i2b2 Web Client Help
The Find Terms view is designed to allow users to search for concepts. Users can search by the name or by a particular code. Once the appropriate concept is found it can be used in many of the i2b2 views and plug-ins, such as the Query Tool view.
This section describes the layout and contents of this view.
The Find Terms view allows users to search for a concept, group of concepts, and their associated modifiers. There are basically two methods of searching available;(1) by name and (2) by code.
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NOTE: Regardless of how you search for the concept the layout of both tabs is the same. |
This section has two tabs; one is to Search by Name and the other Search by Code. Depending on which tab is active will determine which search method is used to find the concept.
There are three fields in this section; (1) Qualifier, (2) Text and (3) Category
The qualifier is used to tell the system whether or not you are looking for an exact match or just a partial match. There are four different options to choose from.
The text box is where you will enter what you are searching for.
The category / coding system selection field allows you to narrow down the search to a particular table or set of codes.
The results section displays the concepts that were found based on the search criteria.
The clinical vocabulary that resides in the Ontology Management Cell was partially built using terminology from several standard coding systems. These codes can be used to search for a particular term (see section on Search by Code). The following are some examples of standard coding systems.
Example:
Code: 414.9
Description: Chronic Ischemic Heart Disease, unspecified
Example:
Code: 13969-1
Description: CPK-MB
Example:
Code: 12783-*178-87
Description: Briston-Myers Squibb, Pravachol, 20 mg tablets
Example:
Code: C0001403
Description: Addison's Disease
An additional section called Find Modifiers is located at the bottom of the Find Terms view. This section is only visible once you find a term and select to find the modifiers from the pop-up menu (see section on Finding Modifiers).
The functionality of finding modifiers is very similar to finding terms in that you can search by name or by code and you can define the search criteria to be used when performing the search.
There are two fields in this section; (1) Qualifier, and (2) Text
The qualifier is used to tell the system whether or not you are looking for an exact match or just a partial match. There are four different options to choose from.
The text box is where you will enter what you are searching for.
There are three methods of searching for a modifier; (1) Find Name, (2) Find Code and (3) Get All.
The text entered will be used to search for the name of the modifier.
Example:
Severity: Mild
The text entered will be used to search for the code of the modifier.
Example:
255604002 (this is the SNOMED code for Mild Severity)
The Get All button will return all the modifiers associated with a term regardless of what qualifier and text have been entered.
The results section displays the concepts that were found based on the search criteria.
Depending on the search criteria, the results section may display groups of concepts which are contained in folders as well as individual concepts. The folders can be expanded to see the listing of concepts in that grouping by clicking on the plus sign (
) or negative sign (
) next to the folder icon.
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NOTE: The ability to expand and collapse folders also extends to the modifier result section which can contain modifiers. |
) next to the folder in the results section of Find Terms view or the Modifier folder in the Find Modifiers section.
) next to the folder in the results section of Find Terms view or the Modifier folder in the Find Modifiers section.
Users can define how many concepts to display and whether or not to show hidden terms and/or synonyms. The display options are set in the Find Terms Options dialog window, which can be accessed by clicking on the Show Options button (
).
The Maximum number of children to display is used when retrieving the search results to be displayed in the results section of the Find Terms view. Once the maximum number is reached a message will appear informing you that the query has reached the maximum number of terms and suggests you try searching again with a more specific query. Running a search with a more specific query will narrow your results as the selection criteria will not be as broadly defined.
In the metadata table, an attribute is set to determine whether or not a term is active, inactive or hidden. If an item is marked as hidden it will not appear in the list of terms. Selecting Show Hidden Terms will display those items marked to be hidden. For easy identification, hidden terms will be red when displayed in the results list.
Some terms may be flagged in the metadata table as a synonym of another term. Selecting Show Synonymous Terms will display both the original term and the synonym in the Find Terms view. For easy identification, synonymous terms will be blue when displayed in the results list.
The Enable patient counts option will display the total number of patients that have an observation fact entered for that item.
By default, the tooltip that displays when you hover over an item will contain the entire path name and the tooltip that is specific to that item. Enabling the Use short tooltips option will only display the tooltip information; the path will not be included.
In addition to showing the tooltip, this option will also display the concept_cd associated to the item.
The ability to search for modifiers will not be available if the Disable modifiers option is checked off.
This section describes how to search for a term using one of the two available methods; (1) Search by Name and (2) Search by Code.
Regardless of whether you are searching by name or by code, the first step in entering the search criteria is defining a qualifier. The first field is the “qualifier” and it is a drop-down list with four options:
The results returned will contain only those terms whose name or code begins with the text entered in the search box.
The results returned will contain only those terms whose name or code ends with the text entered in the search box.
The results returned will be those terms whose name or code ends with the text entered in the search box.
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NOTE: This search will return the broadest range of results. |
The results returned will be those terms whose name or code matches exactly to the text entered in the search box.
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NOTE: This search will return the narrowest range of results. |
The method of searching by the name is exactly what it sounds like; you can search for a concept by its name.
Some of the concepts have a standard code associated with them. This code can be used to search for a specific concept or a grouping of concepts.
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NOTE: The steps listed in this section walk you through a code search using LOINC codes. These same steps can be used when doing a search of any type of code. In step 4, replace LOINC with the coding system you want to search. |
A modifier is associated with a single term or a group of terms. Therefore in order to search for a modifier you must first search for the term. Once the term is found you can begin the process of finding the modifier. Overall the process of finding modifiers is very similar to searching for a term; you can search by name or by code.
