Representation of Cancer Phenotypes
| Date | Day | Time (MT) | Location (Virtual option will be available*) |
|---|---|---|---|
| Sept 23, 2023 | Saturday | 9am - 5pm | Venue (TBD) |
| Sept 24, 2023 | Sunday | 9am - 5pm | Venue (TBD) |
| Sept 25, 2023 | Monday | 9am - 3pm | Venue (TBD) |
*Zoom link will be shared with registered guests.
Workshop organizers
- Peter Robinson, JAX
- Justin Reese, LBNL
- Melissa Haendel, CU Anschutz
- Monica Munoz-Torres, CU Anschutz
- Umit Topaloglu, NIH/NCI
- Daoud Meerzaman, NIH/NCI
Workshop goals
- Harmonize multimodal cancer data
- Assess the suitability of existing terminologies and value set mappings for describing cancer phenotypic data
- Transform cancer phenotypic data into Phenopackets using LinkML
- Design an API for cancer phenotypic data access
- Complete development of the C2P package to transform cancer data into Phenopackets (see https://github.com/monarch-initiative/c2p/blob/main/notebooks/Individual.ipynb), connecting the current elements of the Phenopacket schema to the existing ETL platform from the Cancer Data Aggregator (CDA)
- Leverage modeling and mapping work done by the Center for Cancer Data Harmonization (CCDH) in the software engineering of the C2P/Phenopackets project and use them together to support AI/ML
- Launch molecular data pilot to represent epidermal growth factor receptor (EGFR) variants.
Agenda Overview
| Day | Time | Topic |
|---|---|---|
| Sat, Sept 23 | 9:00 am - 5 pm | Day 1 |
| Sun, Sept 24 | 9:00 am - 5 pm | Day 2 |
| Mon, Sept 25 | 9:00 am - 5 pm | Day 3 |
Detailed Agenda
Saturday, September 23, 2023
- Welcoming remarks – logistics, goals
- Introductions
- Intro to the landscape of existing resources
- Exploring the CCDH model, LinkML, and the Phenopackets schema
Sunday, September 24, 2023
- Cancer phenotypic data modeling discussion
- Transformation pipeline: CRDC → LinkML → phenopackets
- Building a basic API endpoint
- Connecting elements of the Phenopacket Schema to ETL code from the Cancer Data Aggregator (CDA) and its API
Monday, September 25, 2023
- Launch the pilot to test the molecular hypothesis about variants in EGFR
- Wrap up collaborative work, plan next steps, issue a list of actionable items, and identify product owners
Resources
- Phenopackets Documentation & Repositories
- C2P Repository
- CCDH Pilot Demonstration (2021)
- CRDC Data Workflow End to End Analysis
COVID-19 policy
- If possible, we request that everyone test for COVID-19 prior to gathering in person for the workshop.
Code of Conduct
Link TBD
Funding
This workshop is supported by the NIH BD2K conference grant “Forums for Integrative Phenomics” to Melissa Haendel and Peter Robinson: U13CA221044.