Note: the examples in this tutorial are based on OAIOnline as it existed on July 2007. Additional visits and data have been added since then, so there may be differences in screen shots and data results, but the basic layout is the same.
This tutorial walks you through the variety of tools available for touring and understanding the clinical data.
Below is the home page or initial page for OAIOnline. On the home page, a summary of the new information regarding data releases can be found in the Data News section.
Displaying the Tutorial
We recommend that you size the OAIOnline window, as shown below, to sit side by side with the tutorial window so that you try the steps mentioned in the tutorial. Various formats of the tutorial are available from the links at the bottom of the tutorial page (lower green circle). The default format is "Text Mostly," which combines text with images. You might find the handout version useful if you want to print out the tutorial. To move through the tutorial, please use the previous and next links at the top of the tutorial (upper green circle).
Study Overview & Design Protocol
In order to understand the data, it is helpful to begin from the macro perspective by looking at the purpose, design, and measurements to be performed over the life of the study. To access the study objectives and protocol documents please go to the "About OAI" page by clicking About OAI in the upper menu. Links under "The Osteoarthritis Initiative (OAI)" lead to the study objectives, design protocol, and design protocol appendices. Under "Visit Schedule and Assessments" links to information about type and frequency of examination and questionnaire measurements can be found.
Visit Schedule & Assessments
The Visit Schedule and Assessments links are to PDF documents of tables showing the schedule of questionnaire and exam measures. Besides being found on the About OAI page, these links are also conveniently placed at other locations such as on the "Clinical Data," "Forms," and "Operations Manuals" pages. A portion of the questionnaire measures PDF is shown below.
Let's say after looking at the study design protocol and planned measurements, you decide that you are interested in learning more about how physical activity and knee symptoms are related. This could be posed as the following research question:
What is the relationship between physical activity and knee symptoms?
OAIOnline's resources can help you find data and documentation related to this question and assist you in the formulation and refinement of this and other research questions.
The rest of the tutorial will use this research question for demonstration purposes.
Most of the OAIOnline resources are located in the Data & Documentation area of the website. Let's look next at how you access this area.
Account & Logon I
OAIOnline requires an account and logon for all users that want to access the Data & Documentation portion of the website. When you click on the Data & Documentation link in the upper menu, you will be prompted to enter your username and password as shown below. Please create an account now if you don't already have one by clicking on the link Create My Account, otherwise please logon.
Account & Logon II - account info
After you logon, your username (TutorialUser was used for this tutorial) and a logoff link appears in the far right top corner of the web page. The web page My Account, which is used for viewing and editing your account information, is shown below. There is also an Account Summary which shows a number link to your carts (0 means no carts have been created yet) and the status of your acceptance of the Data Use Agreement, which is required if you plan on downloading datasets. Please click on the Data Use Agreement link to read and then accept the terms. The Data Use Agreement will always be available from the My Account page in case you want to read over the agreement again later.
Annotated Data Collection Forms I - forms page
From the Data & Documentation tab there is a link to forms which contains an expandable/collapsible list of links to the data collection forms ordered by visit.
The forms are annotated with variable root names for the data points collected or derived according to the conventions detailed in the Annotated Form Conventions. When you click "Expand All " you will see each form followed by a short outline of the form's topics. You can peruse these outlines for your topics of interest.
Annotated Data Collection Forms II - expanded tree
After expanding the Baseline Clinic Visits and the 12-month Follow-Up Visit, you will notice topics that may be related to physical activity and knee symptoms, which are related to our research question. Let's take a closer look at the Enrollment Visit Workbook in the next slide.
NOTE: Please don't forget to consult the How to disable Acrobat PDF from displaying in the browser link on the "forms" page for step-by-step instructions on the optimal way to view PDFs with OAIOnline.
Annotated Data Collection Forms III - PDF view
The first page of the Enrollment Visit Workbook contains a linked table of contents. Click on "Walk, 20-meter" and you will jump to that section of the 60-page PDF. Viewing the form will give you a clearer idea about the context of the data collection, a good practice before going on to viewing data longitudinally, our next topic.
One of the most powerful tools that OAIOnline offers for familiarizing users with the study data is search/browse. It allows you to search or browse categorized variable documentation and see the results displayed longitudinally. Each variable label is in turn linked to statistics, comments, and the page from the annotated data collection form that the variable originally appeared on.
