br />
<br />
4. Any new questionnaires and cover letters must be approved by the responsible physician before being sent out.<br />
<br />
IV. Receiving letters and questionnaires<br />
<br />
Open LetterReceived wizard.<br />
Page 1-Lists number of letters received, returned to sender, and pending.<br />
Page 2-Instructions for processing the letters as they are received<br />
Page 3-Instructions for entering data from the questionnaire<br />
Page 4-Instructions/criteria for changing the patient’s contact status<br />
NeedMD_Contact<br />
<br />
1) Call the physician’s office and explain that you will be sending an authorization to get medical records for a patient. Ask if they prefer to fax the authorization or send it in the mail. If they prefer sending it by mail, send cover letter to physician along with patient’s signed consent. Alternatively, if a fellow or medical student calls the doctors office, they can get the information over the phone. Copies of the medical records are still needed.<br />
2) Once this is done, enter the action MD_Contacted in the actions tab.<br />
3) Once the medical records are received, enter the data, or change the patient’s contact status to NeedDataEntry, if the data can’t be entered right away.<br />
<br />
==== NeedMD_ToCallPt ====<br />
If the patient hasn’t responded after sending three letters, change the patient’s contact status to '''NeedMD_ToCallPt'''-patients who have been in the category '''Letter3_Sent''' and have had no action entered for 6 weeks. MDs (mainly research fellows) will then call the patient to collect a history, physician contact info, and get authorization.<br />
<br />
The following is a list of pertinent questions to ask a patient if a fellow or medical student calls the patient. These can also be used when they call a patient’s doctor for records:<br />
## Other treatments since RP?<br />
## Have you had any problems with urination since the surgery (difficulty passing urine; urinary retention) Have you had any treatments for urethral strictures?<br />
## Have you had any other '''procedures''' for prostate cancer-related problems/urinary dysfunction?<br />
## Do you wear protective pads for urine loss/incontinence? How many pads do you wear during the day? How many pads do you wear at night? Have you had any treatment for incontinence (AUS)?<br />
## Do you have any spontaneous erections sufficient for intercourse? Are you capable of intercourse without erectile aids? If you use aids, which aids are you using? If you take Viagra, which dose are you using? Do you use injection therapy or urethral suppositories? Have you had any surgical treatment for impotence (prosthesis)?<br />
## Follow up lab reports since last records at your site? (total PSA, testosterone, free PSA)<br />
## Are you being followed by a physician; may we have your physician’s address and mail you a permission form to request your records from your physician?<br />
## Would you like to be mailed a QOL questionnaire that will ask questions about your general state of health and urologic function since your surgery?<br />
<br />
# After calling the patient, enter the action '''Patient_WasCalled''' in the actions tab.<br />
# Enter updated information in the database.<br />
# Change the patient’s contact status to<br />
** '''Current''' if you do not need to contact their physician, and have up to date information.<br />
** '''NeedPtAuthorization''' if you need to send them a Release of Information form to sign.<br />
** '''NeedMD_Contact''' if you need to contact their physician.<br />
<br />
==== NeedPtContactInfo ====<br />
