# Presentation: 948412

## The University of PittsburghCancer InstituteCenters for Oncology and Pathology Informatics 

- 	 **CaBIG Kickoff Meeting**
**	**** ****Vocabulary/CDE WG**
**	**** ****Feb 19-20, 2004**
**	**** ****Rebecca Crowley, MD, MS****	**

## Outline

- Ideas about priorities
- Pitt involvement in other projects of interest
- What we can do to work best with Domain Workspaces
- What we can contribute – Framework for Free-Text concept coding and IE
- Some initial thoughts on CDE Development

## Ideas about priorities:

- Work with Domain Space Developers – bottom up development of CDEs
- Decide on general purpose **applications **as well as **processes** for CDE development
- Work with the Architecture Group to understand and adapt to architecture for interoperability
- Select or develop solutions for certain general vocabulary-based tasks (free-text coding of clinical documents might be one of these tasks)

## University of Pittsburgh  - Oncology and Pathology Informatics

- 	  _Roles In CaBIG:_
- Developers in Clinical Trials Workspace
- Developers in TBPT Workspace
- Member of Architecture WG
_**Other collaborative projects we have been involved with:**_
- Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC) – Abramson Cancer Center (U Penn), Fox Chase Cancer Ctr, Kimmel Cancer Ctr (TJU), Penn State Cancer Center (Hershey) and Wistar Institute
- Shared Pathology Informatics Network (SPIN) – Harvard, UCLA, Univ Indiana
- Cooperative Prostate Cancer Tissue Resource (CPCTR) – GWU, Howard Univ, Med College of Wisconsin, NYU and VA
- Patient Safety Database – Kaiser Permanente, Henry Ford, Univ Iowa and West Penn Allegheny
- Early Detection Research Network – Numerous sites; data sharing model
- Molecular Reclassification of Cancer/Director’s Challenge – numerous sites, have shared data with caBIG through GEDB portal

## Pittsburgh Tissue Banking and PathologyDevelopers Proposal

- We propose a project with three related phases running in parallel depending on feedback from the adopter sites
**The basic systems to support “best practices” in tissue banking**
- Universal Consent, Sample Inventory, Manual Annotation using local data elements, Web Based Query and Display of Tissue Bank Data
- Existing UPMC or Adopter production software will be used
**Common Data Elements & Sharing of Data and Applications in caBIG**
- Applications based on a CDE Registry, Mapping Application (local Data Elements to CDE)
- Existing production software will have to be hardened and extended
**Establishment of Automated Tissue Annotation**
- Allow clinical systems (AP-LIS, CP-LIS, Cancer Registry, WSI) and Major Research Labs to provide annotation data directly
- Aggregation and Mapping tools are available at UPMC, but local expertise and implementation is necessary
- Free text De-identification (production) and UMLS Autocoding (beta) software is available

## Relevant Standards currently in use in Pittsburgh TBPT Applications

## CTMA Overview

- Supports a range of users including
- Nurse Coordinators
- Data Managers
- Clinicians
- Administrators
- Researchers
- Manages all or part of 250 active protocols representing in-house, Co-op, NCI and pharmaceutical-sponsored trials
- Contains clinical data for approximately 16,000 patients (including legacy systems)
- Currently deployed at UPCI
- Deployment at three community hospitals is underway

## Relevant Standards currently in use in Pittsburgh Clinical Trials Application (CTMA)

## Ideas for collaborating with Domain WG

- Assign liaisons to WG; ask for liaisons on Domain side as well
- Identify existing use cases, object models and work processes within Domain WS and evaluate how well they generalize
- Develop inventory (checklist style) of current data standards, terminologies used among all the developer and adopter sites in CaBIG – relevant to the three Domain WS
- Identify and work with content developers in domain WS to inventory and prioritize most important necessary additions to the existing NCI terminologies
- Survey recent CDE development initiatives at NCI and any process artifacts; identify best practices, common problems
- Vocabulary/CDE WG meetings should collocate with Domain and Architecture WG on a rotating basis, or else one of us should attend a selection of meetings of each Domain WS
- Develop initial (draft) timeline for CDE and intra-operability goals in collaboration with domain and architecture WG
- Develop appropriate infrastructure that constrains CDE development to underlying data and work process models

## Modular tools for Concept Annotation of Clinical Free-Text

***Problem addressed:***
- Information about phenotype is very often stored in clinical documents as free-text .
- Researchers might want EVS-concept based access to de-identified clinical documents.
- Tissue Banking and Pathology Tools WG developers are proposing projects that will require concept coding of free text documents. Many other potential uses.
***Proposed solution:***
- Extend existing GATE-based pipeline for concept annotation of Pathology Reports – This is developed on an open source Java framework (GATE) for concept coding of Pathology Reports. This software was developed by us for the Shared Pathology Informatics Network (SPIN) a consortium grant from NCI Cancer Diagnosis Branch
- This software is open source under GNU license – current version available at: _[http://](http://opidev.upmc.edu/aaci/spin/)__[opidev](http://opidev.upmc.edu/aaci/spin/)__[.](http://opidev.upmc.edu/aaci/spin/)__[upmc](http://opidev.upmc.edu/aaci/spin/)__[.](http://opidev.upmc.edu/aaci/spin/)__[edu](http://opidev.upmc.edu/aaci/spin/)__[/](http://opidev.upmc.edu/aaci/spin/)__[aaci](http://opidev.upmc.edu/aaci/spin/)__[/spin/](http://opidev.upmc.edu/aaci/spin/)__   (download SPIN.zip) _
- We could modify this to use EVS, create more flexibility in choosing source vocabularies, coding other report types, offering choice of output formats, and adding simple interfaces for report coding and querying