To begin, click on the search/browse link in the upper menu under Data & Documentation and the following window below will be shown. The two red arrows below point to the search and then the browse input areas respectively.
First we will examine how to use the browse feature, then the search feature, and finally a combination of both.
Browse Categories I - select
Since the example research question concerns knee symptoms and physical activity, we will select these categories and browse through all the related variable labels.
1. Select "Knee symptoms" from the list by clicking on it.
2. Scroll down to "Physical activity," press "Ctrl" and then select "Physical activity" by clicking on it.
You now have both categories selected.
3. All the visits available are selected by default. Leave this as is for our example, but note that in the future you can uncheck visits to filter your results.
4. Click the "Search/Browse" button to generate a longitudinal display of the selected categories.
Browse Categories II - results
The results of browsing the categories "Knee symptoms" and "Physical activity" is shown below.
The Summary of Results shows a count of all the variable labels found and a linked table of contents that allows you to jump to a specific category or subcategory within the results.
Below the "summary of results" is a longitudinal table which shows the variable labels sorted by category, subcategory, visit, order of the data collection forms, and order of appearance of the variable on the form. Skip patterns in the form logic and the resulting dependency trees (parent/child) are shown through indentation and color coding (grey for children).
Each label row contains the variable label and root followed by markers (PDF icons) indicating at which visit(s) (P02, P01,V00, V01) a data point was collected. The variable names used in the datasets are a combination of the visit prefix and root. For more help on variable names please click the Variable Name link. Besides being visit markers, the PDF icons also link to the page of the annotated data collection form on which the variable appears.
Please click on the label "Right knee pain, aching or stiffness: any, past 12 months" (KPNR12) to see more details.
Browse Categories III - categorical variable longitudinal details
Below are the details for the label "Right knee pain, aching or stiffness: any, past 12 month" (KPNR12).
Dataset: the functional dataset that the variables are found in.
Descriptive Statistics: statistics based on variable type (categorical or continuous). Since this label is for categorical variables, you see the frequencies of all possible values and any special missing values. Variable Name: (P01KPNR12 and V01KPNR12). Full variable name by visit. The PDF icon links to the page of the annotated form on which the variable appears.
SAS Format Name: (YNDK) Link to a full description of the format.
Related Labels: other labels from the same family tree. The selected label is highlighted in light orange.
Please click on the PDF icon next to P01KPNR12 to see the annotated form.
Browse Categories IV - single-page annotated PDF
Below is the single-page annotated data collection form linked to the label "Right knee pain, aching or stiffness: any, past 12 month" (P01KPNR12). This page gives you insight into the form context under which a variable was collected. Single-page annotated PDFs can be accessed via the PDF icon links from the variable details page or the search/browse results page. Next we will examine a format. Please click "back" to return to the details page if you are still in a browser or close the PDF if you are not.
Browse Categories V - format
Shown below is a part of the details page for the label "Right knee pain, aching or stiffness: any, past 12 month" (KPNR12). Click the "YNDK" link and you will see that SAS Format.
The YNDK format contains two possible values and a number of SAS missing value codes. From this web page you can:
Select Format to view another format; or
click the See Variables link, which will show you a list of all the variable labels that use the "YNDK" format.
Next we will look at a continuous variable. Please click "back" in your browser twice and return to the browse results page. This may take awhile.
Browse Categories VI - jump to a category
The Summary of Results seen below is returned when "knee symptoms" and "physical activity" are selected from the Browse/Limit category list. The continuous variable that we want to examine is in the PASE subcategory, so please click on that subcategory in the summary of results table of contents and you will jump down to PASE.
Next let's examine the details for the PASE label. Please click the link "Physical Activity Scale for the Elderly (PASE) score (calc)" (PASE).
Browse Cats VII - continuous variable details
Below are the details for the label "Physical Activity Scale for the Elderly (PASE) score (calc)" (PASE).
This is a label for a continuous calculated variable. The descriptive statistics for a continuous variable show mean, standard deviation(SD), number(N), specific percentile values, and some special missing values.
Since PASE is calculated from a scoring algorithm, it is marked with a calculator icon. You can click on the calculator to jump to the comments regarding the calculation or simply scroll down to the comments. Next click on the "PASE" link in the comments area to see the code used to make the calculation.
