CaTISSUE Suite
Download
1 / 34

CaTISSUE Suite Nov. 2007 - PowerPoint PPT Presentation


  • 126 Views
  • Uploaded on

CaTISSUE Suite Nov. 2007. Rakesh Nagarajan, M.D., Ph.D. Mark A. Watson, M.D., Ph.D. Washington Univ. / Siteman Cancer Center. Srikanth Adiga Kapil Kaveeshwar Poornima Govindrao Aarti Sharma Gautam Shetty Mandar Deshmukh. caTISSUE. 050107. Suite. http://caBIG.nci.nih.gov.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' CaTISSUE Suite Nov. 2007' - herrod-acosta


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

CaTISSUE Suite

Nov. 2007

Rakesh Nagarajan, M.D., Ph.D.

Mark A. Watson, M.D., Ph.D.

Washington Univ. / Siteman Cancer Center

Srikanth Adiga

Kapil Kaveeshwar

Poornima Govindrao

Aarti Sharma

Gautam Shetty

Mandar Deshmukh

caTISSUE

050107

Suite

http://caBIG.nci.nih.gov


  • caTISSUE Core 1.1 (WU) – Core object model and reference inventory system for research biospecimen management.

  • caTISSUE Clinical Annotation Engine 1.2 (UPMC) - Annotation of biospecimens with pathology data using CAP protocol data elements.

Tissue Banks and Pathology Tools (December 2006)

caTIES 2.0 (UPMC) - Text extraction and de-identification of surgical pathology reports. Query and request system for archived tissue blocks.


caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006)

  • Resolution of caTISSUE Core bugs based upon ‘real life’ utilization

  • Improved usability and workflow of caTISSUE Core based upon ‘real life’ utilization

  • Integration of caTIES and caTISSUE Core

    • UML modeling

    • Updating HL7 data loader with matching algorithms and new model support

    • User interface to view pathology reports along with associated biospecimen data objects


caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006)

  • Integration of caTISSUE CAE and caTISSUE Core

    • UML modeling of CAP protocol CDEs to backbone objects

    • Less detailed but more comprehensive pathology representation

    • Clinical data:

      • Environmental exposure (Smoking, Alcohol)

      • Family history

      • Clinical events / follow-up

      • Therapy

  • Dynamic data extensions

    • User interface to add data elements

    • Query based on local data elements


caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006)

  • Informed consent tracking

  • Biospecimen request and fulfillment

    • Based on pathology report cases (caTIES)

    • Biospecimens

    • Biospecimen derivatives

    • Biospecimen arrays

  • Integrated query interface

    • Support queries across biospecimens, reports, annotation, and data extensions.

    • Query across multiple instances of caTissue

    • Temporal query

    • New query interface

    • Ability to store queries & results

    • Ability to join query results


caTISSUE Suite Dynamic Extensions

  • Create new classes (entities) dynamically and associate them with the caTISSUE Core static model

    • Class, attribute, and associated metadata - Add/Edit/Delete

    • Data entry form generation: Form view and spreadsheet view

    • Validation rules (UI as well as backend)

    • Permissible values support (custom, EVS, CDE)

    • Security for identified attributes

    • Entity reuse - Copy & share attributes

    • XMI: Import and export

    • caCORE API to add, edit and read


Metadata structure
Metadata structure

MODEL

EVS

1..*

CLASS

1..*

Concept Code

1..*

ATTRIBUTES

Download value domain

Class reuse

1..*

PERMISSIBLE VALUES

CDE reuse

caDSR


Dynamic extension use cases

Administrator creates new custom annotations

System stores metadata and creates RDBMS tables to store actual data

CREATE

Technician wants to add custom annotation

System auto generates web page to add custom annotation

System adds data to the database

DATA

Researcher query for Specimens based on custom annotation

System auto generates query criteria pages and provides ability to query across static and dynamic model

QUERY

Dynamic extension use cases


Sample entity creation user interface
Sample entity creation user interface

Build a Form

1. Define Form 2. Build Entity 3. Preview

Case

Add new attribute

Current Attributes

Text Field

Name Text Field

CDE:

Label :

Datatype

Size:

Default Value:

Permissible

values:

Check Box

Get info from caDSR

ID Text Field

Radio Button

Disease Check Box

Type List

List

Tissue

File Upload

Hierarchical Tree

Add

Grid

URL

Add associated class

Save & Add

Down

Up

Delete

Previous

Next


Consent Tracking Requirements for caTISSUE Suite

  • July 19, 2006

End users meet to discuss requirements for caTISSUE Suite.

Consent tracking given high priority.

Consent tracking working group formed.

(MD Anderson, PENN, UPMC, Dartmouth, Duke, TJU, NCI)

  • August 2006

Consent tracking working group identified key requirements for consent tracking functionality.

  • Sept. 2006

Summary document of consent tracking requirements created and reviewed by DSIC (see CVS).

  • Oct. 2006

Formal software requirements and wire frames for UI created by caTISSUE Suite development team (see CVS).

  • Dec. 2006

First iteration prototype of caTISSUE Suite application with consent tracking.























caTISSUE Iterative Development Plan

Milestone 1 (Dec. 15, 2006)

  • Harmonized UML model (in progress)

  • Dynamic extensions – simple object creation (in progress)

  • Design of query Interface (in progress)

  • Documentation (done)

    Milestone 2 (Jan 2007)

  • HL7 path data loader (in progress)

  • Distribution (in progress)

  • Consent tracking (SRS done)

  • Updates to UML model

  • Dynamic extensions – complex object creation

  • Query Interface

  • Finalize usability enhancements

  • Incorporate adopter comments

  • Documentation

  • APIs


caTISSUE Iterative Development Plan

Milestone 3 (Feb. 2007)

  • DE-ID pipeline changes (in progress)

  • Dynamic extensions – Support for permissible values

  • Integrated query Interface

  • Implement usability enhancements

  • Incorporate adopter comments

  • Documentation

  • API

    Milestone 4 (March 2007)

  • Concept coding pipeline changes

  • Dynamic extensions

  • Integrated query interface

  • Implement usability enhancements

  • Incorporate adopter comments

  • Documentation

  • Installer

  • API


caTISSUE Iterative Development Plan

  • Milestone 5 (April 2007)

    • Installer

    • Integrated query interface

    • Bug fixing and testing

    • Documentation

    • API

  • Milestone 6 (May 2007)

    • Bug fixing and testing

    • Documentation

    • API


ad