TIES Cancer Research Network
Y3 Face to Face Meeting
U24 CA 180921
Session 7 Year 3 Development Plan
October 9th, 2015
University of Pennsylvania
Agenda
• Update on Year 2 Releases
– TIES v5.4 Demo – virtualslides and structured data support
– Plans for TIES v5.5
• Discussion – Y3 development needs for new
sites, pilot projects.
• Y3 Project Plan
Year 2 Releases
• v5.1 – Released on 01/15/2015
– Attach and store IRB documents related to studies.
– Node Control Panel to customize a node after installation.
– TCRN registration licensing for non-member institutions.
– Improved Login screen.
– Manually scrub identifiers.
– Add patient information to QA View.
– Add patient name to exported CSV for honest broker order
export.
– Support partial matches in concept search in diagram view.
Year 2 Releases
• v5.2 – Released on 03/25/2015
– Internal release to TCRN members only
– Node management tool
– Patient name deidentifier
Year 2 Releases
• v5.3 – Released on 06/01/2015
– Installer for TCRN Node
– New Metadata storage system (preliminary)
– New search mechanism (preliminary)
– Node management tool
– Patient name, MRN, SSN and accession no. de-identifiers
– Whole Slide Imaging
– Account Lockout
• We put in place a release process that supports a smooth transition
for TCRN nodes running different versions of TIES.
Year 3 Planned Releases
• v5.4 – Scheduled for 10/15/2015
– New structured data storage system (final)
– New search mechanism (final)
– Data Cleanup Utility
– Patient initials de-identification
– Auditing Support
Structured Data Support – Why?
• Common requests from users:
– Can I get outcomes data for patients?
– I want to limit my search to patients that have not had a
recurrence of the cancer.
• Every research study collects, curates and generates data on patients
that is then trapped within that research group. How can we leverage
that data for fulfilling future data requests?
Structured Data Support
• Allows you to import data from data sources, e.g. Cancer Registry,
Tissue Bank etc.
• Combine search criteria across all data sources and the TIES concept
coded reports.
• Easy to setup and user. Ability to import from MS Excel/CSV/BSV or
other delimited file formats.
• You can also search data sets from other institutions.
Structured Data Support
Patient
Pathology
Report
Patient
Or Report
Cancer Registry
Tissue Bank
Dataset
• Disease free
survival
• Recurrence
• Materials
Available
• IPOX Stains
• ER Status
• PR Status
• Materials
Available
• IPOX Stains
• No. of lymph
nodes
…
•
•
•
•
Text Attribute
Numeric Attribute
Category Attribute
Boolean Attribute
Structured Data
Model
10
New utility to load delimited files into TIES
11
Configuration File
Data File
12
Virtualslide Support
• Uses OpenSlide library that supports a wide range of
formats(http://openslide.org/)
– Aperio (.svs, .tif) Hamamatsu (.vms, .vmu, .ndpi) Leica (.scn) MIRAX
(.mrxs) Philips (.tiff) Sakura (.svslide) Trestle (.tif) Ventana (.bif, .tif)
• Can connect to native image servers or OpenSlideServer.
• Load image data using Structured Data Loader Utility.
Configuration File
Data File
14
Demonstrate new features in the upcoming TIES v5.4 release
DEMO
15
Virtual Slide Support
16
Virtual Slide Support
Structured Data Search
18
Structured Data Search
19
Year 3 Planned Releases
• v5.5 – Scheduled for 02/15/2016
– LDAP Authentication
– Updated case set and query management
• Easily share/import/export case sets and queries.
• Template queries
– API access to hub – users, case sets and orders.
– TMA Support
LDAP Authentication
• Will use LDAP Binding
• TIES Nodes will be configured during installation
– Existing nodes will be configured during upgrade
• LDAPs on different networks for the same site can be supported.
– Will require an IP specific firewall exception to allow TIES node
server to connect to LDAP server on another network.
Do you have multiple networks that you need to support?
YEAR 3 PROJECT PLAN
What is left over from Y2…
• We adapted to changing requirements and priorities, hence we did
not get to these features:
– Different de-identifier (MIST)
– Publicly accessible statistics on node
– Patient level visualization
– Detailed data loading report
– Remove outside consult from cases
What are your top 3 pain points / feature requests?
DISCUSSION – PARTNER INSIGHTS
Y3 Project Plan
• Identify non-software goals (Rebecca).
• Prioritize software features.
• Create a rough project schedule.
Feature
RPCI
GRU
PENN
Whole Slide Image (WSI) TIES Integration
D.1.4 Add virtual slide visualization to TIES. We will add virtual slide visualization to support review of
FFPE before tissue transfer, block annotation for paraffin registries, development of TMAs, and
nondestructive tissue uses. We will leverage the open source SlideServer and SlideViewer software
developed in our group to deliver and display virtual slide images for another NIH funded project50.
SlideViewer uses native file format readers and the OpenSlide library (http://openslide.org/) to
support all major whole slide image file formats ensuring maximum compatibility.



implement a scalable architecture for
associating whole slide images to
documents
implement virtual slide metadata
creation and query modules
update the UI to allow for limiting
searches to virtual slides, querying
virtualslide metadata and displaying
virtual slides in the TIES client.
+
Open Slide Server
OpenSlide is a product of the research
group of M. Satyanarayanan (Satya) in
the Carnegie Mellon University School
of Computer Science.

C library with Java and Python bindings
http://openslide.org
Supports multiple vendors

Free and Open Source
•
Aperio (.svs, .tif)

Has a basic Java client
•
Hamamatsu (.vms, .vmu, .ndpi)
•
Leica (.scn)
•
MIRAX (.mrxs)
•
Sakura (.svslide)
•
Trestle (.tif)
•
Generic tiled TIFF (.tif)
Can convert images to deep zoom
format to display in OpenSeadragon
HTML5 viewer

HTTP image server using this library
has been developed at University of
Pittsburgh

How TIES connects to Whole Slide Images (WSI)



TIES
node
TIES
Public
Database

User finds a de-identified
report of interest in TIES
Report happens to have WSI
related metadata attached to it
s.a. image server URL, image
path etc.
TIES client loads a WSI
directly from the image server
IF image server is behind an
institutional firewall, THEN
access to images is restricted
to people within that institution
How TIES load WSI related data




TIES requires a delimited file (spreadsheet) s.a. CSV or BSV that contains:
 WSI accession number
 WSI image type.
Ex: aperio
 WSI server URL. Ex: http://image.upmc.edu:8080/
 WSI image path.
Ex: GI/test2/image3.svs
 Other useful metadata s.a. Stain, Part, Block, Level, Institution
Accession number is used to cross-reference WSI with an identified report
in TIES private database.
Once identified report is found, WSI metadata is associated with TIES deidentified UUID and non-PHI attributes are transferred to TIES public
database where both report and image are de-identified
Accession number is the only way we can link WSI with text report