If a letter gets returned undeliverable, and there is no forwarding address, enter an action, '''ReturnedToSender'''. Then change the patient’s contact status to '''NeedPtContactInfo'''. The following steps can be taken to obtain their contact info. Enter an action after each step is taken.<br />
<br />
# Call the numbers listed in the database or DMS (patient’s numbers, emergency contact numbers).<br />
# Call information (411) to check to see if there are any listings in their area code.<br />
# Try their physicians listed to see if they have updated contact information.<br />
# Search the internet. <br />
# Try your site's Tumor registry to see if they can help. They can give you the last vital status they have for a patient or the last contact information for the patient. <br />
# If you obtain updated contact information through any of these steps, update Caisis, enter the action '''AddressUpdated''', and then change the patient’s contact status back to '''NeedLetter1, 2, or 3''', depending on where they are in the process.<br />
# If no contact information is obtained after all these steps, update the patient’s contact in the database to '''LTF''' “Lost to follow-up”.<br />
<br />
==== Ordering Supplies ====<br />
# Order institutional letterhead and envelopes.<br />
# Business Reply envelopes are ordered as follows:<br />
<br />
== Caisis Demographics Contact Status ==<br />
<br />
{|<br />
! PtContactStatus || Drop downActionItem Drop down<br />
|-<br />
| Current || CaseReviewed<br />
|-<br />
| DoNotContactPerMD || <br />
|-<br />
|DoNotContactPerPt || DataReceived<br />
|-<br />
| Letter1_Sent || &nbsp;<br />
|-<br />
| Letter2_Sent || Letter2_Sent<br />
|-<br />
| Letter3_Sent || Letter3_Sent<br />
|-<br />
| LostToFollowup || PtWebSearched<br />
|-<br />
| MD_Contacted || MD_Contacted<br />
|-<br />
| NeedDataEntry || DataEntered <br />
|-<br />
| NeedLetter1 || Letter1_Sent<br />
|-<br />
| NeedLetter2 || SentToCDB<br />
|-<br />
| NeedLetter3 || SentToEMR<br />
|-<br />
| NeedMD_Contact || VitalStatusChecked<br />
|-<br />
| NeedMD_ToCall || PtWasCalled<br />
|-<br />
| NeedPtAuthorization || &nbsp;<br />
|-<br />
| NeedPtContactInfo || PtContactInfoUpdated<br />
|-<br />
| NeedVitalStatus || LetterReturnedToSender<br />
|}<br />
<br />
==== Actions table Trigger ====<br />
Whenever a user edits or inserts a record in the Actions table (Immediate Response- Should remain simple or as simple as possible) <br />
<br />
<code><br />
UPDATE Patients<br />
SET PtContactStatus = CASE WHEN i.ActionItem = 'VitalStatusChecked' AND PtContactStatus = 'NeedVitalStatus' THEN 'Current'<br />
WHEN i.ActionItem = 'Letter1_Sent' AND PtContactStatus = 'NeedLetter1' THEN 'Letter1_Sent'<br />
WHEN i.ActionItem = 'Letter2_Sent' AND PtContactStatus = 'NeedLetter2' THEN 'Letter2_Sent'<br />
WHEN i.ActionItem = 'Letter3_Sent' AND PtContactStatus = 'NeedLetter3' THEN 'Letter3_Sent'<br />
WHEN i.ActionItem = 'LetterReturnedToSender' AND PtContactStatus LIKE 'Letter[1-3]%Sent' THEN 'NeedPtContactInfo' WHEN i.ActionItem = 'MD_Contacted' AND PtContactStatus = 'NeedMD_Contact' THEN 'MD_Contacted' WHEN i.ActionItem = 'PtWasCalled' AND PtContactStatus = 'NeedMD_ToCallPt' THEN 'Current' WHEN i.ActionItem = 'DataReceived' AND PtContactStatus IN ('Letter1_Sent','Letter2_Sent','Letter3_Sent','MD_Contacted') THEN 'NeedDataEntry' WHEN i.ActionItem = 'DataReceived' AND PtContactStatus = 'NeedPtAuthorization' THEN 'NeedMD_Contact' WHEN i.ActionItem = 'DataEntered' AND PtContactStatus = 'NeedDataEntry' THEN 'Current'<br />
WHEN i.ActionItem = 'PtContactInfoUpdated' AND PtContactStatus = 'NeedPtContactInfo' THEN 'Current' END<br />
FROM Patients INNER JOIN Inserted i ON Patients.PatientId = i.PatientId WHERE PtContactStatus <> CASE<br />
WHEN i.ActionItem = 'VitalStatusChecked' AND PtContactStatus = 'NeedVitalStatus' THEN 'Current'<br />