Regardless of whether you are searching by name or by code, the first step in entering the search criteria is defining a qualifier. The first field is the “qualifier” and it is a drop-down list with four options:
The results returned will contain only those modifiers whose name or code begins with the text entered in the search box.
The results returned will contain only those modifiers whose name or code ends with the text entered in the search box.
The results returned will be those modifiers whose name or code ends with the text entered in the search box.
|
NOTE: This search will return the broadest range of results. |
The results returned will contain only those modifiers whose name or code matches exactly to the text entered in the search box.
|
NOTE: This search will return the narrowest range of results. |
The method of searching by the name is exactly what it sounds like; you can search for a modifier by its name.
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NOTE: As stated above you must first search for the term before you can find the associated modifiers. |
) or folder (
).
) or folder ().
) or folder ().
) or folder ().
Some of the modifiers have a standard code associated with them. This code can be used to search for a specific modifier or a grouping of modifiers.
|
NOTE: As stated above you must first search for the term before you can find the associated modifiers. |
) or folder ().
In the Find Modifiers section of the Find Terms view there is a Get All button. This button will return all the modifiers associated to a term.
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NOTE: As stated above you must first search for the term before you can find the associated modifiers. |
) or folder ().
This section describes how to use a concept or group of concepts.
Individual as well as groups of concepts and modifiers can be dragged and dropped (copied) from the Find Terms View to other views in the i2b2 Web Client.
A folder () and all its concepts (children) can be added to other views by dragging the folder name from Find Terms to one of the following views.
A modifier folder (
) and all its concepts (children) can be added to other views by dragging the folder name from Find Terms to one of the following views.
A concept () can be added to other views by dragging the name of the concept from Find Terms to one of the following views.
A modifier (
) can be added to other views by dragging the name of the modifier from Find Terms to one of the following views.
A folder, individual concept, or modifier can be added to the query tool view by simply dragging the item from Find Terms view and dropping it into one of the panels in the Query Tool view.
) by clicking on the name of the folder.
) by clicking on the name of the concept.
) by clicking on the name of the modifier.
Information in the workplace is related to the most common concepts and queries that an individual uses and in essence becomes their personal workplace.
) by clicking on the name of the folder.
) by clicking on the name of the concept.
) by clicking on the name of the modifier.
The Navigate Terms view is designed to display the i2b2 vocabulary concepts that are maintained in the Ontology Management Cell of the i2b2 Hive. These concepts are used in many of the i2b2 views and plug-ins, such as the Query Tool view.
This section describes the layout and contents of this view.
The Navigate Terms view displays the terms listed in the metadata table(s). These terms are grouped (categorized) with other similar items. These groupings are displayed in a hierarchal tree that can be expanded to view all the concepts and modifiers in the associated category.
As stated above, the Navigate Terms view is hierarchical display of the concepts and modifiers in the metadata table(s). The modifiers will always appear with their associated concept.
There are several branches or components of the tree that display.
The highest level is the name of the metadata table that stores the vocabulary. This level cannot be used when creating a query.
A container (
) has other folders, concepts and / or modifiers. It can be expanded and collapsed by clicking on the plus sign () or minus sign () next to it. It can not be dragged to other views.
A modifier container (
) has other modifier folders and / or modifiers. It can be expanded and collapsed by clicking on the plus sign () or minus sign () next to it. It can not be dragged to other views.
A folder () contains other folders, concepts and / or modifiers. It can be expanded and collapsed by clicking on the plus sign () or minus sign () next to it. It can also be dragged to other views.
A modifier folder (
) contains other modifier folders and / or modifiers. It can be expanded and collapsed by clicking on the plus sign () or minus sign () next to it. It can also be dragged to other views.
The concept () is the lowest level of the hierarchy and cannot be expanded further.
The modifier () is the lowest level of the hierarchy and cannot be expanded further.
Users can expand or collapse a folder by clicking on the plus sign () or negative sign () next to the folder icon.
) next to the folder in the Navigate Terms view.
) next to the folder in the Navigate Terms view.
Users can define how many concepts to display and whether or not to show hidden terms and/or synonyms. The display options are set in the Navigate Terms Options dialog window, which can be accessed by clicking on the Show Options button ().
The Maximum number of children to display is used when expanding a folder in the Navigate Terms view. Once the maximum number is reached a message will appear informing you that you have reached the maximum and continuing to retrieve all the concepts in the list may affect performance. You will have the option to continue or to cancel the action.
In the metadata table, an attribute is set to determine whether or not a term is active, inactive or hidden. If an item is marked as hidden it will not appear in the list of terms. Selecting Show Hidden Terms will display those items marked to be hidden. For easy identification, hidden terms will be red when displayed in the results list.
Some terms may be flagged in the metadata table as a synonym of another term. Selecting Show Synonymous Terms will display both the original term and the synonym in the Find Terms view. For easy identification, synonymous terms will be blue when displayed in the results list.
The Enable patient counts option will display the total number of patients that have an observation fact entered for that item.
By default, the tooltip that displays when you hover over an item will contain the entire path name and the tooltip that is specific to that item. Enabling the Use short tooltips option will only display the tooltip information; the path will not be included.
