TIES Researcher Training
Elizabeth Legowski
Department of Biomedical Informatics
University of Pittsburgh School of Medicine
[email protected]
• TIES stands for Text Information Extraction
System
• Deployed UPMC-approved system for
retrieving de-identified data and identifying
and ordering images and tissue using
clinical radiology and surgical pathology
reports
• Provides access to 19 million radiology and
4 million pathology reports across all UPMC
hospitals from 2003-present
– Updated monthly and automatically from
clinical systems
Introduction to TIES
http://ties.upmc.com
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De-identification
Access from anywhere
Concept-based queries
Hierarchical indexing
Negation
Temporal queries
Honest broker support
Role-based access
Introduction to TIES
http://ties.upmc.com
Introduction to TIES
http://ties.upmc.com
http://ties.upmc.com
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Access the TIES Application
Submit account requests
How to videos and manuals
Get status updates
Helpdesk contact information
Introduction to TIES
http://ties.upmc.com
• Windows / MAC / Linux
• Java 1.5+
– Download latest version at
http://www.java.com
Logging In
http://ties.upmc.com
The TIES client is served as a Java Webstart application
To access TIES:
1. Access the website: http://ties.upmc.com
2. Click the ‘Launch TIES’ button:
3. Click the ‘Run’ button on the Java Webstart window.
It will take a short time to download the TIES application to your
computer. Fortunately, this only happens the first time you are
accessing TIES. After Webstart has finished downloading, you will
be asked to pick a data network to access.
Logging In
http://ties.upmc.com
1. Select ‘Test Data Network’ from the drop down
box and then click the ‘OK’ button
The Test Data Network contains dummy data (not real
data) and is used for training purposes.
2. Enter your username and password and click
the ‘Login’ button.
Logging In
http://ties.upmc.com
For TIES users, there are three roles to choose from:
Honest Broker, Researcher and Preliminary User.
3. Select ‘Preliminary User’ as the role from the
drop down box, and the appropriate study. Click
on ‘OK’ to finish the logging in process.
Logging In
http://ties.upmc.com
4. Read USAGE AGREEMENT and click ‘Accept’ if
you agree to the 3 terms provided in the box.
Logging In
http://ties.upmc.com
Current role and distribution protocol for this session
Tab bar is used to switch
between open tabs
Tool bar provides
quick access
Preliminary User Perspective
http://ties.upmc.com
Switch
between query
and results
Type search terms here
‘Advanced Dashboard’ link
Select report
type and
sections to
search
Query Builder pane
Preliminary User Perspective
Chart
options
Switch query
views
‘Start Search’ and
‘Start Over’ buttons
Dashboard View
http://ties.upmc.com
All of the
search terms
must be
present
At least 1 of
the search
terms must
be present
Search term
must be
present in
the negated
form
Query Builder pane
Preliminary User Perspective
Text search not available in
‘Preliminary User’ perspective
‘Start Search’ and
‘Start Over’ buttons
Advanced Dashboard
http://ties.upmc.com
Filters
palette
for
adding
and
deleting
filters.
Filters
can also
be added
by right
clicking
in the
diagram.
Currently
selected
filter
‘Start Search’ and
‘Start Over’ buttons
Diagram View
Query Builder Pane
Preliminary User Perspective
http://ties.upmc.com
• The simple dashboard query works very much like a Google™ search bar. It is
designed for very basic queries like: “Search for reports with adenocarcinoma”
• TIES selects the best matching NCI metathesaurus concept for each search
term entered, and returns the reports that contain the concept. If there are
multiple search terms, the returned reports contain all of the matching
concepts.
Enter
search
terms
here
NOTE: Race is NOT
consistently captured
on UPMC System
Dashboard Query Builder
http://ties.upmc.com
• If a word is misspelled, it will appear with red wavy lines
underneath, like this:
• To correct the spelling, right click on the word and choose the
correctly spelled word from the drop downs.
• Preliminary Users are not able to conduct Text Searches or create
Temporal Queries at this time.
• Print Screen function can capture results – which can be placed in
grants, reports and preliminary research documents.
• All Dashboard queries (Basic or Advanced) will translate into
Diagrams when you switch to the Diagram View. However, not all
Diagram queries can be shown in the Dashboard View.
Dashboard Query Builder
http://ties.upmc.com
• Treating search terms as Concepts generally returns more
accurate results.
• Concept searching returns reports containing the search term,
as well as reports containing synonyms of the search term.
– For example, when searching for reports containing ‘Bronchiolitis
Obliterans Organizing Pneumonia’, Text search will only return reports
containing exactly that string, whereas Concept search will also return
reports containing BOOP, COP, and any other synonyms of BOOP.