WHEN i.ActionItem = 'Letter1_Sent' AND PtContactStatus = 'NeedLetter1' THEN 'Letter1_Sent'<br />
WHEN i.ActionItem = 'Letter2_Sent' AND PtContactStatus = 'NeedLetter2' THEN 'Letter2_Sent'<br />
WHEN i.ActionItem = 'Letter3_Sent' AND PtContactStatus = 'NeedLetter3' THEN 'Letter3_Sent'<br />
WHEN i.ActionItem = 'LetterReturnedToSender' AND PtContactStatus LIKE 'Letter[1-3]%Sent' THEN 'NeedPtContactInfo'<br />
WHEN i.ActionItem = 'MD_Contacted' AND PtContactStatus = 'NeedMD_Contact' THEN 'MD_Contacted' WHEN i.ActionItem = 'PtWasCalled' AND PtContactStatus = 'NeedMD_ToCallPt' THEN 'Current' WHEN i.ActionItem = 'DataReceived' AND PtContactStatus IN ('Letter1_Sent','Letter2_Sent','Letter3_Sent','MD_Contacted') THEN 'NeedDataEntry' WHEN i.ActionItem = 'DataReceived' AND PtContactStatus = 'NeedPtAuthorization' THEN 'NeedMD_Contact' WHEN i.ActionItem = 'DataEntered' AND PtContactStatus = 'NeedDataEntry' THEN 'Current'<br />
WHEN i.ActionItem = 'PtContactInfoUpdated' AND PtContactStatus = 'NeedPtContactInfo' THEN 'Current' END<br />
</code><br />
<br />
Nightly Job(Delayed Response, Can be complex)<br />
<br />
<code><br />
CREATE PROCEDURE dbo.spFollowupUpdatePtContactStatus<br />
AS<br />
BEGIN TRANSACTION<br />
--Change to current if null<br />
UPDATE Patients<br />
SET PtContactStatus = 'Current'<br />
WHERE PtContactStatus = '0' OR PtContactStatus IS NULL<br />
/*<br />
If they are Current and (no data in the last 14 months or dead)<br />
and (vital status has not been checked in the last 60 days) then<br />
change to NeedVitalStatus<br />
*/<br />
UPDATE Patients<br />
SET PtContactStatus = 'NeedVitalStatus' FROM Patients LEFT OUTER JOIN FJ_CurrentDataView ON Patients.PatientId = FJ_CurrentDataView.PatientId<br />
LEFT OUTER JOIN FJ_VitalStatusCheckedView ON Patients.PatientId = FJ_VitalStatusCheckedView.PatientId<br />
WHERE PtContactStatus = 'Current' AND<br />
FJ_CurrentDataView.PatientId IS NULL AND FJ_VitalStatusCheckedView.PatientId IS NULL<br />
/*<br />
If they are Current and (no data in the last 14 months or dead)<br />
and (vital status has been checked in the last 60 days) then<br />
change to next letter/contact, If the last LetterX_Sent was more<br />
than 90 days ago then move to NeedLetter1 so can restart the process */<br />
UPDATE Patients<br />
SET PtContactStatus =CASE<br />
WHEN LastLetterSent IS NULL THEN 'NeedLetter1' WHEN LastLetterSent LIKE 'Letter1%Sent' THEN 'NeedLetter2'<br />
WHEN LastLetterSent LIKE 'Letter2%Sent' THEN 'NeedLetter3'<br />
WHEN LastLetterSent LIKE 'Letter3%Sent' THEN 'NeedPtContactInfo'<br />
END FROM Patients LEFT OUTER JOIN FJ_CurrentDataView ON Patients.PatientId = FJ_CurrentDataView.PatientId<br />
INNER JOIN FJ_VitalStatusCheckedView ON Patients.PatientId = FJ_VitalStatusCheckedView.PatientId<br />
LEFT OUTER JOIN FJ_LastLetterSentView ON Patients.PatientId = FJ_LastLetterSentView.PatientId<br />
WHERE PtContactStatus = 'Current' AND<br />
FJ_CurrentDataView.PatientId IS NULL<br />
/*<br />
If they are LetterX_Sent or NeedLetterX or NeedVitalStatus and<br />
(no LetterX_Sent in the last 90 days) and (have data in the last 14 months or dead) change to Current */<br />
UPDATE Patients<br />
SET PtContactStatus = 'Current'<br />
FROM Patients INNER JOIN FJ_CurrentDataView ON Patients.PatientId = FJ_CurrentDataView.PatientId<br />
LEFT OUTER JOIN FJ_RecentLetterSentView ON Patients.PatientId = FJ_RecentLetterSentView.PatientId<br />
WHERE (PtContactStatus LIKE 'Letter[1-3]%Sent' OR<br />
PtContactStatus LIKE 'NeedLetter[1-3]' OR<br />
PtContactStatus = 'NeedVitalStatus') AND<br />
FJ_RecentLetterSentView.PatientId IS NULL<br />
/*<br />
If they are LetterX_Sent only and (no LetterX_Sent in the last 90 days) and (no data in the last 14 months or dead) and<br />
