# Presentation: 769403

## Identification of High-Impact Common Data Elements 

***CDE Leadership Group***

**January 30, 2008**

## Agenda

**Introduction**
**What are High Impact CDEs?**
**Approach**
**Manual Identification**
**Automated Identification**
**Work Done to Date**
**High Impact Information**
**Issues to Consider**
**Next Steps**

## Introduction

**CDEs designated as caBIG Standards by the caBIGTM Community should be reused.**
**‘****High impact’ CDEs are CDEs that are pervasive through many developer projects and are ‘touch points’ for semantic interoperability. **
**To permit interoperability, the classes and attributes in the UML models for different applications should be semantically annotated to be the same.**
**Some examples of high impact CDEs include those where the object class is patient, participant, biospecimen, genes or gene products.**

## Approach

**Manual Identification**
**Automated Identification**

## Manual Identification of High Impact CDEs

**Models under review are available at GForge-UML model projects (**_[https://gforge.nci.nih.gov/frs/?group_id=64](https://gforge.nci.nih.gov/frs/?group_id=64)_**)**
**Some examples include Bioconductor, caBIO, caCORE, caFE Server, caIntegrator, caMOD, caTIES, caTissue Core, Clinical Genomics, Gene Connect, protLIMS etc.**

- Identify commonly
- reused
- objects/attributes

- Review UML models

- Extend
- backbone
- model

- Propose
- as
- standard

## Backbone Model

## Backbone Model

- ICR-TBPT Links

## Backbone Model:  ICR

## Backbone Model:  TBPT

## Automated Identification of High Impact CDEs

**One of the Compatibility Review System v2.0 requirements is to calculate CDE reuse.**
**This will include not only CDE reuse, but DEC, class and attribute reuse as well.**
**This component will be run against the caDSR to review all loaded models and identify examples of full or partial reuse.  **
**This will lead to the identification of potential touch points or high impact CDEs.**

## Automated CDE Reuse Report

## Models Reviewed Manually

**Tumor registry**
**TrAPSS**
**Training Data Model**
**caElmir**
**SPORES**
**Seed**
**Reactome FKA caBIOExtensions**
**protLIMS**

**Protein Identification**
**NHIS Tobacco Survey**
**NCIA**
**NCI-60 SKY**
**CPAS**
**IVI Middleware**
**NCI-60 Drug Screen  **

**Notes:**
15 out of total 76 models reviewed.

## High Impact

| Information captured | Models |
| --- | --- |
| MRN | Training data model; Tumor Registry |
| Patient | Training data model; Tumor Registry ; NCIA |
| Participant | protLims (as “Donor Information”); SPOREs (as “Person”); caElmir (as “User”); NCI-60 Drug Screen ( as “Study Subject”) |
| Demographics | Training data model; Tumor Registry; protLims; NHIS Tobacco Survey; NCIA |
| Diagnosis-histologic, clinical | Training data model ; Tumor Registry |
| Address | Training data model ; caElmir ; SPOREs (as “Contact info”); Tumor Registry |
| Treatment | Training data model; SPOREs; Tumor Registry  |
| Organization/institution | caElmir; NCI-60 Drug Screen;  |
| Specimen  | caElmir (as “Tissue”, “Slide”); protLims (as “Sample”); NCI-60 SKY (as BioSample); CPAS (as Material) |
| genomic identifier
 | TrAPSS (as “Gene”, “Transcript”); caBIOExtensions (as “Reference RNA”/ “Reference gene” and “Reference protein”); Seed (as ”proteinEncodingGeneFeature”) |
| Species | protLims; caBIOExtensions (as “Taxon”); Seed (as “Organism”) |
| Genotype | protLims; caElmir |

## High impact 

| Information captured | Models |
| --- | --- |
| Chromosome | NCI-60 SKY |
| Copy Number | NCI-60 SKY |
| Protocol | NCIA; CPAS (as Protocol Application); NCI-60 Drug Screen |
| Phase | NCI-60 Drug Screen |
| Event | NCI-60 Drug Screen |
| Disease/Tumor  | NCI-60 SKY |
| Image | NCIA |
| "Metadata" | In vivo imaging Middleware (Underspecified class) |
| Tandem Mass Spectra |   CPAS |
|   Peptides | CPAS |
|   Protein Sequences | CPAS |
|   Publication | NCI-60 Drug Screen (as “Study Publication”) |
|   "Observation" Data |   NCI-60 Drug Screen (Underspecified) |
|   Cohort | NCI-60 Drug Screen (as “SubjectGroup”) |

**Notes:**
Phase is e.g Phase of a study
Event in NCI-60 Drug Screen (as “ScheduledTimeLineEvent” and “ScheduledEvent”)

## Why reuse did not occur?

**Patient/Participant: ****“Donor information” in protLIMS; “person” in ****SPOREs****;“u****ser” in caElmir; “animal” in caElmir**
**genomic identifier: ****“Gene”, “Transcript” (TrAPSS); “Reference RNA”/ “Reference gene” and “Reference protein”(caBIOExtensions); “proteinEncodingGeneFeature” (Seed)**
**Underspecified Modeling: ****In caBioExtensions “referenceDatabase” and “identifier” could be represented by one e.g pubMedIdentifier.**
**Need ways of mapping combination of CDEs into single CDE in caDSR**

## Need ways of mapping combination of CDEs into single CDE in caDSR

- Where referenceDatabase = pubMed
- Identifier = 1007457

- Where pubMedIdentifier =1007457

## Next Steps

- Complete manual review (15/76 models completed to date).
- Complete automated review using CRS v2.0 software.
- Determine extension of the backbone model based on findings.
- Creation of standard CDEs that may be shared more broadly.

## 

				Questions?

**	****	****	****	****Questions?**