In addition to showing the tooltip, this option will also display the concept_cd associated to the item.
The ability to search for modifiers will not be available if the Disable modifiers option is checked off.
This section describes how to use a group of concepts, a single concept, and a modifier.
Individual as well as groups of concepts can be dragged and dropped (copied) from the Navigate Terms view to other views in the i2b2 Web Client.
A folder () and all its concepts (children) can be added to other views by dragging the folder name from Navigate Terms to one of the following views.
A modifier folder () and all its concepts (children) can be added to other views by dragging the modifier folder name from Navigate Terms to one of the following views.
A concept () can be added to other views by dragging the name of the concept from Navigate Terms to one of the following views.
A modifier () can be added to other views by dragging the name of the modifier from Navigate Terms to one of the following views.
A folder, individual concept, or modifier can be added to the query tool view by simply dragging the item from Navigate Terms view and dropping it into one of the panels in the Query Tool view.
) by clicking on the name of the folder.
) by clicking on the name of the concept.
) by clicking on the name of the modifier.
Information in the workplace is related to the most common concepts and queries that an individual uses and in essence becomes their personal workplace.
) by clicking on the name of the folder.
) by clicking on the name of the concept.
) by clicking on the name of the modifier.
The Previous Query view is designed to display the most recent queries run by a user. The results associated to the query are also available for viewing.
This section describes the layout and contents of the Previous Query view.
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NOTE: There are two types of queries that can be run in the i2b2 Web Client;
Both of these types of queries will appear in the Previous Query view and throughout this document they will both be referred to as a "Previous query".
For more detailed information on the distinction of these two types of queries please see the Query Tool help. |
A previous query (
/ 
) is created when a query is run from the Query Tool.
The query is stored and displayed in the Previous Query view. These previous queries can be used to run new queries or to easily populate other views.
The query in the previous query view is comprised of multiple hierarchical levels that can be seen by expanding each level of the tree. These levels are outlined below.
The name of the previous query is the top level of the hierarchal tree and is comprised of these three components.
The Results folder (
) contains the results of the query. To see the query results simply expand the folder by clicking on the plus sign () located next to the result name.
The results associated with a previous query are determined by the query result type(s) that are selected when the query is run in the Query Tool view.
The Patient set (
) appears if Patient set or Timeline was checked at the time the query was run. The set contains all the patients who met the defined search criteria.
The Encounter Set () appears if Encounter set was checked at the time the query was run. The set contains all the patients whose encounters met the defined search criteria.
The Number of Patients (
) appears if Number of Patients was checked at the time the query was run. The results are a total count for those patients who met the defined criteria.
The Gender patient breakdown (
) appears if Gender patient breakdown was checked at the time the query was run. The results are a breakdown by gender for those patient who met the defined criteria.
The Vital Status patient breakdown () appears if Vital Status patient breakdown was checked at the time the query was run. The results are a breakdown by vital status for those patient who met the defined criteria.
The Race patient breakdown () appears if Race patient breakdown was checked at the time the query was run. The results are a breakdown by race for those patient who met the defined criteria.
The Age patient breakdown () appears if Age patient breakdown was checked at the time the query was run. The results are a breakdown by age for those patient who met the defined criteria.
Users can rename a previous query from the list by selecting Rename from the popup menu.
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NOTE: When dragging a previous query to another view the new name will appear when it is dropped. |
Users can rename a previous query from the list by selecting Delete from the pop-up menu.
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WARNING: Once you click on Delete, the previous query will be removed from the view and there is no way to restore it. Therefore you need to make sure you want to remove it from the list. |
Users can refresh the list of previous queries from the list by selecting Refresh All from the pop-up menu.
Users can define how many previous queries to display and the order in which they will appear in the list. The display options are set in the Options for Previous Queries window, which can be accessed by clicking on the Show Options button ().
The Maximum number of queries to display defines how many previous queries will be visible in the Previous Query view. Once the maximum number is reached the oldest query will no longer appear in the view.
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TIP: Recommendation: Use the Workplace view to save those previous queries that will be used often. In addition to being more convenient it will also prevent you from loosing a common query if the maximum number to display has been reached. |
Selecting to sort By Create Date will sort the queries in the Previous Query view by the date and time the query was created. Once you select to sort by the creation date, you need to define whether or not it will be in ascending or descending order.
Ascending: displays the oldest query first.
Descending: displays the newest query first.
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NOTE: Renaming a query will not affect the sort order as the date and time is stored with the previous query. |
Selecting to sort By Query Name will sort the queries in the Previous Query view alphabetically by the name of the query. Once you select to sort by name, you need to define whether or not it will be in ascending or descending order.
Ascending: queries are displayed in alphabetical order with the beginning of the alphabet at the beginning of the list. (A to Z)
Descending: queries are displayed in alphabetical order with the beginning of the alphabet at the end of the list. (Z to A)
This section describes how to use a previous query.
Different parts of the previous query can be dragged and dropped (copied) from the Previous Query view to other views in the i2b2 Web Client.
Associated with each previous query ( / ) are the items used to run the query, any constraints that were defined, and the results. A previous query can be added to other views by dragging the previous query name from Previous Query view to one of the following views.
A specific set of patients can be added to other views by dragging the Patient set () from Previous Query view to one of the following views.
A specific set of encounters (visit list) can be added to other views by dragging the Encounter Set () from Previous Query view to one of the following views.
