April 2014
Copyright© 2014 University of Washington
Created and published by the National Alzheimer’s Coordinating Center (Walter A. Kukull, PhD, Director). All rights reserved.
This publication was funded by the National Institutes of Health through the National Institute on Aging (Cooperative Agreement U01 AG016976).
Requirements. . . 2
Contact us . . . 2
The software . . . 2
Backups . . . 2
Security . . . 2
What CSF data should be submitted . . . 2
Methods of submitting data . . . 2
Database storage . . . 3
Steps involved in submitting via file upload. . . 3
Steps involved in submitting via web data entry . . . 3
Disclaimer . . . 3
General operation of the CSF Data Submission System . . . 4
Accessing the system . . . 4
Navigating the system . . . 4
Upload and pre-process files. . . 5
Uploading . . . 5
Pre-processing . . . 6
Web data entry . . . 7
Editing an ID . . . 8
Error check . . . 11
Finalize data . . . 13
Reports. . . 15
Download data . . . 16
Documentation . . . 17
Introduction
Using NACC’s CSF Data Submission System, Centers can submit CSF data for subjects in the Uniform Data Set (UDS) or Minimum Data Set (MDS). The values can be uploaded or entered directly.
Requirements
The following are recommended for use with the CSF Submission System:
• A hard-wired internet connection. A modem can be used instead, but it may be slow and tedious.
• Browser: Microsoft Explorer (version 8.0 or later) or Firefox (version 1.0 or later). Other browsers and versions will work, but the displays may be difficult to use.
• Screen size of at least 17 inches. Smaller sizes will work but will be more difficult to use.
The software
The data are stored in Oracle 10g, with SAS 9.3 used as the front-end software;
most of NACC’s programs for web data entry, file uploading, error checking, and data access are therefore written in SAS. An automated data element dictionary has been written into the database, as well as version control and error checking.
Backups
All data are backed up every night, and monthly backups are archived. Backups are stored offsite in case of disaster.
Security
Only authorized personnel have access to the system. Users must be approved by their Center to obtain a user name and password from NACC to upload data. Users have access only to data from their own Center, not data from other ADCs. All data transmitted across the Internet is encrypted with at least a 256-bit encryption suite.
What CSF data should be submitted
NACC would like each Center to submit all CSF values held at the Center for subjects in the UDS. This information is used to further research by investigators using the NACC database.
Methods of submitting data
NACC currently accepts form data from Centers in two ways:
• direct data entry through the NACC website
• uploading through the NACC website Contact us
If you have questions or comments or would like to obtain the access needed to submit CSF data, please contact NACC:
email [email protected] phone (206) 543-8637
Uploaded files must be in one of the following formats:
• the specified ASCII fixed-field format *
• comma-delimited
• SAS version 7, 8, or 9
• tab-delimited
*(see the Data Templates and Quick Reference Coding Guide in the DoCumenTaTion section of the CSF Submission System) Database storage
The database for forms is divided into three areas:
• Working Database: holds data when it is first uploaded or entered; may contain errors
• Current Database: holds error-free data
• Frozen Database: holds archived copies of the current database, used for research and reports
Data are stored as they are uploaded (i.e., not error checked).
Steps involved in submitting data via file upload
Following is an outline of the process; for more detailed instructions, see the section “Upload and pre-process files” on page 5.
1. Create file from Center’s local database using NACC’s CSF Data Template for guidance.
2. Upload the file to the NACC website using the Upload Files process.
3. Correct the file if prompted to do so during pre-processing; repeat until accurate.
4. Using the error CheCks process, execute Form CheCk and correct any errors. Forms may be corrected using web data entry, or you may correct them within your local database and re-upload the files to NACC.
5. Re-run error checks until all forms are accurate.
6. Using the Finalize process, execute Finalize data to move the IDs to the current database. If an ID has an error, correct the error and then re- finalize.
Steps involved in submitting data via web data entry
Following is an outline of the process; for more detailed instructions, see the section “Web data entry” on page 7.
• Select Web data entry
• Select edit id
• Select the ID to edit
• Input the requested data and click sUbmit
Disclaimer
Because all websites are dynamic by nature, the sample screens provided in this manual may not be an exact representation of the most current page on the NACC website itself. Although details may change, the sample screens still provide the user with a visual companion to the written instructions, as well as navigational orientation.
General operation of the CSF Data Submission System
Accessing the system
• Go to https://www.alz.washington.edu
• Click adCs
• Click data Cores / data managers (on left side of page)
• Click genetiC data
• Enter your user name and password
• Find and select the name of your Center
• Click CsF data sUbmission system
Navigating the system
The first page of the system will be shown (Figure 1):
FIGURE 1 Submission system
main page
This menu provides access to the entire CSF Submission System. The buttons down the left side of the page (Upload and Pre-Process Files, Web Data Entry, etc.) represent the major sections of the CSF Submission System.
The buttons across the top of the page link to other areas of the NACC website.