Browse Categories VIII - comment
The comment web page for the calculated PASE calculated variable pops up in a new window. When you click the PASEG.sas link, you will see the SAS code created by a UCSF analyst.
Search Text I - in label
In addition to browsing by category, you can also access variable documentation by searching for keywords that appear in the variable label, root, or category. Following our sample research question, let's search for variables associated with knee symptoms. From the single-page annotated PDF, for "knee symptoms," which we saw earlier in this tutorial, we know that "stiffness" is a key related term.
To begin, please click on the search/browse link in the upper menu under Data & Documentation to bring up the search/browse interface. Next type "knee stiffness" into the Keyword or phrase box and press the "Search/Browse" button. Notice that your search phrase is bold and highlighted in yellow where it matches in a label.
Also notice the labels with the grey background (WOMSTFR). As the key explains, these labels are suggested labels that ascend up the family tree of form logic and help reveal the broader context of your search phrase.
Search Text II - in categories
Let's do a search where the search phrase is found in a category name. In the Keyword or phrase box please type "knee symptoms," which is one of the terms from our sample research question, and then press the "Search/Browse" button. Notice that the search phrase is bold and highlighted in yellow where it matches a category or subcategory name in the Summary of Results table of contents.
A new section called Related Category is shown. This section lists all the categories with a subcategory name that contains your search phrase. It is designed to help you find similar topical areas.
Please scroll down the page, and you will see the rest of the search results as shown in the next slide.
Search Text III - in categories continued
Since "knee symptoms" was our search phrase, the results below show that category highlighted in yellow followed by every label/root that belongs to that category beginning with KSX.
Notice that the two prior categories "Joint Imaging" and "Knee pain/OA status" do not have any highlighted labels or roots. So why do these categories appear in the results? They appear because they contain labels that also belong to the targeted "knee symptoms" category. A label can belong to multiple categories or subcategories. As you can see on this slice of the page, KSX belongs to both "Knee pain/OA status" and "Knee symptoms." RSXKOA, LSXKOA, SXKOA, etc. also belong to the category "Knee symptoms" (scroll down the page to see this) and are therefore part of the results. Also note that if you would like to see all the labels in a subcategory then please click the link See All Labels in Subcategory.
Search Text IV - in root
In addition to searching through label and category name text, you can search variable root names. In the Keyword or phrase box please type "KPNR12," which is from the single-page annotated PDF which we saw earlier in the tutorial, and then press the "Search/Browse" button.
Notice that the root is bold and highlighted in yellow. Suggested labels are shown with a grey background.
Search Text V - filter by category
A search can be filtered (narrowed) by restricting the results to one or multiple categories. Let's restrict a text search by one category. Please type "knee" into the Keyword or phrase box. Then select "physical activity" from the Browse/Limit Category dropdown list. Finally, press the "Search/Browse" button. There are 26 records in the results. Next we will look at filtering the results even more by restricting visits.
Search Text VI - filter by visit
A search can be filtered (narrowed) by restricting the results to one or multiple visits. Let's add to the restrictions of the text search in the last slide by limiting the results to only variables collected at the enrollment and first follow-up visits. Please deselect visits P02 and P01. Then select "physical activity" again from the Browse/Limit Category dropdown list, and press the "Search/Browse" button. There are now only 11 records in the results. 15 records were filtered out, because we searched 2 fewer visits.
My Cart I - add variables
You can store a list of variable labels that interest you by adding them to a personal cart. Given the search results from the last slide, please add three labels to your cart by checking the box next to the desired labels and then clicking the Save Icon (Diskette) at the top of the table or the Add Checked Items to Cart button at the bottom of the page.
Note that you will be able to access your cart later by selecting the My Account tab and clicking the link to the my cart page.
My Cart II - contents
The three variable labels you selected in addition to a suggested label with a grey background are shown in your current cart below. The cart item count is 3 because suggested labels are not added to the count. The count can be found in the upper right corner of the web page and at the top of your current cart. To add the suggest label click the "ADD" link, but for now, do not add the suggested label. Notice that this cart is temporary (temp unsaved cart). In order to preserve your selections for use in future browser sessions and to enable custom codebooks and dataset filtering, you have to save your cart. Please type "activities" in the Save Cart section and press the button Save New.