(vital status has not been checked in the last 60 days) change to NeedVitalStatus<br />
*/<br />
UPDATE Patients<br />
SET PtContactStatus = 'NeedVitalStatus' FROM Patients LEFT OUTER JOIN FJ_CurrentDataView ON Patients.PatientId = FJ_CurrentDataView.PatientId<br />
LEFT OUTER JOIN FJ_RecentLetterSentView ON Patients.PatientId = FJ_RecentLetterSentView.PatientId<br />
LEFT OUTER JOIN FJ_VitalStatusCheckedView ON Patients.PatientId = FJ_VitalStatusCheckedView.PatientId<br />
WHERE PtContactStatus LIKE 'Letter[1-3]%Sent' AND<br />
FJ_CurrentDataView.PatientId IS NULL AND FJ_RecentLetterSentView.PatientId IS NULL AND<br />
FJ_VitalStatusCheckedView.PatientId IS NULL<br />
/*<br />
If they are LetterX_Sent and (no LetterX_Sent in the last 90 days) and (no data in the last 14 months or dead) and<br />
(vital status has been checked in the last 60 days) then change to next letter/contact */<br />
UPDATE Patients<br />
SET PtContactStatus =CASE<br />
WHEN PtContactStatus LIKE 'Letter1%Sent' THEN 'NeedLetter2'<br />
WHEN PtContactStatus LIKE 'Letter2%Sent' THEN 'NeedLetter3'<br />
WHEN PtContactStatus LIKE 'Letter3%Sent' THEN 'NeedPtContactInfo' END FROM Patients LEFT OUTER JOIN FJ_CurrentDataView ON Patients.PatientId = FJ_CurrentDataView.PatientId<br />
LEFT OUTER JOIN FJ_RecentLetterSentView ON Patients.PatientId = FJ_RecentLetterSentView.PatientId<br />
INNER JOIN FJ_VitalStatusCheckedView ON Patients.PatientId = FJ_VitalStatusCheckedView.PatientId<br />
WHERE PtContactStatus LIKE 'Letter[1-3]%Sent' AND<br />
FJ_CurrentDataView.PatientId IS NULL AND FJ_RecentLetterSentView.PatientId IS NULL /*<br />
If patient is dead change ContactStatus to Current but only if ContactStatus is not already Current and ContactStatus NOT LIKE '%DoNotContact%'<br />
*/<br />
UPDATE Patients<br />
SET PtContactStatus = 'Current'<br />
FROM Patients WHERE (PtContactStatus <> 'Current' AND PtContactStatus NOT LIKE '%DoNotContact%') AND<br />
(PtDeathDateText IS NOT NULL)<br />
COMMIT TRANSACTION<br />
GO</code><br />
<br />
<br />
Queries used by Nightly Job<br />
<br />
<code><br />
CREATE VIEW dbo.FJ_CurrentDataView<br />
AS<br />
--Not all tables are represented here Includes deceased patients SELECT a.PatientId AS PatientId<br />
FROM<br />
(<br />
SELECT BxDate AS SortDate, 'Biopsies' AS TableName, PatientId<br />
FROM Biopsies WHERE BxDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT BxDate AS SortDate, 'BiopsiesProstate' AS TableName, PatientId<br />
FROM BiopsiesProstate WHERE BxDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT ClinStageDate, 'ClinicalStages', PatientId<br />
FROM ClinicalStages<br />
WHERE ClinStageDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT DxDate, 'Diagnostics', PatientId<br />
FROM Diagnostics<br />
WHERE DxDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT LabDate, 'LabTests', PatientId<br />
FROM LabTests WHERE LabDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT MedTxDate, 'MedicalTherapy', PatientId<br />
FROM MedicalTherapy WHERE MedTxDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT OpDate, 'Procedures', PatientId<br />
FROM Procedures<br />
WHERE OpDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT SurgDate, 'Surgery', PatientId<br />
FROM Surgeries<br />
WHERE SurgDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT EndoDate, 'Endoscopy', PatientId<br />
FROM ProcEndoscopies<br />
WHERE EndoDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT CytoDate, 'Cytology', PatientId<br />
FROM Cytologies<br />
WHERE CytoDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT BrachyDate, 'BrachyTherapy', PatientId<br />
FROM BrachyTherapy WHERE BrachyDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT RadTxDate, 'RadiationTherapy', PatientId<br />