The Query Tool view is designed to simplify the process of retrieving information from the database associated to the i2b2 Web Client.
Within the Previous Query view there are several items that can be used in the Query Tool view to run a query. The following sections explain how to add the previous query, patient set and encounter set to the Query Tool view.
Within the Query Tool view, a previous query can be added to one of the following two locations.
| Query Name field | The items and constraints from the original query will be used to create a new query. This information can be edited to make a new query or can be used as is to run the query again. |
| Panel (Group) | Used within a new query (query-in-query). The information associated with the previous query can not be edited. Add additional search criteria (items) to be used in the new query. |
/ ) by clicking on the name of the query.
|
NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
/ ) by clicking on the name of the query.
) next to the name of the previous query that contains the patient set.
) next to the results folder.
) by clicking on its name.
) next to the name of the previous query that contains the encounter set.
) next to the results folder.
) by clicking on its name.
Information in the workplace is related to the most common concepts and queries that an individual uses and in essence becomes their personal workplace.
/ ) by clicking on the name of the query.
) next to the name of the previous query that contains the patient set.
) next to the results folder.
) by clicking on its name.
) next to the name of the previous query that contains the encounter set.
) next to the results folder.
) by clicking on its name.
The Query Tool view is designed to simplify the process of retrieving information from the database associated to the i2b2 Web Client.
This section describes the layout and contents of this view.
The Query Tool view is used to define and run a "select query" that will retrieve information from the database associated to the i2b2 Web Client.
The Query Tool view can be broken down into several sections which are defined below.
The name of a query will be assigned when it is run and will display in the Query Name field.
The only time a query name will appear prior to running the query is when you drag a previous query from either the Previous Query or Workplace views and drop it into the Query Name field.
The Temporal Constraint is defined on the query level and depending on what is selected will set the default for the panel timing.
A panel is the section of the Query Tool view that contains information about a group of concepts. The panel can be broken down into the following sections.
The heading is a label to easily identify the collection of terms. Each heading will contain "Group" followed by a sequential number.
Example: Group 1, Group 2, Group 3, etc.
This area of the panel is used to define date selections and other constraints.
The panel timing defines the constraint on the panel level and uses the patient's visits in determining eligibility.
This section contains the terms that will be used during the process of querying the database.
The content in the information box will change depending on whether or not a term is listed in the panel / group.
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NOTE: Once you add an item to a panel, an additional information box will appear between the two panels containing the text "AND". This is to indicate that each panel will be joined with an AND operator when the SQL query is created. |
The toolbar is the bottom section of the Query Tool view and contains several buttons that perform various actions.
On the toolbar for the Query Tool there is a single button for running and canceling a query. Depending on the circumstances defined below the label on this button and its associated action will change to one of the following: (1) Run Query or (2) Cancel Query.
Clicking on the button labeled Run Query will run your query with the defined search criteria.
Once you start running a query, the label will change to Cancel Query. Clicking on the button when it says Cancel Query will cancel the query and free up the Query Tool / Web client so that you can continue to do other things.
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NOTE: Clicking on Cancel Query in the Query Tool will only cancel the web client piece of the process. The server side will continue to run. |
The Clear button will reset the view to the default; this includes deleting the concepts listed in the panel and removing any constraint that have been defined.
The Print button will open a window with the query information in a printable format.
The Query Status view is located below the Query Tool view and contains information regarding the status of a query that is either running or has just finished as well as the results of a previous query.
While a query is running you will see the name of the query and how long it has been running.
Once the query has finished, the number of patients meeting the search criteria will appear in this view. You will also see the length of time it took to retrieve the requested information. This is a display only view.
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NOTE: The result types that appear will depend on what you have selected when running the query.. |
Users can define how long to wait before a query will time out. This setting is defined in the Query Tool Options, which can be accessed by clicking on the Show Options button ().
The default setting is 180 seconds, which means the web client will wait for a response from the server for 180 seconds. Once it reaches that time it will display a message saying the query has timed out and will continue to run in the background.
This section describes the process of adding items to the query tool, "AND" / "OR" operators and setting constraints.
In order to create your query, you will need to define what information will be retrieved from the databases. Selected items from other i2b2 Web Client views can be dragged and dropped (copied) into the Query Tool view.
Concepts () can be defined as terms, results, providers, etc. They can be added as a group (folder ()) or individually by dragging the item(s) from Navigate Terms, Find Terms, and Workplace views.
Modifiers () are associated with a concept or group of concepts. They can be added as a group ( modifier folder ()) or individually by dragging the item(s) from Navigate Terms, Find Terms, and Workplace views.
A new query can be created from one that has already been run by dragging the previous query (
) from Previous Query and Workplace views.
A patient set () can be can be used in a query by dragging the patient set from Previous Query and Workplace views . When you run the query it will use the patient set to query against.
An encounter set () can be used in a query by dragging the patient set from Previous Query and Workplace views. When you run the query it will use the encounter set to query against.
There are two operators, known as SQL Logical Operators, which are necessary when running a query that has more than one item. These operators provide a way to specify exactly what you want to retrieve. The operators are the 'AND' and 'OR' operators.
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IMPORTANT: The query tool knows which operator to use based on the panels used when defining the query. It is important to verify you are setting up your query correctly as each operator will return different results. |
The AND operator returns a record if both the first condition and the second conditions are true.