• In the Advanced Dashboard, search terms entered in the NOT
box (bottom empty search box) should be absent from the
report text when doing a Text search. When performing a
Concept search, the search term will need to be presented in
the negated form within the report.
– For example, if you enter ‘Adenocarcinoma’ in the NOT box for a Text
search, it will return all reports that do not contain the word
‘Adenocarcinoma’. If you do a Concept search, only reports containing
phrases such as ‘No evidence of adenocarcinoma’ or ‘Adenocarcinoma
not found’ will be returned.
Dashboard Query Builder
http://ties.upmc.com
Queries with a single word search term
Problem: Search for pathology reports with adenocarcinoma.
STEP 1: Type ‘adenocarcinoma’ in the search box. The text will turn blue once it matches to a concept.
STEP 2: Select the ‘Pathology’ checkbox under Report Types to limit your search to pathology reports.
STEP 3: Click on ‘Start Search’ button.
STEP 1
STEP 3
STEP 2
Dashboard Query Builder
http://ties.upmc.com
Can change search parameters
Can change type
of chart displayed
Number of
matches
returned in
‘any
section’
40 Matches from 2005
Can
change
sub- &
category
Bar Chart View
Chart Legend
Browsing Results
10 Matches from
2006
Hit ‘Update Chart’
button if any
changes are made
to chart type or
categories
Matches categorized by
‘Collection Year’
http://ties.upmc.com
Changes to query results
Problem: Change chart type to a pie chart showing age distribution.
STEP 1: Click on ‘Pie’ Chart Type.
STEP 2: Click on ‘Age’ in Categorize By drop down menu.
STEP 3: Click on ‘Update Chart’ button.
STEP 2
STEP 3
Dashboard Query Builder
http://ties.upmc.com
Each age
range
shown
Pie Chart View
Majority of matches
in 40-49 age range
Color coding for age range legend
Browsing Results
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Queries with a multi-word search term
Problem: Search for reports with atypical ductal hyperplasia.
STEP 1: Since “atypical ductal hyperplasia” is one concept, we type these words in the ‘All of these Concepts’ field.
Type ‘atypical ductal hyperplasia’ in the search box.
STEP 2: Click on ‘Start Search’ button.
STEP 1
STEP 2
Dashboard Query Builder
http://ties.upmc.com
Queries with multiple concepts
Problem: Search for reports with biopsies indicating atypical ductal hyperplasia.
STEP 1: Type ‘atypical ductal hyperplasia’ in the search box, a comma ‘,’, and then type ‘biopsy’.
STEP 2: Click on ‘Start Search’ button.
STEP 1
STEP 2
Dashboard Query Builder
http://ties.upmc.com
Queries with demographics
Problem: Create a bar chart of 30-40 year old females with atypical ductal hyperplasia categorized by event
STEP 1: Type ‘atypical ductal hyperplasia’ in the search box.
STEP 2: Under Age, select ‘ranging between’; type ‘30’ in the Min box; type ‘40’ in the Max box.
STEP 3: Select ‘Female Gender’.
STEP 4: Choose ‘Bar Chart’.
STEP 5: Categorize by ‘Event Year’.
STEP 6: Click on ‘Start Search’ button.
STEP 1
STEP 5
STEP 3
Dashboard Query Builder
http://ties.upmc.com
Click on ‘Switch Role’ button and
change to ‘Researcher’ perspective
Researcher Perspective
http://ties.upmc.com
Read USAGE AGREEMENT and click ‘Accept’ if you
agree to the 4 terms provided in the box.
Researcher Perspective
http://ties.upmc.com
Can now set “Number of Results”
Note expanded toolbar
Researcher Perspective
http://ties.upmc.com
For more advanced queries, switch to the “Advanced Dashboard” by
clicking on the blue link under “More options?”
To switch to the ‘Advanced
Dashboard’ – click on this blue link
Advanced Dashboard Query Builder
http://ties.upmc.com
The Advanced Dashboard is always synced with the Simple Dashboard, so if you had a query
already entered in the Simple Dashboard, it will be copied over to the Advanced Dashboard.
To switch back to the
‘Basic Dashboard’ click on this blue link
Same as ‘Basic Dashboard’ box
Additional search boxes let you
specify boolean OR and NOT logic
Select ‘Concept’ to map the search terms to NCI
metathesaurus concepts and search with those concepts.
Select ‘text’ to treat the search terms as text strings.