FROM RadiationTherapy WHERE RadTxDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT StatusDate, 'Status', PatientId<br />
FROM Status<br />
WHERE StatusDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT PtProtocolStatusDate, 'Protocols', PatientId<br />
FROM PatientProtocols INNER JOIN PatientProtocolStatus ON PatientProtocolStatus.PatientProtocolId = PatientProtocols.PatientProtocolId<br />
WHERE PtProtocolStatusDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT EncDate, 'Encounters', PatientId<br />
FROM Encounters WHERE EncDate > DATEADD(m,-14,GETDATE())<br />
UNION<br />
SELECT SurveyDate, 'Surveys', PatientId<br />
FROM Surveys<br />
WHERE SurveyDate > DATEADD(m,-14,GETDATE())<br />
--Add in deceased patients classified as having a DeathDateText<br />
UNION<br />
SELECT PtDeathDate, 'Patients',PatientId<br />
FROM Patients<br />
WHERE (PtDeathDateText IS NOT NULL)<br />
) AS a<br />
GROUP BY a.PatientId<br />
CREATE VIEW dbo.FJ_VitalStatusCheckedView<br />
AS<br />
SELECT DISTINCT PatientId<br />
FROM Actions<br />
WHERE ActionItem = 'VitalStatusChecked' AND<br />
ActionDate >= DATEADD(d, - 60, GETDATE())<br />
CREATE VIEW dbo.FJ_LastLetterSentView<br />
AS<br />
SELECT Actions.PatientId AS PatientId, ActionItem AS LastLetterSent<br />
FROM<br />
(<br />
SELECT MAX(ActionDate) AS LastLetterDate, PatientId<br />
FROM Actions<br />
WHERE (ActionItem LIKE 'Letter[1-3]%Sent') AND ActionDate >= DATEADD(d, - 90, GETDATE())<br />
GROUP BY PatientId<br />
) AS a INNER JOIN Actions ON a.PatientId = Actions.PatientId AND<br />
a.LastLetterDate = Actions.ActionDate<br />
WHERE (ActionItem LIKE 'Letter[1-3]%Sent')<br />
CREATE VIEW dbo.FJ_RecentLetterSentView<br />
AS<br />
SELECT DISTINCT PatientId<br />
FROM Actions<br />
WHERE ActionItem LIKE 'Letter[1-3]%Sent' AND<br />
ActionDate >= DATEADD(d, - 90, GETDATE())</code><br />
<br />
[[Image:FollowupDiagram.JPG]]</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T20:48:39Z<p>Fearnp: /* Features */</p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a Windows security group with permissions to read data on your Caisis SQL Server warehouse<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Splash Screen. This form opens automatically when you open the Export Analysis Utility. It displays the location of the MDB file and the database your tables are linked to, and it provides buttons to launch each of the following features.<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through Metadata tables) The recode feature is exclusively available through the Caisis system admin tool.<br />
* [[Nomograms]]. Links to [http://nomograms.org web nomograms] on [http://www.mskcc.org MSKCC web site]. Also includes functions for calling nomogram library to calculate nomogram predictions for sets of patients in a tables or spreadsheet.<br />
* [[Longitudinal Followup]]<br />
<br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=NomogramsNomograms2007-12-20T20:30:35Z<p>Fearnp: </p>
<hr />
<div>Download the following 3 files:<br />
*Caisis.Nomogram.dll<br />
*Caisis.Nomogram.reg<br />
*Caisis.Nomogram.tlb<br />
<br />
<br />
# Double-click the Caisis.Nomogram.reg file to register this DLL<br />
# Open a VBA Module in the Export Analysis Utility<br />
# Click Tools, References, Browse and open the Caisis.Nomogram.tlb file<br />
<br />
<code><br />
Public Function TestMe()<br />
Dim score As Double<br />
Dim prp As Caisis_Nomogram.ProstatePreRPNew<br />
Set prp = New Caisis_Nomogram.ProstatePreRPNew<br />
With prp<br />
.NAHormones = False<br />
.NAXRT = False<br />
.psa = 2#<br />
.TStage = "T2a"<br />
.PrimaryGleason = 2<br />
.SecondaryGleason = 3<br />
.PositiveCores = 10<br />
.NegativeCores = 3<br />
