i2b2 Workplace View

Information in the Workplace View is related to the most common concepts and queries that an individual uses and in essence becomes their personal workspace.  The main objectives of this view are:

§         Save and organize user specific items.

§         Share information with other project users.

§         Project managers can view the workplace for individual team members.

 

The items stored in the Workplace View can be used in many of the i2b2 views, such as Query Tool, Timeline and Export Data.

 

Table of Contents

i2b2 Workplace View... 1

Introduction.. 2

Layout of the Workplace View... 2

User Folder. 3

Folders. 3

Items. 4

Navigation.. 4

Expand/Collapse a Folder.. 4

Expand (Open) a Folder. 4

Collapse (Close) a Folder. 4

Add a Folder.. 4

Rename a Folder.. 6

Annotate a Folder.. 8

Delete a Folder.. 10

Rename Items. 12

Annotate Items. 13

Delete Items. 15

Adding Items to Workplace View... 17

Draggable Items. 17

Add Folders. 18

Add Folder From Find Terms View.. 18

Add Folder From Navigate Terms View.. 19

Add Concepts. 19

Add Concept From Find Terms View.. 19

Add Concept From Navigate Terms View.. 19

Add Previous Query.. 19

Add Previous Query From Previous Query View.. 19

Add Patient Set.. 20

Add Patient Set From Previous Query View.. 20

Add a Single Patient.. 20

Add A Patient From Previous Query View.. 20

Add Patient Count.. 21

Add Patient Count From Previous Query View.. 21

Add Group Template.. 21

Add Group From Query Tool View.. 21

Add Query Definition.. 22

Add Query Definition From Query Tool View.. 22

Using Items in Workplace View... 22

Draggable Items. 22

Using Concepts. 24

Add Concept To Query Tool View.. 24

Add Concept to Timeline View.. 26

Using Group Templates. 27

Add Group Template To Query Tool View.. 28

Add Group Template To Timeline View.. 30

Using Previous Query.. 32

Add Previous Query To Analysis View.. 32

Add Previous Query To Query Tool View.. 34

Add Previous Query To Timeline View.. 36

Using Query Definition.. 38

Add Query Definition To Query Tool View.. 38

Using Patient Set.. 40

Add Patient Set To Timeline View.. 40

 

Introduction

This section describes the layout and contents of this view.

 

Layout of the Workplace View

Information in the Workplace View is related to the most common concepts and queries that an individual uses and in essence becomes their personal workplace.

 

Figure 1         Workplace View

 

 

The Workplace view is hierarchical display of the items added by the user.  There are three main branches or components of the tree that displays.

 

User Folder

The highest level is the individual user folder ().  This folder is automatically created with the user’s name and it stores items added by the individual user. This level cannot be used when creating a query.

 

Note: This also includes the Shared folder.

 

 

Folders

A folder () contains other folders and/or items added by the user.  It can be expanded and collapsed by clicking on the plus () or minus () sign next to it.   A user defined folder cannot be dragged to other views.  It can be moved around within the workplace view.

 

 

Items

Items are the lowest level of the hierarchy. They cannot be expanded further.  Some examples of items are listed below.

§         concepts ()

§         group of concepts (ontology folder) ()

§         group templates ()

§         patient lists ()

§         query definitions ()

 

 

Navigation

 

Expand/Collapse a Folder

Users can expand or collapse a folder by clicking on the plus sign () or negative sign () next to the folder.

 

Expand (Open) a Folder

Click on the plus sign () next to the folder in Workplace View.

1.       The folder will open and all the items in the folder will display.

 

Collapse (Close) a Folder

1.       Click on the negative sign () next to the folder in Workplace View.

2.       The folder will close and all the items in the folder will no longer appear in the view.

 

 

Add a Folder

Users can add a folder to either their folder or to the shared folder.