Specify demographic criteria for patient here
Advanced Dashboard Query Builder
http://ties.upmc.com
Queries with OR
Problem: Search for reports with cicatrix or radial scar.
STEP 1: Type ‘cicatrix’ in the OR search box, followed by a comma ‘,’ and ‘radial scar’.
STEP 2: Specify the ‘No. of Results:’ to ‘100’.
STEP 3: Click on ‘Start Search’ button.
STEP 2
STEP 1
Advanced Dashboard Query Builder
http://ties.upmc.com
‘Change’ returns to
original query
Patient details
Results in
tree
format.
Report details
Choose how report text
is visually displayed
Reports
grouped
by
patient.
Click on
any report
in the tree
to view.
Can save
reports in
separate
case sets.
Later,
case sets
can be
viewed or
submitted
as orders
for tissue.
Browsing Results
Report results in
text format
http://ties.upmc.com
• Report options available in the File Menu
– Print
– Export
– QA options
 Request Review
o Use for flagging problematic reports (ex: report doesn’t
fit search criteria, concepts are not colored correctly in
the annotations)
 Quarantine
o Use for reports that are not completely de-identified.
o Once quarantined, reports are not available for searches
until un-quarantined by a system administrator.
Report Options
http://ties.upmc.com
Diagram button
Filters
palette
for
adding
and
deleting
filters.
Filters
can also
be added
by right
clicking
in the
diagram.
Diagram Query Builder
Initial diagram with a
single search term box
http://ties.upmc.com
• A query diagram consists of boxes connected by
arrows.
• A box in the diagram view is used to represent a filter
constraint on the query. The arrows indicate the
order in which the various constraints are checked on
any report.
• The placeholders, ‘All Reports’ and ‘Filtered Reports’,
are special boxes that represent the start and end of
the diagram.
• The results of the query are all the reports that make
it to the ‘Filtered Reports’ Placeholder.
• Forks in the path indicate boolean OR conditions.
• Filters on the same path are logically ANDed together.
Diagram Query Builder
http://ties.upmc.com
•Report Type
•Search Term
• NOT Search Term
• Event Year
• Gender
• Age
Diagram Query Builder
http://ties.upmc.com
• Right clicking on any part of the diagram will display a
context sensitive menu
– Add/remove filter boxes, edit filter properties, or add/remove
temporal sub-queries
– Menu options differ based on what was right clicked.
• All elements in the diagram can be moved around by
selecting them and dragging the mouse pointer.
• You can resize any filter box by dragging any of the 8 small
squares displayed around it when selected.
• Filter boxes (except the ‘All Reports’ and ‘Filtered Reports’
placeholders) can be deleted by:
– Selecting it and pressing the ‘Delete’ key on the keyboard OR
– Right clicking on the filter box and selecting ‘Delete Filter’
• Can also use the Filters palette to add/remove filter boxes
Diagram Query Builder
http://ties.upmc.com
Query requiring Boolean AND
Problem: Search for reports with biopsies indicating
atypical ductal hyperplasia.
STEP 1: Right-click on the green ‘Search Term’ box.
A dropdown menu will appear. Choose Edit filter
properties. Alternatively, double click the green
‘Search Term’ box.
STEP 3
STEP 2: Type ‘atypical ductal hyperplasia’ in the ‘add
concept here’ textbox
STEP 1
STEP 3: Click the + button, or press Enter.
STEP 4: Select the term(s) that best fit(s) your
concept. You can select multiple concepts if you feel
they are both good matches. When multiple concepts
are added to a single box, they are ORed together.
STEP 4
STEP 5
STEP 5: Click the ‘Done’ button.
continued on next slide…
STEP 5
Diagram Query Builder
http://ties.upmc.com
STEP 6: Step 5 will send you automatically back to the original ‘Search Term
Filter Properties’ popup window. Click the ‘Save’ button.
To add a filter box for biopsy we will use the Filters palette on the left-hand
side of the screen:
STEP 7: Click the
button in the Filters palette.
STEP 8: Similar to how we added a concept for ‘atypical ductal hyperplasia’ we
need to add a concept for biopsy. Repeat steps 2-6, this time for ‘biopsy’ .
Your final diagram should look like this:
STEP 6
Diagram Query Builder
http://ties.upmc.com
Query with Boolean OR
Problem: Search for reports with either lobular
carcinoma with microcalcification in the breast or
primary carcinoma of the liver with cirrhosis.
STEP 1: We will reuse the empty search term box
that is added when a new query is created. Modify
its properties to add ‘breast’ as a concept.