The query tool uses the AND operator when concepts are listed in different panels.
Example:
WHAT: Return only those patients who have Acute Myocardial Infarction AND Angina Pectoris.
HOW: In the query tool add the concept Acute Myocardial Infarction to Group 1 and then add the concept Angina Pectoris to Group 2.
RESULT: The population is limited by requiring the patients fulfill both requirements.
The OR operator returns a record if either the first condition or the second conditions are true.
The query tool uses the OR operator when concepts are listed in different panels.
Example:
WHAT: Return only those patients who have Acute Myocardial Infarction OR Angina Pectoris.
HOW: In the query tool add both concepts Acute Myocardial Infarction and Angina Pectoris to Group 1.
RESULT: The population is broadened to include all patients who fit either one of those criteria.
Concepts can be added to the Query Tool view by simply dragging the concept from one of the following views.
How to add a concept from each of these views is explained in the next few sections.
The Navigate Terms view contains a hierarchical display of all the items that can be used to search the database.
|
NOTE: How the items are grouped and displayed is dependent on how the database is setup. |
) or folder () by clicking on its name.
The Find Terms view provides a way to search for a particular concept.
|
NOTE: For detailed information on how to search for terms, please see the i2b2 Find Terms help. |
) or folder () by clicking on its name.
Information in the workplace is related to the most common concepts, modifiers, and queries that an individual uses and in essence becomes their personal workplace.
) or folder () by clicking on its name.
Modifiers can be added to the Query Tool view by simply dragging the modifier from one of the following views.
How to add a modifier from each of these views is explained in the next few sections.
The Navigate Terms view contains a hierarchical display of all the items that can be used to search the database.
|
NOTE: How the items are grouped and displayed is dependent on how the database is setup. |
) or modifier folder () by clicking on its name.
The Find Terms view provides a way to search for a particular concept and modifier.
|
NOTE: For detailed information on how to search for terms and modifiers, please see the i2b2 Find Terms help. |
) or modifier folder () by clicking on its name.
Information in the workplace is related to the most common concepts, modifiers, and queries that an individual uses and in essence becomes their personal workplace.
) or modifier folder () by clicking on its name.
A previous query can be used to run a new query or as an item within a query (query-in-query). To add a previous query to the Query Tool view simply drag the query name from one of the following views.
Within the Query Tool view, the previous query can be added to one of the following two locations.
| Query Name field | The items and constraints from the original query will be used to create a new query. This information can be edited to make a new query or can be used as is to run the query again. |
| Panel (Group) | Used within a new query (query-in-query). The information associated with the previous query can not be edited. Add additional search criteria (items) to be used in the new query. |
How to add a previous query from each of the views listed above is explained in the next few sections.
The Previous Query view displays the queries that were run by the user.
) by clicking on its name.
|
NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
) by clicking on its name.
Information in the workplace is related to the most common concepts, modifiers, and queries that an individual uses and in essence becomes their personal workplace.
) by clicking on its name.
|
NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
) by clicking on its name.
|
NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
A patient set can be added to the Query Tool view by simply dragging the list of patients from one of the following views.
How to add a patient set from each of these views is explained in the next few sections.
The Previous Query view displays the queries that were run by the user.
) next to the name of the previous query that contains the patient set.
) next to the results folder.
) by clicking on its name.
Information in the workplace is related to the most common concepts, modifiers, and queries that an individual uses and in essence becomes their personal workplace.
) by clicking on its name.
An encounter set can be added to the Query Tool view by simply dragging the encounter set from one of the following views.
How to add an encounter set from each of these views is explained in the next few sections.
The Previous Query view displays the queries that were run by the user.
) next to the name of the previous query that contains the patient set.
) next to the results folder.
) by clicking on its name.
Information in the workplace is related to the most common concepts, modifiers, and queries that an individual uses and in essence becomes their personal workplace.
) by clicking on its name.
|
NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
Three panels are typically displayed as part of the standard Query Tool view. Some complex queries may require the use of additional panels.
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NOTE: In order to add a panel, the previous panels must contain at least one concept. |
On the toolbar at the bottom of the view, there are additional navigational buttons that will become active when more than three panels are being used.
 |
Begin button | will move the display to show the first panel |
 |
End button | will move the display to show the last panel in use |
 |
Previous button | will move the display back one panel |
 |
Next button | will move the display forward one panel |
There are three options for removing a concept from the Query Tool view. Users can (1) reset all the groups, (2) clear all items in a panel, or (3) delete an individual item from the group.
|
WARNING: Once you click on the clear button, all items in every group; and the constraints will be removed, therefore you need to make sure you want to delete ALL items. |
) located in the top right corner of the panel (next to the Group name).
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WARNING: Once you click on the delete button, all items in every group; and the constraints will be removed, therefore you need to make sure you want to delete ALL items. |
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WARNING: Once you click on the delete, any constraints specific to that item will be removed, therefore you need to make sure you want to delete that item. |
Constraints are used to narrow down the search criteria to a particular time frame, number of occurrences or a specific value or range of values. In i2b2, there are several types of constraints that can be defined in the Query Tool view.
| Constraint Type | Description |
|---|---|
| Temporal | Constraint is defined on the query level and utilizes the patient encounters and / or instance number when determining eligibility. |
| Panel Timing | Constraint is defined on the panel level and utilizes the patient encounters and / or instance number when determining eligibility. |
| Date | Constraint uses a date range when determining eligibility. |
| Occurrence | Constraint is by the number of occurrences an item is documented. |
| Exclusion | Constraint will not include patients with the concepts listed in the panel. |
| Value | Constraint is by the value associated to a concept or modifier. Not all items have values. |
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NOTE: In the client, the value constraints are currently the only ones that directly correspond to a single concept. All others are defined on the query or panel level. |
Both temporal and panel constraints are very similar in that both utilize the visit / encounter information along with the concepts defined to determine if a patient meets the search criteria.
