# Presentation: 847584

## caBIG Silver Compatibility Reviews & Recommendations

- C3PR, caTRIP
- July 12, 2007

## C3PR v. 1.0

## Team members

- Supporting members
- Michael Keller (BAH)
- Robert Freimuth (Mayo)
- Patrick McConnell (Duke )

- Reviewers
- George Joseph (Wash U)
- Linda Schmandt (UPCI)
- Lynne Wilkens (U.Hawaii )
- Xin Zheng (AECOM)
- Julie Zhu (NW)

## C3PR v. 1.0	

- Recommendation:   Not silver-compatible
- Inadequate information in original submission
- After 30+ days, no response from development team to request for information

## C3PR v 1.0 Overview

- The Cancer Central Clinical Participant Registry (C3PR) was designed to assist in registering patients to clinical trials.
- The developers provided the following documents for compatibility review:
**information model: **
- C3PR.EAP
- C3PR EA Documentation.doc
**common data elements (CDE): **
- C3PR CDE Use Report.xls
- C3PR Value Domain Report.xls
- C3PR Standards Report.doc (empty)
**vocabularies and ontologies: **
- C3PR Vocabulary Report.doc
- EVS Report_fixed_C3PR.csv
- Annotated_fixed_C3PR_v1_1_rv1.xmi
**programming and messaging interfaces (APIs): **
- C3PR API Description.doc
- C3PR Adopter Test Log.doc

## Review Process

- The notations in the main review document are highlighted to indicate degree of compliance:
- Red:  Unresolved.  Issues that need to be corrected
-  Orange:  Unresolved.  Issues that may need to be corrected
-  Yellow:  Points of concern
-  Green:  No issues, or issues have been addressed
-  Gray:   Not reviewed
- The review team requested written responses to all issues categorized as red, orange or yellow

## C3PR v. 1.0 Review Issues	

- Information Model
- 2 associations with no directionality
- Associations with wrong cardinality (e.g. Protocol to Protocol Amendment should be one to many, not one to one.)
- Some classes incorrectly/unclearly defined (e.g. Registration.funding source is defined as ‘source of funding for patient on a trial’.   Permissible values x, y, z indicate that it represents the insurer.)
**Some class names are used in attribute names, e.g. Race.raceDesc **
**Some attribute names do not convey clear meaning, e.g**. **Registration.institutionCode would be more clearly named  Registration.CtepInstitutionCode.**

## C3PR Vocabulary Review

- Vocabulary and ontologies
- EVS is used to define all concepts in information model.
- Instances of mis-mapped concepts
- e.g. Class ProtocolParticipant for staff of clinical trial is mapped to concept ‘Participant’ used by many other applications to mean patient/subject/tissue donor.
- e.g. Registration.PatientPositionID was mapped to C25339, which is defined as ‘the particular portion of space occupied by a physical object’, while the attribute is a sequence number having nothing to do with physical position.

## C3PR CDE review

- The permissible values of certain CDEs do not fit the description of the attributes
- e.g. RegistrationDisease.ID was defined as “Values should comply with the latest version of the CTEP Disease Codes for Protocols available on the following site: _[http://](http://ctep.cancer.gov/guidelines/codes.html#disease)__[ctep.cancer.gov/guidelines/codes.html#disease](http://ctep.cancer.gov/guidelines/codes.html#disease)_”. The assigned Value domain 2019312, a diagnosis code, does not reference CTEP
- e.g. protocol.protocolPhaseDesc  is defined as “phase of the protocol”  but has values of *mFOLFOX6 +/- bevacizumab, Bevacizumab alone, Post-therapy, Double-blinded*, and *Open)*
- Standards Report not submitted, so no justification of the many instances where an existing standard was not used.

## C3PR API Review

- Did not provide sufficient document for review.  The API document submitted only contains a list of objects without any methods defined. According to the follow up email response from the developer, there is no java docs or other documentation was ever produced.
- A broken URL ( http://c3pr-qa.nci.nih.gov/c3prapi/Happy.jsp) was included as a test log and developer did not provide other information

## Vote on C3PR recommendation

## caTRIP

## Team members

- Supporting members
- Lewis Frey (Utah)
- Tahsin Kurc (Georgetown )
- Brian Davis (3rd Mill.)
- Michael Keller (BAH)

- Reviewers
- George Joseph (Wash U)
- Linda Schmandt (UPCI)
- Baris Suzek (OSU)
- Xin Zheng (AECOM)
- Hemant Shah (City of Hope)

## caTRIP

- Recommendation:  Silver-compatible
- Review group requested several changes after initial review.  Development team made many and committed to others in next release.
- 2 models:
- Tumor registry
- Annotation engine (only 4 of the classes; the rest were used as is for CAE and thus reviewed previously)
- 31 classes, 224 attributes

## caTRIP compatibility review

- Information Model
- Many classes with only inherited attributes (next page)
- Associations not named per caCore rules, but API not generated with caCore so this is OK
- Developers corrected the definitions of several attributes
- Class names repeated in attribute names:  to be addressed in a future release
- Acronyms in attribute names:  AJCC, SEER, TNM (staging).  Reviewers agreed these do not need to be spelled out

## Slide 16

## caTRIP compatibility review

- Vocabulary and ontologies
- Review team suggested some changes in/additions to mapping.  Developers made several changes and resubmitted model; others will be made in a future release.
- API
- Not generated with caCore SDK, but judged to be compatible.

## Issues for discussion

- Best practices with respect for specifying enumerated values (or not)
- Best practices for resolving tension between requirements of individual cancer center and those of the wider group.
- MedicalRecordNumber has  1..0* association to Patient, not associated with a location or hospital.
- Association between Diagnosis and Address
- Patient.autopsy: Definition:  “Text indicating whether or not an autopsy was performed”, with data type java.lang.string. Review team suggested data type boolean; developers noted that they capture it as text.

## Vote on caTRIP recommendation