.PredMonths = 120<br />
score = .Calculate<br />
End With<br />
TestMe = score<br />
End Function<br />
</code><br />
<br />
To unregister this DLL if you make a mistake...<br />
Go to Start, Run, cmd<br />
Bug Brandon to fix this!</div>Fearnphttp://caisis.org/wiki/index.php?title=NomogramsNomograms2007-12-20T20:21:16Z<p>Fearnp: </p>
<hr />
<div>Download the following 3 files:<br />
*Caisis.Nomogram.dll<br />
*Caisis.Nomogram.reg<br />
*Caisis.Nomogram.tlb<br />
<br />
<br />
# Double-click the Caisis.Nomogram.reg file to register this DLL<br />
# Open a VBA Module in the Export Analysis Utility<br />
# Click Tools, References, Browse and open the Caisis.Nomogram.tlb file<br />
<br />
<code><br />
Public Function TestMe()<br />
Dim score As Double<br />
Dim prp As Caisis_Nomogram.ProstatePreRPNew<br />
Set prp = New Caisis_Nomogram.ProstatePreRPNew<br />
With prp<br />
.NAHormones = False<br />
.NAXRT = False<br />
.psa = 2#<br />
.TStage = "T2a"<br />
.PrimaryGleason = 2<br />
.SecondaryGleason = 3<br />
.PositiveCores = 10<br />
.NegativeCores = 3<br />
.PredMonths = 120<br />
score = .Calculate<br />
End With<br />
TestMe = score<br />
End Function<br />
</code><br />
<br />
To unregister this DLL if you make a mistake...</div>Fearnphttp://caisis.org/wiki/index.php?title=NomogramsNomograms2007-12-20T20:10:32Z<p>Fearnp: </p>
<hr />
<div>Download the following 3 files:<br />
*Caisis.Nomogram.dll<br />
*Caisis.Nomogram.reg<br />
*Caisis.Nomogram.tlb<br />
<br />
<br />
# Double-click the Caisis.Nomogram.reg file to register this DLL<br />
# Open a VBA Module in the Export Analysis Utility<br />
# Click Tools, References, Browse and open the Caisis.Nomogram.tlb file<br />
<br />
<code><br />
Public Function TestMe()<br />
<br />
Dim score As Double<br />
Dim prp As ProstatePreRPNew<br />
<br />
Set prp = New ProstatePreRPNew<br />
<br />
prp.NAHormones = False<br />
prp.NAXRT = False<br />
prp.psa = 2#<br />
prp.TStage = "T2a"<br />
prp.PrimaryGleason = 2<br />
prp.SecondaryGleason = 3<br />
prp.PositiveCores = 10<br />
prp.NegativeCores = 3<br />
prp.PredMonths = 120<br />
<br />
score = prp.Calculate<br />
<br />
TestMe = score<br />
<br />
End Function<br />
</code></div>Fearnphttp://caisis.org/wiki/index.php?title=NomogramsNomograms2007-12-20T20:02:28Z<p>Fearnp: New page: Download the following 3 files: *Caisis.Nomogram.dll *Caisis.Nomogram.reg *Caisis.Nomogram.tlb # Open a Module in the Export Analysis Utility: # Click Tools, References, Browse and open t...</p>
<hr />
<div>Download the following 3 files:<br />
*Caisis.Nomogram.dll<br />
*Caisis.Nomogram.reg<br />
*Caisis.Nomogram.tlb<br />
<br />
# Open a Module in the Export Analysis Utility:<br />
# Click Tools, References, Browse and open the Caisis.Nomogram.tlb file<br />
<br />
<code><br />
Public Function TestMe()<br />
<br />
Dim score As Double<br />
Dim prp As ProstatePreRPNew<br />
<br />
Set prp = New ProstatePreRPNew<br />
<br />
prp.NAHormones = False<br />
prp.NAXRT = False<br />
prp.psa = 2#<br />
prp.TStage = "T2a"<br />
prp.PrimaryGleason = 2<br />
prp.SecondaryGleason = 3<br />
prp.PositiveCores = 10<br />
prp.NegativeCores = 3<br />
prp.PredMonths = 120<br />
<br />
score = prp.Calculate<br />
<br />
TestMe = score<br />
<br />
End Function<br />
</code></div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T19:36:49Z<p>Fearnp: /* Features */</p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a Windows security group with permissions to read data on your Caisis SQL Server warehouse<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Splash Screen. This form opens automatically when you open the Export Analysis Utility. It displays the location of the MDB file and the database your tables are linked to, and it provides buttons to launch each of the following features.<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through Metadata tables) The recode feature is exclusively available through the Caisis system admin tool.<br />