 

1.       Using the right mouse button click on your folder in Workplace View.

2.       A menu will open saying New Folder.

 

Figure 2         Add New Folder

 

 

3.       Click on New Folder.

4.        A dialog box will open allowing you to enter a name for the new folder.

 

Figure 3         New Folder Dialog Box

 

 

5.       Enter the name you want to be displayed.

6.       Click on the OK button.

7.       The new folder will appear in the workplace view.

 

Figure 4         New Folder Added

 

 

 

Rename a Folder

Users can easily rename an existing folder.

 

1.       Using the right mouse button click on the folder you want to rename.

2.       A menu will open with several options.

 

Figure 5         Menu: Rename Folder

 

 

3.       Select Rename from the list.

4.        A dialog box will open allowing you to change the name of the folder.

 

Figure 6         Rename Folder Dialog Box

 

 

5.       Enter the name you want to be displayed.

6.       Click on the OK button.

7.       The folder will appear in the workplace view with the new name.

 

Figure 7         Folder Renamed

 

 

 

Annotate a Folder

Users can change the default annotation for any of their folders in Workplace View. 

 

Note: The annotation is what is displayed in the tool tip.

 

1.       Using the right mouse button click on the folder you want to annotate.

2.       A menu will open with several options.

 

Figure 8         Menu: Annotate Folder

 

 

3.       Select Annotate from the list.

4.        A dialog box will open allowing you to enter the text you want to appear displaying the tool tip.

 

Figure 9         Annotate Folder Dialog Box

 

 

5.       Enter the text want to be displayed.

6.       Click on the OK button.

7.       Using the mouse hover over the folder you just annotated.

8.       The text you entered will display as a tool tip.

 

Figure 10       Annotated Folder

 

 

 

Delete a Folder

Users can remove a folder from the Workplace View.

 

Warning: All items in the folder will be deleted when the folder is deleted. It is recommended that you move items that you want to keep to another folder.

 

1.       Using the right mouse button click on the folder in Workplace View.

2.       A menu will open with several options.

 

Figure 11       Menu: Delete Folder

 

 

3.       Select Delete from the list.

4.       A dialog box will open warning you the contents of the folder will also be deleted.

 

Figure 12       Delete Folder Warning

 

 

5.       Click on the Yes button.

6.       The folder and all of its contents will no longer appear in the workplace view.

 

 

 

Rename Items

Users can easily rename an item in Workplace View.

 

1.       Using the right mouse button click on the item you want to rename.

2.       A menu will open with several options.

 

Figure 13       Menu: Rename Item

 

 

3.       Select Rename from the list.

4.        A dialog box will open allowing you to change the name of the folder.

 

Figure 14       Rename Item Dialog Box

 

 

5.       Enter the name you want to be displayed.

6.       Click on the OK button.

7.       The item will appear in the workplace view with the new name.

 

Figure 15       Renamed Item

 

 

 

Annotate Items

Users can change the default annotation for any of the items in their folder in Workplace View. 

 

Note: The annotation is what is displayed in the tool tip.

 

1.       Using the right mouse button click on the item you want to annotate.

2.       A menu will open with several options.

 

Figure 16       Menu: Annotate Item

 

 

3.       Select Annotate from the list.

4.        A dialog box will open allowing you to enter the text you want to appear displaying the tool tip.

 

Figure 17       Annotate Item Dialog Box

 

 

5.       Enter the text want to be displayed.

6.       Click on the OK button.

7.       Using the mouse hover over the item you just annotated.

8.       The text you entered will display as a tool tip.

 

Figure 18       Annotated Item

 

 

 

Delete Items

Users can remove items from the Workplace View.

 

1.       Using the right mouse button click on the item in Workplace View.

2.       A menu will open with several options.

 

Figure 19       Menu: Delete Item

 

 

3.       Select Delete from the list.

4.       A dialog box will open warning you it is about to delete the item.

 

Figure 20       Delete Item Warning

 

 

5.       Click on the Yes button.

6.       The item will no longer appear in the workplace view.

 

 

 

Adding Items to Workplace View

This section describes how to add items to the Workplace view.