Upload and pre-process files
Uploading
To upload data files from your local computer to the NACC database, click Upload and pre-proCess Files, then biomarker data. The following page will be displayed (Figure 2):
FIGURE 2 Upload CSF files
Files must be in the correct format. ASCII files must conform to the correct column alignment, as described in the Data Template and the Data Element Dictionary (available on the CSF Submission System’s Documentation page). Only the following file types, with the extensions shown, are accepted:
FORMAT EXTENSION
ASCII . . . txt comma-delimited . . . csv SAS . . . sas7bdat Tab-delimited. . . tsv
To upload a file, select the type to be uploaded, and use the broWse button to look for files on your local computer, or type in the path and filename. When the filename is displayed in the box, click Upload!, and the file will be uploaded and pre-processed.
Common pre-processing errors are:
• Missing data elements
• Extra data elements
• Wrong type for data
• Wrong Center number (ADCID)
• Data in separator columns (applies to ASCII files only)
• IDs not in the UDS Pre-processing
Once a file is uploaded, the software will verify that it’s in the correct format and test for non-numeric characters in numeric fields, characters where blanks should be, and illegal characters. In addition, all IDs will be checked to verify that they are already in the UDS database. When pre-processing is complete, a report page is displayed. If there are no errors, click sUbmit to add the uploaded data to the Working Database. If there are any errors, the file will be unusable, and the user will have to correct the file and upload again. Following is an example of a pre- processing report (Figure 3):
FIGURE 3 Pre-processing report
These errors must be corrected before the file can be uploaded. If there are no errors, a message to that effect will be displayed. Then once sUbmit is clicked, the following page will be displayed (see Figure 4):
FIGURE 4
Add using batch input
Type your email address in the box as requested and then select start batCh Job.
This will submit a job that will move the file into the CSF database. The beginning page will be displayed. You should receive an email in a few minutes (or longer, if the server is very busy) describing the file uploaded.
Web data entry
CSF data forms to be added, edited, and deleted via web data entry. When you select Web data entry, you have access to all the form data in your Working Database — both data you have uploaded from files and data you have entered through the website.
Editing an ID
This is accessed by clicking edit a CsF biomarker Form. All of the IDs currently in your Working Database will be displayed for editing (see Figure 5):
FIGURE 5 Edit CSF biomarker form
FIGURE 6 Edit form data
Select an ID and date, and then click edit. This will display the form for editing (see Figure 6):
To edit, click the box for the data element to be edited. Select the desired value or use the scroll bars to display and select the value.
Next, click Update CsF biomarker Form at the bottom. This will range-check and then update the data in the Working Database.
To add a new form, click add a neW sample inventory Form. This will display the page in Figure 7:
FIGURE 7
Add sample inventory form
FIGURE 8
Form for adding CSF values Select an ID, and then click ContinUe. This will display the form for adding the
CSF values (see Figure 8):
Click each box and enter or select the values. The date of the lumbar puncture is required in order to add a new CSF. Once a date is entered and the form added, the date CANNOT be changed. Click add a neW biomarker CsF Form. The form will be added. This form can be modified later using the edit a CsF biomarker Form functions.
To delete a CSF form, first click delete a CsF biomarker Form. This will display the page in Figure 9:
FIGURE 9 Delete a CSF biomarker form
Select the patient ID and date to delete, and then click delete. The CSF form for that ID and date will be deleted.
FIGURE 10 Errors check page
Error check
Select error CheCk, then error CheCk CsF biomarker Form, and the following page will be displayed (Figure 10):
Click the ID to be error-checked or click all ids to check all available IDs. Each ID’s CSF forms are checked for data- element range errors and other inconsistency errors. Following is an example of errors and alerts (Figure 11):
These errors must be corrected before the forms can be moved to the Current Database.
FIGURE 11 Sample errors and alerts
FIGURE 12
Finalize CSF biomarker form
Finalize data
When all errors have been corrected, the data can be finalized. This involves moving the data from your Working Database to the Current Database. Click Finalize, and then Finalize CsF biomarker Form, and the page below will be displayed (Figure 12):
Select the CSF forms to finalize and then click Finalize biomarker. This will move the data into the Current Database.
IDs with errors in any form will not be moved. A list will be generated showing the number moved and the number with errors (Figure 13):
For CSF forms with no errors, the CSF form data may be copied to the Current Database by clicking Copy paCkets Using batCh inpUt. Once the button is clicked, a page will be displayed asking for your email address (Figure 14):
FIGURE 13 IDs processed and IDs with errors
A report will be sent to this address detailing the CSFs finalized to the current database. It is recommended that you keep these emails. The programs normally are complete within 10 minutes, although completion can take as long as two hours when the system is busy. You will receive your email shortly thereafter.
Reports
Click reports to display the reports page (Figure 15):
FIGURE 15 Generate reports
The Total CSF Biomarker Data Forms report will help you manage your CSF data.
Click doWnload asCii File, and the following page will be displayed (Figure 17):
Download data
Click doWnload data, and then asCii Files, and the following page will be displayed (Figure 16):
FIGURE 16 Download data
FIGURE 17 Download ASCII file
NOTE: This manual uses the ASCII button as an example; however, all of the download file procedures are the same except that different types of files will be created and downloaded.
Select CliCk here to doWnload asCii File. You will be asked whether you want to save or open the file. Open the file and check it or just save the file.
Documentation
Click doCUmentation, and the following page will be displayed. Use the links to access the various guidebooks and forms, available in PDF (Figure 18):
FIGURE 18 Documentation page
