NIH | National Cancer Institute | NCI Wiki  

  • Created by Unknown User (decorons), last modified on Jun 04, 2018

 

Held: May 15/16 2018

 

The goal of the Workshop is to define semantic requirements and approaches to support query, submission, and analytical functions of the NCI CRDC. A particular focus will be on semantics that will inform plans for a Cancer Data Aggregator that will enable queries across commons nodes (e.g. different sources and data types) through their exposed metadata.  

The expected outcomes of the workshop and its follow-up documentation will be
(1) A requirements and evaluation document that identifies and summarizes a set high level requirements as well as including a variety of competency questions for semantic design and evaluation testing of the Cancer Data Aggregator.
(2) A set of options/pros/cons for using and/or extending current approaches and resources in support of both semantic query capabilities and approaches to facilitate metadata annotation, validation, and submission.
(3) A set of recommendations to support ongoing engagement with the community such that the semantics behind the Cancer Data Aggregator improve and evolve as people contribute to and use the CDA.

Two pre-workshop webinars are being held to provide background information about the NCI CRDC and semantic resources, as well as Use cases for the CRDC.

  1. Tuesday April 24 1-2:30 pm– Pre-Workshop Webinar: Cancer Research Data Commons and Semantic Resources: 
    1. Powerpoint presentations .  See Attachments to this page (paperclip icon upper left, or ... icon upper right)
      •Overview of Cancer Moonshot and Cancer Research Data Commons –  Tanja Davidsen 
      •Cancer Data Aggregator - goals/requirements – Todd Pihl
      •GDC – Overview of model/querying/pain points – Mark Jensen  
      •Overview of NCI Semantic Resources
      •Enterprise Vocabulary Services (EVS) – Margaret Haber
      •Structured Metadata Resources (caDSR and MDR plans) – Denise Warzel
      •CDISC Standards Overview – Bron Kisler
      •Semantics of Monarch Overview –  Chris Mungall
    2. Recorded Webinar (as an MP4) file - (You can run the recording by clicking on the attachment)
    3. Cheat Sheet of acronyms   
  2. Tuesday May 8 1-2:30 pm – Pre-Workshop Webinar: Representative Use Cases for the CRDC
    1. Powerpoint presentations See Attachments to this page (paperclip icon upper left, or ... icon upper right)
      •HTAN – Human Tumor Atlas Network - driving project for Cancer Data Aggregator – Sean Hanlon
      •PDC - Protein Data Commons / CPTAC – Ratna Thangudu
      •CIDC - Cancer Immunologic Data Commons – David Patton
      •SEER - Surveillance data linkage and discovery – Paul Fearn
      Broadening Genomic Data Storage - diversity of data types  – Ian Fore
    2. Recorded Webinar (as an MP4) file

 

The Workshop was held on May 15/16.  Many thanks to those who participated, and special thanks to the speakers and facilitators!  We are happy to be able to continue engaging with participants and the community in the next steps.

  1. Agenda: Facilitators - Melissa Haendel and Bron Kisler (See Attachments to this page)
  2. Presentations from Day 1 of Workshop: (These have been loaded as attachments to this page)

    1. Pediatric Cancer Data Commons – Sam Volchenboum 

    2. APOLLO: A High Profile Use Case with Unique Challenges for the CRDC – Kathleen Darcy

    3. Project GENIE and other relevant SAGE Activities: James Eddy/Sara Gosline  

    4. NCIt OBO Edition and its Use in Phenotype/Genotype Efforts across Non-Cancer and Cancer Diseases – Jim Balhoff

    5. Modeling Landscape Analysis, Bron Kisler

Raw Notes from the workshop are on the shared Google folder:   bit.ly/nci_semantics  

Summary materials and outputs from the workshop will be sent to attendees, and our thanks to a number of attendees agreeing to continue working with us on Recommendations, Queries to feed into Requirements, and a possible White Paper.

 

 

 

 

 

 

  • No labels