STEP 2
STEP 1
STEP 4
STEP 2: To add ‘liver’, with an OR relationship to
‘breast’ we will select the ‘breast’ box as the
reference box and right click. From the dropdown
menu, choose ‘Add ORed Filter’ and click ‘OK’ for
‘Search Term’ filter type.
STEP 3: Type ‘liver’ in the ‘add concept here’
textbox.
STEP 4: Click the + button, or press Enter.
STEP 5: Select the term(s) that best fit(s) your
concept.
STEP 6: Click the Select Concepts ‘Done’ button.
STEP 7: Click the ‘Save’ button.
continued on next slide…
STEP 6
STEP 7
Diagram Query Builder
http://ties.upmc.com
STEP 8: Now we need to add ‘lobular carcinoma' and ‘microcalcification’ with a boolean AND relationship to the
breast box, and add ‘primary carcinoma' and ‘cirrhosis’ to the liver box. Using steps learned before, add these
search terms.
Your final diagram should look like this:
Diagram Query Builder
http://ties.upmc.com
Temporal Query
Problem: Search for patients with a benign biopsy followed by a report indicating carcinoma within 5 years.
STEP 1: For a temporal query, we create the first part of the query just as we did in earlier exercises. Your
diagram should look like the one shown here.
continued on next slide…
Diagram Query Builder
http://ties.upmc.com
STEP 2: Now we add another query to represent the second part of the query. Right click on any clear area within
the box enclosing the query to popup the query menu, and select ‘Add Temporally related sub-query’ from the
menu. Alternatively, click the Patient Event button in the Filters palette. Your diagram should now look like this:
continued on next slide…
Diagram Query Builder
http://ties.upmc.com
STEP 3: Edit the search term box in the second query to specify a ‘carcinoma’ concept. Your diagram should now
look like this:
continued on next slide…
Diagram Query Builder
http://ties.upmc.com
STEP 4: The last thing is specifying the temporal constraint. Double click on the arrow connecting the subqueries to specify it, or right click the arrow and select ‘Modify Temporal filter properties’. Then select the
‘equal/less/greater” radio button and specify less than 5 years using the widgets. Press ‘OK’ to finish.
continued on next slide…
Diagram Query Builder
http://ties.upmc.com
Now, your diagram should look like this:
The Patient Events can be as complex as you want and there can be more temporal events following Patient
Event 2.
Diagram Query Builder
http://ties.upmc.com
Diagram Exercise:
Find patients who had no evidence of thyrotroph
adenoma less than 3 years prior to being diagnosed with
Brain Hemangioma
Diagram Query Builder
http://ties.upmc.com
Solution:
Diagram Query Builder
http://ties.upmc.com
You can save queries in TIES for later retrieval by using the
‘Save Query’ button or ‘Save Query’ and ‘Save Query As’
options in the file menu. The ‘Save Query As’ dialog box is
shown here:
Queries already saved
by this user
Name and description for
the query
Saving & Loading Queries
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You can open queries previously saved by you, or other
members of your distribution protocol.
Go to File and choose ‘Open Query’. The ‘Open Query’ dialog
box is shown here:
View queries created by
others using the
dropdown menu here
Saving & Loading Queries
http://ties.upmc.com
• Researchers can group reports into case sets.
• Case sets can be used to group interesting cases
together and can be viewed and modified by all
researchers in the distribution protocol.
• Case sets can be submitted as orders for
tissue/data.
• Tissue ordering in TIES is a multi-step process
involving communication with the honest broker
to confirm the order.
Case Sets
http://ties.upmc.com
Researchers create case sets by clicking the + button
under Case Sets in the Results view.
Reports can be added to existing case sets by dragging
reports to the desired case set.
Case Sets
http://ties.upmc.com
Submit or delete an order here
Order View
Case set name
3 reports added as
order items. Click on
an order item to load
its view in the right
pane.
All orders are
classified into Case
Sets, Submitted, or
Completed orders
Case Sets
http://ties.upmc.com
Area to specify ordering
instructions specific to
this case
De-identified pathology
report for this case
Case Sets
http://ties.upmc.com
Researchers can submit a case set by selecting it in the ‘My Case
Sets’ tab and clicking on the ‘Submit’ button in the ‘Available Tasks’
section.
TIES will add the order to the honest broker’s queue. It will also
move the order to the ‘Submitted Orders’ group for the researcher.
Case Sets
http://ties.upmc.com
Rebecca Jacobson ( Principal Investigator )
[email protected]
Girish Chavan ( Project Manager )
[email protected]
Kevin Mitchell ( Developer )
[email protected]
Elizabeth Legowski ( User Support )
[email protected]
http://ties.upmc.com