The main difference between a temporal and a panel timing constraint is that temporal constraints are defined at the query level and panel timing constraints are defined at the panel level.
As stated in the previous section the Temporal Constraint is defined at the query level.
Users can select one of three available options:
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NOTE: In order to be considered the same instance, the facts have to have the same patient number, encounter number, concept, provider, start date, and instance number. |
Example:
Patient has a medication with a dose greater than 500 mg and a medication that is taken once a day documented at any time in their history.
RESULTS: there are 47 patients who have had a medication with a dose of 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where medication dose and frequency have the same patient_num.
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IMPORTANT: The panel timing will override the temporal constraint setting. |
Example:
Patient has a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same visit.
RESULTS: there are 41 patients who have had a medication with a dose of 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num.
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IMPORTANT: The panel timing will override the temporal constraint setting. |
Example:
Patient has a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same instance.
RESULTS: there are 36 patients who have had a medication with a dose of 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num , concept_cd, provider_id, start_date, AND instance_num.
As stated in the previous section the Panel Timing Constraint is defined at the panel level and can only be changed when the temporal constraint is defined as Selected groups occur in the same financial encounter or Items instance will be the same.
Users can select one of three available options:
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NOTE: In order to be considered the same instance, the facts have to have the same patient number, encounter number, concept, provider, start date, and instance number. |
The items (facts) listed in the panel can occur at any time in the patient's history.
The items (facts) listed in the panel occur during same visit (financial encounter).
In the example shown below, the items (facts) listed in the panel for Group 1 can occur at any time in the patient's history while the items in Group 2 and 3 have to occur during the same visit.
Example:
Patient has a diagnosis of Acute MI documented at any time in their history and they have a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same visit.
RESULTS: there are 4 patients who have had a medication with a dose greater than 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num AND the diagnosis of acute MI, the medication dose and frequency all have the same patient_num
The items (facts) listed in the panel occur during same instance.
In the example shown below, the items (facts) listed in the panel for Group 1 can occur at any time in the patient's history while the items in Group 2 and 3 have to occur during the same instance.
Example:
Patient has a diagnosis of Acute MI documented at any time in their history and they have a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same instance.
RESULTS: there are 3 patients who have had a medication with a dose of 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num , concept_cd, provider_id, start_date, AND instance_num AND the diagnosis of acute MI, the medication dose and frequency all have the same patient_num
Users can define a date range to be used when querying the database. This date range can be in any one of the following combinations.
The start date associated with the observation is what is used to determine if there is a positive hit.
Only data with activity within the defined date range will be used.
Example:
Concept: Acute Myocardial Infarction
From date: 01/01/2001
To date: 12/31/2005
In this example, if a patient has a diagnosis of Acute Myocardial Infarction (MI) entered on their record from 01/01/2001 to 12/31/2005 then their data will be included. If the patient does have an MI diagnosis but it was entered prior to 01/01/2001 or after 12/31/2005 then their information will not be included.
) to open the calendar view and click on the desired date.
Once you click on the desired date the calendar window will close.
Data from the defined start date to the latest date available. No end date defined.
Example:
Concept: Acute Myocardial Infarction
From date: 01/01/2001
To date:
In this example, if a patient has a diagnosis of Acute Myocardial Infarction (MI) entered on their record any time on or after 01/01/2001 then their data will be included. If the diagnosis was entered prior to 01/01/2001 then it will not be included.
) to open the calendar view and click on the desired date.
Once you click on the desired date the calendar window will close.
All data up until the defined end date. No start date defined.
Example:
Concept: Acute Myocardial Infarction
From date:
To date: 12/31/2005
In this example, if a patient has a diagnosis of Acute Myocardial Infarction (MI) entered on their record prior to and including 12/31/2005 then their data will be included. If the diagnosis was entered after 12/31/2005 then it will not be included.
) to open the calendar view and click on the desired date.
Once you click on the desired date the calendar window will close.
Users can define the number of times an item has to occur in order to be considered a positive "hit".
The exclude constraint will not include patients with the item(s) listed in the panel.
Value constraints can be associated with concept and modifiers but not all of them will have values. For instance, the diagnosis of Acute Myocardial Infarction does not have a value but the tests used to make the diagnosis do have values (high, low, numeric, etc.).
For those items that do have values there are different types of values that may be associated with it.
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NOTE: The different types of constraints and how they work are the same regardless of whether or not it is associated with a concept or a modifier. |
Flags are defined in the source system when the value is entered. The following are some examples that can be found in the i2b2 Demo database.
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NOTE: The value constraint window will open automatically when you drop a concept into a panel in the Query Tool view. This will only happen if the concept is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
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NOTE: The modifier value constraint window will open automatically when you drop a modifier into a panel in the Query Tool view. This will only happen if the modifier is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
The text value is defined in the source system when the value is entered. The following are some examples that can be found in the i2b2 Demo database.
