Genomic Information Commons (GIC)
Overview
The GIC is a continuously updating, queryable, federated genomic data commons. Inspired by a common vision of accelerated genomic research discovery, collaboration, and improved clinical outcomes. The participants are:
- Boston Children’s Hospital (BCH)
- Cincinnati Children’s Hospital Medical Center (CCHMC)
- Children’s Hospital of Philadelphia (CHOP)
- St. Louis Children’s Hospital (SLCH)/Washington University at St. Louis (WUSTL)
- University of Pittsburgh Medical Center (UPMC)
- Riley Children's Health (RHC)/Indiana University Health
- Rady Children's Hospital San Diego (RCHSD)
- LeBonheur Children's Hospital (LBCH)/The University of Tennessee Health Science Center UTHSC)
- Partner: Harvard Medical School
ICS' Role
ICS provides WashU's EHR and genomic data to the portal. We also handle other backend administrative duties.
Contacts
Internal
| Name | Role |
|---|---|
| Nicole Venteris | PM |
| Ian Lackey | Tech |
| Indraniel Das | Tech |
| Madhurima Kaushal | Technical |
| Alvin Ndikefor | Technical |
| Snehil Gupta | Technical |
| Kimberly Turner | PM/Genomic Patient Management |
| Kathleen Sisco | PM/Genomic Patient Management |
| Patricia Dickson | PI |
| Philip Payne | PI |
| Albert Lai | PI |
External
| Name | Role | Contact Info |
|---|---|---|
| Danielle Pillion | Technical PM (at the BCH) | Danielle_Pillion@hms.harvard.edu |
| Kenneth Mandl | PI at BCH (Project Overlord) | kenneth.mandl@childrens.harvard.edu |
| Simran Marwan | Data Analyst (BCH) | simran_makwana@hms.harvard.edu |
| Anil Kumar Degala | Software Engineer (BCH) | anilkumar.degala@hms.harvard.edu |
| Luke Sikina | Software Engineer (BCH) | lucas.skina@childrens.harvard.edu |
| Rachel Payne | PM | rachel.paynea@childrens.harvard.edu |
| James Jones | PM (PM to Ken Mandl) | James_Jones@childrens.harvard.edu |
Project Management
Major Tasks & Initiatives
Important Dates & Notes
Important Deadlines
- Nephrotic Project Deliverables: tbd
Deliverables
Standard Meetings
| Name | Occurrence | Frequency | Zoom Link | Occurrence | Attendees | Description |
|---|---|---|---|---|---|---|
| BMI Working Group | W 130-230pm (every 2 weeks) | bi-weekly | https://bostonchildrens.zoom.us/j/94337735996?pwd=aTFZK3UrVDNlSHROSlVxSkxYSnZCZz09 | Every other wednesday 1-2pm CT | Madhu, Niel, Nicole, Ian (sometimes Albert) | GIC Consortium Meeting on Informatics related affairs |
| GIC Governance Committee Call | W 3-345pm (once a month) | monthly | https://bostonchildrens.zoom.us/j/96385225078?pwd=SER3WFMzcmpRMS85N09IMzZ0aHZ4Zz09 | Every other wednesday 3-4pm CT | Madhu, Niel, Nicole, Patti Dickson (occasionally Ian & Albert) | GIC News & Discussion from a high-level (meant for project PIs) |
| GIC Monthly Meeting | W 1-130pm | monthly | https://wustl-hipaa.zoom.us/j/99478769665?pwd=RDYyQlViWERtZ0ZXMXBrQ3cxTXpQQT09 | Once a month (usually Wednesdays 230-3pm) | Madhu, Niel, Nicole, Kimberly, Kathy Sisco, Patti Dickson, Albert | High-level internal GIC discussion (WashU aspects only) |
| GIC Updates and Review | M 11-1130am | weekly | https://wustl-hipaa.zoom.us/j/98256406372?pwd=udeChYCHNlpzCoZtYlzYa8pieaeb97.1 | Tentatively every Monday 11-12pm CT | Madhu, Niel, Nicole, Kimberly | Overall week-to-week GIC activities |
| GIC Tech Check-in | Tu 11-1130am | weekly | https://wustl-hipaa.zoom.us/j/94928225743?pwd=c244NVk1dXp5eDg5ckN5OEdkaG1rdz09 | Tentatively every other Tuesday 11-12pm CT | Madhu, Niel, Nicole, Ian | Overall week-to-week GIC activities (tech aspects only) |
| GIC SDAC Meeting | Th 2-3pm | monthly | https://wustl-hipaa.zoom.us/j/94928225743?pwd=c244NVk1dXp5eDg5ckN5OEdkaG1rdz09 | Tentatively every other Tuesday 11-12pm CT | Madhu, Niel, Nicole, Ian | Overall week-to-week GIC activities (tech aspects only) |
Biomedical Informatics Working Group (BMI) is responsible for developing architectures, processes, and metrics to harmonize and share high quality data within the GIC.