My Cart III - manage saved carts
Since you have saved your "activities" cart, you can now manage your saved carts. That is, you can:
Retrieve a cart and make it your current cart, replacing the contents in your current cart; or
Delete a cart.
In your Current Cart navigation box, there are two new links in addition to "Add Items" and "Jump to Save":
Build Codebook -- creates an html codebook of each variable label in your cart.
Get Datasets -- links to a filtered list of downloadable datasets. The only datasets shown are those containing the variable labels in your cart.
At the bottom of the current cart is a list of all Dataset(s) for [your] cart. In this example there is only one.
Notice that the Save Cart section now allows you to Save changes to the current cart or Add To an existing cart.
My Codebook I - select cart
From the My Account tab there is a link to the my codebook page (and the my cart page where you just came from in the last slide). On the my codebook page, you can create a codebook based on a saved cart.
To build the codebook, select "activities" from the drop-down list of saved carts and press the Build button. Please do not click the Build button a second time as this will start a duplicate build and drastically slow done the creation process. Some large codebooks of 100 plus items can take over 2 minutes to generate. Please be patient.
My Codebook II - results
Part of the codebook for the "activities" cart is shown below. Near the top of the codebook is a table of contents of variable root links ordered from left to right by category and then order on the data collection form. The information for each variable label is the same as that shown for the variable details on search/browse. Please follow the instructions below for saving this codebook to your computer if you would like to view it offline. For our next slide, please click the home link at the top of the page and then the Data & Documentation link in the upper menu.
My Codebook III- research question sample
One of the OAI analysts kindly prepared a document (see the Variables for Sample Research Question link at the bottom of the page below) with a list of variable labels related to our sample research question: What is the relationship between physical activity and knee symptoms?
As a practice exercise, you can create your own cart and codebook with all the variables on this list.
Downloadable Datasets & Doumentation
From the top menu choose the Data & Documentation tab and click the submenu option clinical. Then click the "datasets" link at the far right of the header "Clinical Data." You can also jump to the "datasets" directly by clicking the "Get Datasets" link from one of your saved carts. If you come from your cart, like shown below, the list of datasets will already be filtered for that cart. As you can see the datasets are listed in tables by visit for the "activities" cart. The first table "Enrollees" always appears as it applies to all visits. You can choose any saved cart from the drop-down list and filter the list so that only the datasets corresponding to the items in your cart appear. If you would like to see all the available datasets then select "None (show all datasets)." As long as you have read and agreed to the "Data Use Agreement," you can click on any dataset link in the SAS Data column and download it in .zip or .exe archived format. Also, we recommend that you download the Documentation files, the SAS Formats and the Getting Started with OAI Data: Overview of Structure, Use, and Conventions, which are all found in the Datasets section of the "Clinical Data" page.
The variable guides are found on the "Clinical Data" page. From the top menu choose the Data & Documentation tab and click the submenu option clinical. Then click the "Variable Guides" link to the right of the header "Clinical Data." The variable guides are an offline alternative to search/browse for looking at the variable documentation. There are three primary guides distinguished by sort algorithm: Variable name (VG_Varname.pdf), Form (VG_Form.pdf), and category (VG_CatSubcat.pdf). For a good introduction to the guides please click on the link Variable Guide Tutorial.
The data explorer is linked to from multiple locations. One option is to click the Data & Documentation link and then click the submenu option DataExplorer.
DataExplorer provides descriptive statistics of the data based on your specifications. You can see cross tabs, subsets, frequency distributions and more. To use DataExplorer you are required to accept the terms of the "Data Use Agreement."
See the Help link for complete details on the use of this tool.
Imaging Content and Sitemap
In addition to the "Clinical Data" page, there is an imaging page and other useful content on OAIOnline.
Please click Data & Documentation and then the imaging link in the upper menu to go to the "Imaging Data" page seen below. This page shows which image release sets are currently available and allows you to download corresponding documentation. The images themselves are not available for download. If you would like to receive them then please click the Requesting Images link for more details. Example images showing the typical images from the OAI are available for viewing from the Example Images link.
To see all the content available on OAIOnline in an outline format, please click the Sitemap link in the upper menu. Enjoy!