 

Draggable Items

Items can be dragged and dropped (copied) into the Workplace View from views in the i2b2 Workbench.

 

1.       Folder

A folder () and all its concepts (children) can be added to Workplace by dragging the folder name from one of the following views.

 

§         Navigate Terms View

§         Find Terms View

 

2.       Concept

A concept () can be added to Workplace by dragging the name of the concept from one of the following views.

 

§         Find Terms View

§         Navigate Terms View

 

3.       Group Template

A group template () can be added to Workplace by dragging the name of the group from the following view.

 

§         Query Tool View

 

4.       Patient

A single patient () can be added to Workplace by dragging the patient number from the following view.

 

§         Previous Query View

 

5.       Patient List

A list of patients () can be added to Workplace by dragging the name of the patient list from the following view.

 

§         Previous Query View

 

6.       Previous Query

A previous query () can be added to Workplace by dragging the name of the previous query from the following view.

 

§         Previous Query View

 

7.       Query Definition

A query definition () can be added to Workplace by dragging the name of the query from the following view.

 

§         Query Tool View

 

8.       Number of Patients

The number of patients () can be added to Workplace by dragging the name of the number of patients from the following view.

 

§         Previous Query View

 

 

 

Add Folders

 

Add Folder From Find Terms View

1.       Highlight the folder () by clicking on the name of the folder.

2.       While holding the left mouse button down, drag the folder over to the Workplace View.

3.       Drop the folder into either your workplace folder or the shared folder

4.       The folder will now display in the Workplace View with the same name.

 

Add Folder From Navigate Terms View

1.       Highlight the folder () by clicking on the name of the folder.

2.       While holding the left mouse button down, drag the folder over to the Workplace View.

3.       Drop the folder into either your workplace folder or the shared folder

4.       The folder will now display in the Workplace View with the same name.

 

 

 

Add Concepts

 

Add Concept From Find Terms View

1.       Highlight the concept () by clicking on the name of the concept.

While holding the left mouse button down, drag the folder over to the Workplace View.

Drop the concept into either your workplace folder or the shared folder

The concept will now display in the Workplace View with the same name.

 

Add Concept From Navigate Terms View

1.       Highlight the concept () by clicking on the name of the concept.

2.       While holding the left mouse button down, drag the folder over to the Workplace View.

3.       Drop the concept into either your workplace folder or the shared folder

4.       The concept will now display in the Workplace View with the same name.

 

 

 

Add Previous Query

 

Add Previous Query From Previous Query View

1.       Highlight the previous query () by clicking on the name of the query.

2.       While holding the left mouse button down, drag the previous query name to the Workplace View.

3.       Drop the previous query into either your workplace folder or the shared folder.

4.       The previous query will now appear in the workplace with the same name.

 

 

 

Add Patient Set

 

Add Patient Set From Previous Query View

1.       Click on the plus sign () next to the previous query that contains the patient set.

2.       Click on the plus sign () next to the results folder.

3.       Click on the name of the patient list ().

4.       While holding the left mouse button down, drag the patient list to the Workplace View.

5.       Drop the patient list into either your workplace folder or the shared folder.

6.       The patient list will now appear in the workplace.

 

 

 

Add a Single Patient

 

Add A Patient From Previous Query View

1.       Click on the plus sign () next to the previous query that contains the patient set.

2.       Click on the plus sign () next to the results folder.

3.       Click on the plus sign () next to patient list.

4.       Click on the patient () to be copied.

5.       While holding the left mouse button down, drag the patient to the Workplace View.

6.       Drop the patient list into either your workplace folder or the shared folder.

7.       The patient will now appear in the workplace.

 

 

 

Add Patient Count

 