Administrative Details
Tracking Time
Please ensure all work is categorized underneath the "GIC" project in Tracking Time.
Digital Landmarks
Project Web Pages
- Main Project Page: https://genomicinformationcommons.org
- Main GIC Service Workbench (SWB)
- https://gic.wustl.edu - WashU's PIC-SURE Production Site (
gic01) - https://gic-test.wustl.edu - WashU's PIC-SURE Develoopment Site (
gic01) - Main GIC PIC-SURE Page -- aka the "Access Portal"
- Development GIC PIC-SURE Page -- aka the "Development/Test Portal"
- GIC Service Desk (Atlassian) -- Select "GIC Technical Support" or email
support.gic@bch-gic.atlassian.net - GIC Main Confluence Overview Page
- GIC Confluence Start Page
- GIC on YouTube
- User access requests to GIC portals | REDCap)
Document Repositories
Interesting Documentation
- Nicole's GIC Meeting Notes on Box
- Monthly Progress Report
- DRAFT: Genomic Information Commons Manual of Operating Procedures (GICMOP).pdf
- GIC: Technical Overview
- PIC-SURE Server Setup: "Common errors and triaging solutions
- Variant Explorer Overview (google doc on shared google drive)
- HMS-DBMI's Documentation on Loading Phenotypic (EHR) Data (github.com)
(this documentation may be out of date at this point but it's linked from the main pic-sure-hpds github README) - Google Spreadsheet: Bioinformatics pipelines
(listing of the various software versions being used for genomic data processing) - Google Spreadsheet: BioSamples and Genomic Data in GIC PIC-SURE
InfoSec Report
- GIC Security Review Folder (Box)
- 2024 Security Review Documents & Notes (DevOps)
- 2021-08-19-02-I2-GIC-ISO Security Review Report.pdf by WashU InfoSec
- 2024-03-31-01-I2-GIC-GENEDX-OIS-Security-Review-Report.pdf by WashU InfoSec
Code Repositories
WashU Repositories
- gic-nephrotic-syndrome
- gic-project
- gic-toolkit
- gic-ehr-data-quality-study
- pic-sure-extras
- pic-sure-etl-toolkit (github) - identical to the DevOps
pic-sure-extrasrepository
BCH/HMS Repositories
- https://github.com/hms-dbmi/pic-sure-gic-institution
- https://github.com/hms-dbmi/pic-sure-all-in-one
- https://github.com/hms-dbmi/pic-sure-hpds
- https://github.com/hms-dbmi/i2b2ACTtoHPDS/blob/master/OMOP to HPDS Data/ACT_OMOP_HPDS_MAP_DEM.tsv -- for the ACT Ontology
- https://github.com/hms-dbmi/i2b2ACTtoHPDS -- repo to map ACT paths/codes to HPDS Paths and OMOP Standard and Source concept IDs
Technical Information
Guides, Tutorials, & References
Genomics Notes
Special Projects
Glossary / Acronyms
| Acronym | Definition |
|---|---|
| PIC-SURE | Patient-centered Information Commons: Standard Unification of Research Elements |
| HPDS | High Performance Data Store |
| SWB | AWS Service Workbench |
| BMI | Bio-Medical Informatics |
| TPC | Tissue Procurement Core |
| SDAC | Sample and Data Access Committee |
PIC-SURE: is Open source platform that integrates different layers of clinical and genomic data from diverse data sources.PIC-SURE node: is an instance of PIC-SURE deployed at each hospital/site.GIC Portal: is an instance of PIC-SURE that queries the hospital/site’s node. No data is stored in the GIC Portal.