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NOTE: The value constraint window will open automatically when you drop a concept into a panel in the Query Tool view. This will only happen if the concept is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
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TIP: To select more than one you can hold down the <Ctrl> key while clicking on each name. On the Macintosh you can hold down the command key instead of the <Ctrl> key. |
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NOTE: The modifier value constraint window will open automatically when you drop a modifier into a panel in the Query Tool view. This will only happen if the modifier is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
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TIP: To select more than one you can hold down the <Ctrl> key while clicking on each name. On the Macintosh you can hold down the command key instead of the <Ctrl> key. |
The numeric value is defined in the source system when the result is entered. The following are some example formats that can be found in the i2b2 Demo database.
Unlike flag and text values, numeric values use operators, such as greater than or less than when setting the constraints. The following is a listing of operators currently in use.
| Operator | Description / Use |
|---|---|
| Less Than (<) | Any value less than the number entered. |
| Less Than or Equal To (<=) | Any value less than or equal to the number entered (inclusive). |
| Equal To (=) | An exact match to the number entered. |
| Between | Any value in the range of numbers entered. |
| Greater Than (>) | Any value greater than the number entered. |
| Greater Than or Equal To (>=) | Any value greater than or equal to the number entered (inclusive). |
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NOTE: The value constraint window will open automatically when you drop a concept into a panel in the Query Tool view. This will only happen if the concept is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
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NOTE: The modifier value constraint window will open automatically when you drop a modifier into a panel in the Query Tool view. This will only happen if the modifier is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
Units in regards to i2b2 are the standard units of measurement associated with a value. For instance, a medication may have "mg" listed as the unit for the dose, while a HGB lab test may have "gm/dL".
The units are defined in the source system and although it is recommended that all numerical facts are stored in normalized units it is recognized that this is not always feasible. Therefore, the Web Client has the ability to convert the units when running a query.
In order for this feature to work a parameter called CRC_ENABLE_UNITCD_CONVERSION must be defined for the project. If this is not defined you need to contact your system administrator.
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NOTE: The modifier value constraint window will open automatically when you drop a modifier into a panel in the Query Tool view. This will only happen if the modifier is set up in the database with XML metadata. The first three steps can be used if you did not add a value constraint when you added the item or if you wish to edit an existing item. |
In the above scenario, the normal units are "mg". When setting up the value constraint the units were changed to "gm" and the numerical value was set to 5. Upon saving the value constraint, the Web Client converted 5 gm to 5000 mg. When the query is run it will look at those facts that have both 5 gm and 5000 mg defined in the observation_fact table.
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NOTE: The unit conversion information is specific to the term and is defined in the i2b2 metadata table. |
This section describes the process of running a query and the output.
When you run a query you need to select what type of result the server will return. There are several result types available, each of which will yield a different output.
| Patient set | Provides a list of patients who met the search criteria. |
| Encounter set | Provides the total number of encounters that met the search criteria. |
| Number of patients | Provides the total number of patients who met the search criteria. |
| Gender patient breakdown | Provides a breakdown of the patients by their gender. |
| Vital Status patient breakdown | Provides a breakdown of the patients by their vital status. |
| Race patient breakdown | Provides a breakdown of the patients by their race. |
| Age patient breakdown | Provides a breakdown of the patients by their age. |
| Timeline | Not used in the Web Client. If selected it will work the same as patient set. |
The result type(s) will appear when you click on the Run Query button and they can be selected in any combination.
This option will return a set of patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a set of encounters for those patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a total count for those patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a breakdown by gender for those patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a breakdown by vital status for those patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a breakdown by race for those patients who meet the defined criteria and will display the appropriate information in the following views.
This option will return a breakdown by age for those patients who meet the defined criteria and will display the appropriate information in the following views.
Once the query criterion has been defined, the final steps are to click on the Run Query button, select the result type(s), and click on the OK button to run the query.
Once you begin the process of running the query the Query Status view will display "Running Query", the name of the query, and the time that has elapsed.
To cancel a query you simply click on the Cancel Query button.
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NOTE: Keep in mind "Cancel Query" and the associated action will only appear when the query is still in the process of running |
This section describes the process of saving queries.
A previous query () is created automatically when a query is run from the Query Tool. The query is stored in the database and displayed in the Previous Query view.
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NOTE: Previous queries can also be seen in Workplace view if the user copied it to their workplace or shared folder in workplace view. |
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NOTE: If the previous query does not appear in the list automatically you can refresh the view to update the list. This is done by using the right mouse button and clicking anywhere in the Previous Query view. |
Users are able to print out the query information if they wish to have a hard copy of the search criteria defined for a query.
When printing a query you can either print the information for a current query or you can drag a previous query to the query tool view and print the information associated with that query.
The following steps outline the process of printing a query once you have the appropriate query in the Query Tool.
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:
The items stored in the Workplace view can be used in many of the i2b2 views and plug-ins, such as the Query Tool view plug-in.
This section describes the layout and contents of this view.
As stated above the Workplace view is a place for users to store and organize those items they use on a regular basis. It is also a way to share these items with other users by placing them in the SHARED folder.
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.
The highest level is the individual user folder (). This folder is automatically created with the user's name and it is used to store items added by the individual user. This level cannot be used when creating a query.