Add Patient Count From Previous Query View

1.       Click on the plus sign () next to the previous query that contains the patient set.

2.       Click on the plus sign () next to the results folder.

3.       Click on number of patients ().

4.       While holding the left mouse button down, drag the number of patients to the Workplace View.

5.       Drop the number of patients into either your workplace folder or the shared folder.

6.       The number of patients will now appear in the workplace as patient count ().

 

 

 

Add Group Template

 

Add Group From Query Tool View

1.       Click on the group name/heading.

 

Figure 21       Group Name in Query Tool View

 

 

2.       While holding the left mouse button down, drag the group name to the Workplace View.

3.       Drop the group into either your workplace folder or the shared folder

4.       The group will now display in the Workplace View with a default.

 

 

 

Add Query Definition

 

Add Query Definition From Query Tool View

1.       Click on the group name/heading.

 

Figure 22       Query Name in Query Tool View

 

 

2.       While holding the left mouse button down, drag the query name to the Workplace View.

3.       Drop the query into either your workplace folder or the shared folder

4.       The query definition will now display in the Workplace View with the same name.

 

 

 

Using Items in Workplace View

This section describes how to use items in the Workplace view.

 

Draggable Items

Items can be dragged and dropped (copied) from the Workplace View to other views in the i2b2 Workbench.

 

1.       Folder

A folder () and all its concepts (children) can be added to other views by dragging the folder name from Workplace to one of the following views.

 

§         Query Tool View

§         Timeline View; Create model for Timeline Tab

 

2.       Concept

A concept () can be added to other views by dragging the name of the concept from Workplace to one of the following views.

 

§         Query Tool View

§         Timeline View; Create model for Timeline Tab

 

3.       Group Template

A group template () can be added to other views by dragging the name of the group template from Workplace to one of the following views.

 

§         Query Tool View

§         Timeline View; Create model for Timeline Tab

 

4.       Patient List

A list of patients () can be added to other views by dragging the name of the patient list from Workplace to one of the following views.

 

§         Timeline View; Create model for Timeline Tab

 

5.       Previous Query

A previous query () can be added to other views by dragging the name of the previous query from Workplace to one of the following views.

 

§         Analysis View

§         Query Tool View

§         Timeline View; Create model for Timeline Tab

 

6.       Query Definition

A query definition () can be added to other views by dragging the name of the query definition from Workplace to the following view.

 

§         Query Tool View

 

 

 

Using Concepts

A concept can be added to other i2b2 views by simply dragging the concept name from the Workplace View to one of the following views.

 

Add Concept To Query Tool View

1.       Find the concept () or group of concepts () you want to add.

 

Figure 23       Workplace View: Concept

 

 

2.       Highlight the concept by clicking on its name.

3.       While holding the left mouse button down, drag the concept to the Query Tool view.

4.       Drop the concept into the panel labeled Group 1.

 

Figure 24       Adding Concept to Query Tool View

 

 

5.       The concept will display.

 

Figure 25       Concept Added to Query Tool View

 

 

 

Add Concept to Timeline View

1.       Find the concept () or group of concepts () you want to add.

 

Figure 26       Workplace View: Concept

 

 

2.       Highlight the concept by clicking on its name.

3.       While holding the left mouse button down, drag the concept to the Timeline View.

4.       Drop the concept into the section that displays the list of concepts.

 

Figure 27       Add Concept to Timeline View

 

 

5.       The concept will display.

 

Figure 28       Concept Added to Timeline View

 

 

 

Using Group Templates

Users can define a group of concepts that they frequently run and save them in their workplace view. This grouping of concepts is referred to as a group template.

A group template can be added to other i2b2 views by simply dragging the group template name from the Workplace View to one of the following views.