## Shared Pathology Informatics Network (SPIN)

**Consortium Grant from the Resources Development Branch of the Cancer Diagnosis Program, NCI**
**Goal:** Provide researchers access to data that describe archived tissue specimens across multiple institutions while maintaining security of Patient Information

- Indiana

- UCLA

- Harvard

- Pittsburgh

## Modular tools for Concept Annotation of Clinical Free-Text

_**Maturity Level:**_ Early beta
_**System Design:**_
- Modular Java application built with GATE – an open source architecture for language engineering – modules may be GATE processing resources, JAPE transducers or our own Java apps
_**Component Details:**_
- Inputs de-identified free text pathology reports (we use a UPMC licensable component  - DeID)
- Tokenizer – tokenizes words, punctuation and spaces
- Section chunker breaks up document by section header (Clinical History, Gross Description, Final Diagnosis)
- UMLS Concept tagger – tags concepts using UMLS (RMI to KSS or local access to UMLS dist) – we can use either our own implementation of simple look-ahead/subsume algorithm or MMTX currently.
- NegEx – tags concepts that are negated
- “There is *<concept>*DCIS*</concept> *but no evidence of <negated><concept> invasive carcinoma </concept></negated>”
- XMLizer outputs XML (based on SPIN CHIRPS schema) for upload into the SPIN node. SPIN submission software validates against CHIRPS schema and loads MySQL db.

## Modular tools for Concept Annotation of Clinical Free-Text

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## Slide 15

## Slide 16

## Slide 17

- Value

## Converted and Validated Against SPIN XML Submission Schema

- <Diagnosis>
- <Term Assertion="affirmation" Code="C0001418" Source="UMLS">ADENOCARCINOMA</Term>
- <Modifier Assertion="affirmation"
- Code="C0205281" Source="UMLS">INVASIVE</Modifier>
- <Modifier Assertion="affirmation"
- Code="C0205616" Source="UMLS">MODERATELY DIFFERENTIATED</Modifier>
- <Modifier Assertion="affirmation"
- Code="C0205428" Source="UMLS">INVOLVING</Modifier>
- <Modifier Assertion="affirmation"
- Code="C0205091" Source="UMLS">LEFT</Modifier>
- <Topology>
- <Term Assertion="affirmation"
- Code="C0033572" Source="UMLS">Prostate</Term>
- </Topology>
- </Diagnosis>

## Modular tools for Concept Annotation of Clinical Free-Text

_**Current and Future Development:**_
- We have processed about 25K documents, currently running 1 million through our pipeline.
- Code Sharing and collaboration with Harvard (Qing Zeng, DSG)
- Currently takes about 20 seconds to process each document and output XML
- Working on lots of additions to the pipeline: corpus and frequency based methods for spelling correction,  document classifier using Jess inference engine and ontology, partial-parser, POS-tagger that uses SPECIALIST Lexicon
- SNOMED, NCI Thesaurus (if it eventually contains the right stuff)
_**Current Relevant Standards:**_
- UMLS, SPIN CHIRPS schema
_**Development Environment:**_
- Java, Interactive Java Development Environments, GATE, Jess
- CVS, Bugzilla
_**Interoperability:**_
- We’d like to create a version that uses CaCORE APIs, NCI EVS

## Modular tools for Concept Annotation of Clinical Free-Text

- Modular
- GATE-based
- tools

- 	**Modular tools for EVS-based annotation**
- 	 - Convert existing SPIN UMLS-taggers to CaBiG EVS-taggers
- 	 - Convert pathology-specific chunker to more general purpose chunker for clinical docs
- 	 - Develop SOAP-driven web-service to expose all this functionality
- 	**User-friendly application for automated annotation and storage of coded clinical docs**
- 	- Create CaBIG pipeline including new EVS-taggers and chunkers, db, query interface
- 	- Build GUI for selection of vocabulary sources, document types, output format and location, etc
**	****Linked repositories of coded clinical documents **
**	**- Extend current XML schema to other clinical document types of interest?
- 	- Develop transaction schema (based on SPIN P2P paradigm or emerging CaBIG architecture)?
-                    - Other development goals?

## Infrastructure for CDE development

***Hard but very important given the scale and complexity***
- All CaBig Workspaces have multiple developers and adopters who will need to collaboratively develop CDE using based on both vocabularies and models. This work is time-critical and needs to:
- Implement an agreed upon DE standard (i.e. ISO 11179)
- Implement an agreed upon process
- Constrain CDE development with underlying terminologies
- Resolve inconsistencies, reduce duplication
- Provide version management
- Control access at several levels
- Eventually we will need to think about both integration and mapping of local DE to canonical CDE, as well go forward CaBIO-based development
***It may be best to use extend existing resources – speed may be most important***
- Can we use Protégé-2000 v2?
- Backend and architecture considerations
- Consider developing Protégé-v2.0 plugin for viewing and multi-user editing of CDE based on ISO/IEC 11179 and NCI terminologies

## Infrastructure for CDE development

- Existing open-source software
- Widely used (14390 reg users) and accepted
- Very well supported
- Plug-in architecture
- Limited need for de novo interface development
- Multi-user access in v 2.0
- OWL plugin – one uniform editing environment including for NCI Thesaurus
- Easy to import content directly for use in inference (Jess, Algernon, PAL)
- Use other Protégé plugins, backends (CTS?)
- Visibility and Marketing of the NCI Resources