* Nomograms. Links to [http://nomograms.org web nomograms] on [http://www.mskcc.org MSKCC web site]. Also includes functions for calling nomogram library to calculate nomogram predictions for sets of patients in a tables or spreadsheet.<br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T19:07:00Z<p>Fearnp: </p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a Windows security group with permissions to read data on your Caisis SQL Server warehouse<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through FieldMetadata table) The recode feature is exclusively available through the Caisis system admin tool.<br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T16:01:10Z<p>Fearnp: data integrity tool feature</p>
<hr />
<div>Translations: [[Export_Analysis_Utility_it|italiano]]<br />
<br />
<br />
The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Data Integrity tool. This form is also available in Caisis system admin (Administer the Syste, System Config, Data Integrity). It allows users to browse contents of every table and every field in the MDB file or the linked SQL Server tables in the warehouse. It also allow the user to view lookup codes associated with each field in the database (through FieldMetadata table) The recode feature is exclusively available through the Caisis system admin tool.<br />
<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T15:23:51Z<p>Fearnp: data integrity tool next steps</p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Data Integrity Tool - compare with colorectal database version<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T15:17:09Z<p>Fearnp: integrate follow-up database</p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* Integrate all differences in follow-up process MDB file (UroShared\_CaisisDB\follow up project\CaisisDB.mdb) into Export Analysis Utility<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T15:11:46Z<p>Fearnp: test linked tables</p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
* With fresh install of Caisis 4.0 from caisis.org download, test setup to be sure no linked tables or steps are MSK-specific.<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T15:06:49Z<p>Fearnp: /* Setup Instructions */</p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
* Create a warehouse copy of Caisis on SQL Server<br />
* Create a secure network folder with read/write permissions for ONLY the few people who will be gatekeepers for the data. These users will be responsible for ensuring that all data requests meet IRB and privacy board requirements and will work with users to generate datasets.<br />
* Place the Microsoft Access file (MDB file) for the Export Analysis Utility in this secure network folder.<br />
* From Export Analysis Utility, open the Linked Table Manager (Tools, Database Utilities, Linked Table Manager) to link all tables to the warehouse copy of Caisis on SQL Server.<br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T14:55:22Z<p>Fearnp: </p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Nomograms, a way to run nomograms on sets of patients<br />
* Reports, quality assurance, operations and common research reports<br />
<br />
== Setup Instructions ==<br />
<br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Export_Analysis_UtilityExport Analysis Utility2007-12-20T14:44:01Z<p>Fearnp: New page: The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including. * Algorithms for generating analysis dat...</p>
<hr />