 

Add Group Template To Query Tool View

1.       Find the group template () you want to add.

 

Figure 29       Workplace View: Group Template

 

 

2.       Highlight the group template by clicking on its name.

3.       While holding the left mouse button down, drag the group template to the Query Tool View.

4.       Drop the group template into the panel labeled Group 1.

 

Figure 30       Add Group Template to Query Tool View

 

 

5.       The concept(s) associated with the group template will display.

 

Figure 31       Group Template Added to Query Tool View

 

 

Add Group Template To Timeline View

1.       Find the group template () you want to add.

 

Figure 32       Workplace View: Group Template

 

 

2.       Highlight the group template by clicking on its name.

3.       While holding the left mouse button down, drag the group template to the Timeline view.

4.       Drop the group template at Panel Name.

 

Figure 33       Add Group Template to Timeline View

 

 

5.       The concept(s) associated with the group panel will display in the list of concepts.

 

Figure 34       Group Template Added to Timeline View

 

 

 

Using Previous Query

A group template can be added to other i2b2 views by simply dragging the group template name from the Workplace View to one of the following views.

 

Add Previous Query To Analysis View

1.       Find the previous query () you want to add.

 

Figure 35       Workplace View: Previous Query

 

 

2.       Highlight the previous query by clicking on its name.

3.       While holding the left mouse button down, drag the previous query to the Analysis View.

4.       Drop the previous query into the Graphic Analyses Section.

 

Figure 36       Add Previous Query to Analysis View

 

 

5.       The analyses associated with the previous query will display in the list and the name of the query will appear at Query Name.

 

Figure 37       Previous Query Added to Analysis View

 

 

Add Previous Query To Query Tool View

1.       Find the previous query () you want to add.

 

Figure 38       Workplace View: Previous Query

 

 

2.       Highlight the previous query by clicking on its name.

3.       While holding the left mouse button down, drag the previous query to the Query Tool View.

4.       Drop the previous query into the Query Name.

 

Figure 39       Add Previous Query to Query Tool View

 

 

5.       The concept(s) associated with the previous query will display in the appropriate group(s) and the name of the query will appear at Query Name.

 

Figure 40       Previous Query Added to Query Tool View

 

 

Note: When you run the query it will receive a new name.  This is to distinguish the first previous query from the second.

 

 

 

Add Previous Query To Timeline View

1.       Find the previous query () you want to add.

 

Figure 41       Workplace View: Previous Query

 

 

2.       Highlight the previous query by clicking on its name.

3.       While holding the left mouse button down, drag the previous query to the Timeline View.

4.       Drop the previous query into the Query Name.

 

Figure 42       Add Previous Query to Timeline View

 

 

5.       Once the previous query is dropped the following will occur:

§         The name of the previous query appears at the Query Name.

§         The name of the results panel associated to the previous query appears at the Panel Name.

§         The concept(s) associated with the previous query display in the list along with any constraints that may have been defined when the query was initially run.

§         The Patient Set will be populated with the patient list associated with the previous query.

 

Figure 43       Previous Query Added to Timeline View

 

 

 

Using Query Definition

A query definition can be added to the query tool view by simply dragging the query name from the workplace view.

 

Add Query Definition To Query Tool View

1.       Find the query definition () you want to add.

 

Figure 44       Workplace View: Query Definition

 

 

2.       Highlight the query definition by clicking on its name.

3.       While holding the left mouse button down, drag the query definition to the Query Tool View.

4.       Drop the query definition into the Query Name.

 

Figure 45       Add Query Definition to Query Tool View

 

 

5.       The concept(s) associated with the query definition will display in the appropriate group(s) and the name of the query will appear at Query Name.

 

Figure 46       Query Definition Added to Query Tool View

 

 

 

Using Patient Set

A list of patients can be added to other i2b2 views by simply dragging the name of the patient set from the Workplace View to one of the following views.

 

Add Patient Set To Timeline View

1.       Find the patient list () you want to add.

 

Figure 47       Workplace View: Patient List

 

 

2.       Highlight the patient list by clicking on its name.

3.       While holding the left mouse button down, drag the patient list to the Timeline view.

4.       Drop the patient list into the Patient Set field.

 

Figure 48       Add Patient List to Timeline View

 

 

5.       The name of the patient list will display.

 

Figure 49       Patient List Added to Timeline View