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NOTE: This also includes the shared folder. |
A folder (
) in the workplace view contains other folders and / or items added by the user. It can be expanded and collapsed by clicking on the plus sign () or negative sign () next to it. A user defined folder can not be dragged to other i2b2 views. It can be moved around within the Workplace view.
Items are the lowest level of the hierarchy. They can not be expanded further. Some examples of items are listed below.
)
)
)
)
)
)
Users can expand or collapse a folder by clicking on the plus sign () or negative sign () next to the folder icon.
) next to the folder in the Workplace view.
) next to the folder in the Workplace view.
Users can easily rename an existing folder.
Users can change the default annotation for any of their folders in the Workplace view.
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NOTE: The annotation is what is displayed in the tool tip. |
Users can remove a folder from the Workplace view.
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WARNING: All items in the folder will be deleted when the folder is removed. It is recommended that you move those items you want to keep to another folder. |
Users can easily rename an item in the Workplace view.
Users can change the default annotation for any of the items in their Workplace folder.
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NOTE: The annotation is what is displayed in the tool tip. |
Users can remove items from the Workplace view.
This section describes how to add items to the Workplace view.
Items can be dragged and dropped (copied) into the Workplace view from other views in the i2b2 Web Client.
A folder () and all its concepts (children) can be added to Workplace by dragging the folder name from one of the following views.
A modifier folder () and all its modifiers (children) can be added to Workplace by dragging the folder name from one of the following views.
A concept () can be added to Workplace by dragging the name of the concept from one of the following views.
A modifier () can be added to Workplace by dragging the name of the modifier from one of the following views.
A Patient set () can be added to Workplace by dragging the name of the patient set from the following view.
An Encounter set () can be added to Workplace by dragging the name of the encounter set from the following view.
A previous query () can be added to Workplace by dragging the name of the previous query from the following view.
The Find Terms view provides a way to search for a particular concept.
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NOTE: For detailed information on how to search for terms, please see the i2b2 Find Terms help. |
) or concept () by clicking on its name.
The Navigate Terms view contains a hierarchical display of all the concepts and modifiers that can be used to search the database.
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NOTE: How the items are grouped and displayed is dependent on how the database is setup. |
) or concept () by clicking on its name.
The Find Terms view provides a way to search for a particular concept.
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NOTE: For detailed information on how to search for terms and modifiers, please see the i2b2 Find Terms help. |
) or modifier () by clicking on its name.
The Navigate Terms view contains a hierarchical display of all the concepts and modifiers that can be used to search the database.
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NOTE: How the items are grouped and displayed is dependent on how the database is setup. |
) or modifier () by clicking on its name.
The Previous Query view displays the queries that were run by the user. Each previous query contains a set of results; within these results are the result options that were selected when the query was originally run. The result options include Patient set, Encounter set, Number of patients as well as various other patient breakdowns
) by clicking on the name of the query.
) next to the name of the previous query that contains the patient set.
) next to the results folder.
) by clicking on its name.
) next to the name of the previous query that contains the encounter set.
) next to the results folder.
) by clicking on its name.
This section describes how to use items in the Workplace view.
Items can be dragged and dropped (copied) from the Workplace view to other views in the i2b2 Web client.
An ontology 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.
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NOTE: User folders can not be dragged from the Workplace view. |
A modifier folder () and all its modifiers (children) can be added to other views by dragging the modifier folder name from Workplace to one of the following views.
A concept () can be added to other views by dragging the name of the concept from Workplace to one of the following views.
A modifier () can be added to other views by dragging the name of the modifier from Workplace to one of the following views.
A previous query () can be added to other views by dragging the previous query name from Workplace to one of the following views.
A specific set of patients can be added to other views by dragging the Patient set () from Workplace to one of the following view.
A specific set of encounters (visit list) can be added to the other views by dragging the Encounter set () from Workplace to one of the following view.
A folder or individual concept can be added to the query tool view by simply dragging the item from Workplace view and dropping it into one of the panels in the Query Tool view.
) by clicking on the name of the folder.
) by clicking on the name of the folder.
A modifier folder or individual modifier can be added to the query tool view by simply dragging the item from the Workplace view and dropping it into one of the panel in the Query Tool view.
) by clicking on the name of the modifier.
A previous query can be used to run a new query or as an item within a query (query-in-query). To add a previous query to the Query Tool view simply drag the query name from the Workplace view.
Within the Query Tool view, the previous query can be added to one of the following two locations.
| Query Name field | The items and constraints from the original query will be used to create a new query. This information can be edited to make a new query or can be used as is to run the query again. |
| Panel (Group) | Used within a new query (query-in-query). The information associated with the previous query can not be edited. Add additional search criteria (items) to be used in the new query. |
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NOTE: The process of adding a previous query to the Query Tool view is the same for both standard i2b2 queries ( |
/ ) by clicking on the name of the query.
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NOTE: When you run the query it will receive a new name. This is to distinguish the first previous query from the second. |
/ ) by clicking on the name of the query.
A Patient set can be used as an item within a query. To add a patient set to the Query Tool view simply drag the name of the patient set from the Workplace view.
) by clicking on its name.
An Encounter set can be used as an item within a query. To add an encounter set to the Query Tool view simply drag the name of the encounter set from the Workplace view.
) by clicking on its name.