<div>The Export Analysis Utility is a Microsoft Access 2000 (convert to 2003 format?) database that contains many add-on features for Caisis, including.<br />
* Algorithms for generating analysis datasets for prostate cancer research<br />
* Longitudinal follow-up process wizard for semi-automated mailouts<br />
* Data Integrity Tool, a simple browser for looking into every table and field in the database<br />
* Reports, <br />
<br />
== Features ==<br />
* Tables<br />
** DistributableObjects. A list of tables, queries, forms, etc that can be publically distributed. Used when preparing a copy of the Export Analysis Utility to post here on Caisis.org. Does not include user-defined or temporary tables, queries and reports.<br />
<br />
== TO DO ==<br />
This is a list of tasks we need to do to prepare the most current version of the Export Analysis Utility for public distribution<br />
<br />
*Remove Nomograms code and provide DLL and instructions for using library<br />
** LifeExpectancies<br />
** NomogramScores<br />
** PartinScores_2001<br />
<br />
*Remove Segments code and replace with DLL and instructions?<br />
<br />
*Create feature to export and import algorithm settings so that different users and sites can reproduce analysis datasets using same settings on their own Caisis datasets.<br />
<br />
*Create easy to use feature to export and import user defined queries and reports</div>Fearnphttp://caisis.org/wiki/index.php?title=Main_PageMain Page2007-12-20T14:32:40Z<p>Fearnp: add export analysis utility</p>
<hr />
<div>Welcome to the Caisis Wiki. We welcome contributions from the Caisis community. <br />
<br />
10.25.2007 Caisis 4.0 is now available! <br />
<br />
Previous Caisis documents page is [http://caisis.org/documentation.aspx here].<br />
<br />
== Technical & Administrator Information ==<br />
<br />
* Caisis 4.0 [[Installation]] documentation.<br />
* Caisis 4.0 [[Release Notes]].<br />
* [[Frequently Asked Questions]]<br />
* Common Customization Tasks<br />
** Creating [[Eforms]] in Caisis<br />
** [[Adding Tables to Caisis]]<br />
* Caisis 4.0 [[Export Analysis Utility]]<br />
<br />
== User Information ==<br />
<br />
<br />
== Presentations ==<br />
* 11.2007 Presentation at Indian Association for Medical Informatic [http://openmed.nic.in/2490/]<br />
* 10.2007 Presentation (with audio) from APIII, Pittsburg[http://apiii.upmc.edu/breakout/archive/2007/Fearn/APIII_Caisis4_DataSupplyChainx.ppt]<br />
* 11.2006 Presentation from Caisis Face-To-Face Meeting in New York[http://caisis.org/downloads/CaisisPresentation2006.ppt]</div>Fearnphttp://caisis.org/wiki/index.php?title=Main_PageMain Page2007-12-18T14:31:21Z<p>Fearnp: add link to previous documents page and links to presentations</p>
<hr />
<div>Welcome to the Caisis Wiki. We welcome contributions from the Caisis community. <br />
<br />
10.25.2007 Caisis 4.0 is now available! <br />
<br />
Previous Caisis documents page is [http://caisis.org/documentation.aspx here].<br />
<br />
== Technical & Administrator Information ==<br />
<br />
* Caisis 4.0 [[Installation]] documentation.<br />
* Caisis 4.0 [[Release Notes]].<br />
* [[Frequently Asked Questions]]<br />
* Common Customization Tasks<br />
** Creating [[Eforms]] in Caisis<br />
** [[Adding Tables to Caisis]]<br />
<br />
== User Information ==<br />
<br />
<br />
== Presentations ==<br />
* 11.2007 Presentation at Indian Association for Medical Informatic [http://openmed.nic.in/2490/]<br />
* 10.2007 Presentation (with audio) from APIII, Pittsburg[http://apiii.upmc.edu/breakout/archive/2007/Fearn/APIII_Caisis4_DataSupplyChainx.ppt]<br />
* 11.2006 Presentation from Caisis Face-To-Face Meeting in New York[http://caisis.org/downloads/CaisisPresentation2006.ppt]</div>Fearnp