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5. Building the Cancer Research Data Commons with Neo4j: The Bento Framework

Mark Jensen, Director, Data Management and Interoperability, Frederick National Laboratory for Cancer Research

Todd Pihl, Director, Technical Project Manager, Frederick National Laboratory for Cancer Research

Ming Ying, Senior Software Engineer, Frederick National Laboratory for Cancer Research

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5. Building the Cancer Research Data Commons with Neo4j: The Bento Framework

  1. 1. DEPARTMENT OF HEALTH AND HUMAN SERVICES • National Institutes of Health • National Cancer Institute Frederick National Laboratory is a Federally Funded Research and Development Center operated by Leidos Biomedical Research, Inc., for the National Cancer Institute Neo4j GovConnect: The Bento Framework for Building Data Commons Biomedical Informatics and Data Science (BIDS) Directorate Frederick National Laboratory for Cancer Research (FNLCR) Todd Pihl, PhD, PMP Ming Ying, MS Mark A. Jensen, PhD, PMP
  2. 2. Frederick National Laboratory for Cancer Research • Why was Bento Framework built? • What is the Bento Framework? • How does it work? • Where does Neo4j fit in? • What’s next?
  3. 3. The NCI Cancer Research Data Commons Ecosystem https://datascience.cancer.gov/data-commons Frederick National Laboratory for Cancer Research
  4. 4. Frederick National Laboratory for Cancer Research Integrated Canine Data Commons • Not data type centric Clinical Trials Data Commons • Genomic data bias
  5. 5. Frederick National Laboratory for Cancer Research o Bento can serve as a framework for CRDC platforms o Each platform can customize the core framework o Bento provides modular, customizable components o QA is baked into Bento development process o Bento can serve as a “foundry” for CRDC Bento’s Core
  6. 6. Frederick National Laboratory for Cancer Research Bento Saves Development Time Integrated Canine Data Commons Clinical Trial Data Commons Bento Based Data Commons 9 MONTHS 4 MONTHS ~4 WEEKS
  7. 7. Frederick National Laboratory for Cancer Research o Microservices in Containers: - User Interface - Backend - Database - Core Data Model o Technology Stack: Neo4J | Java/Python | GraphQL | ReactJS - Neo4j drives both persistence and UI o Loose Coupling of Components Bento Architecture For the Custodian o Pull codebase o Configure locally o Deploy anywhere o Multi-cloud support o Documentation support
  8. 8. Frederick National Laboratory for Cancer Research 1 Bento Core Data Model Bento Core API Bento Core UI Framework ü Bento Core Components work out of the box. ü Bento Custodian need only configure the UI. ü The core components provide a minimal but working application. 2 Bento Core UI Framework Bento Extended Model Bento Extended API ü Bento Core Data Model is extended. ü Bento Core API custom queries updated to provide access to data in the extended sections of the model. ü UI continues to work with the API and data model, without any additional development. ü Bento Core Data Model is extended. ü Bento Core API custom queries updated to provided access to data in the extended sections of the model. ü Core UI built out to display model elements according to your custodian’s specifications. 3 Bento Extended UI Framework Bento Extended Model Bento Extended API Bento - Degrees of Configuration
  9. 9. Model Description Format (MDF) MDF is a compact, human-readable—but computable—format for defining a property graph • Nodes • Node Properties • Relationships • Relationship Properties • Relationship Attributes: direction, multiplicity, required/optional, … • Property Definitions • Property Attributes: allowable value types or sets, required/optional, … Frederick National Laboratory for Cancer Research https://github.com/CBIIT/bento-mdf
  10. 10. MDF Overview Nodes Edges Property Defs Props referenced here … and defined here Entity names are the keys Nodes at the ends, with direction Other attributes specified Constrain the data values to defined types Frederick National Laboratory for Cancer Research
  11. 11. Frederick National Laboratory for Cancer Research Metamodel Database https://github.com/CBIIT/bento-meta CTDC Model in MDB Metamodel "Schema"
  12. 12. Testimonial - ICDC Product Owner Philip Musk 12:06 And let me tell you, with data needs driving many of ICDC's requirements as they are, and have been thus far, being able to both write the requirements, and make the required model changes ahead of engineers doing their thing, is really powerful. I don't have to explain what model changes we need to make to someone else - I can get the model changes done myself, and explain what we need the engineers and the UI to do with those changes.
  13. 13. Data pipeline Frederick National Laboratory for Cancer Research Case file Data-loader (Python) Neo4J Case file Case file Study file Case file Study COTC007B Case COTC007b-0505 Case COTC007b-1605 Case COTC007b-0610 Case COTC007b-0408 Cohort NSC 7067…. Cypher
  14. 14. Backend Backend Architecture Neo4j GraphQL Plugin GraphQL GraphQL Java App Data Data Client Bento Backend Redis GraphQL null GraphQL/Data Frederick National Laboratory for Cancer Research
  15. 15. Neo4j GraphQL Plugin GraphQL Java App Data Client Bento Backend Redis GraphQL Data Frederick National Laboratory for Cancer Research Backend Backend Architecture
  16. 16. Why Neo4j-GraphQL Plugin? • Very easy to setup • Very easy to use • Only one file (the schema file) is needed to setup a GraphQL API • Automatically generated common queries • Supports writing custom queries with Cypher • Very responsive customer support! Frederick National Laboratory for Cancer Research
  17. 17. GraphQL Schema (Cypher Annotated) Frederick National Laboratory for Cancer Research
  18. 18. Frederick National Laboratory for Cancer Research
  19. 19. Frederick National Laboratory for Cancer Research
  20. 20. 0 0 Establish workflow for building reusable Bento components Retool existing sites to use Bento Add authentication and authorization layer Add enhanced data viz capabilities Enhance performance 1 2 3 Bento Roadmap 4 5 1 2 3 4 5
  21. 21. Frederick National Laboratory for Cancer Research The Bento Team Bento Leadership Braulio Cabral John Otridge Todd Pihl Mark Jensen DevOps & Backend Ming Ying Vincent Donkor Michael Fleming Austin Mueller Bento Management Ye Wu Kailing Chen Amit Mukherjee Data Mark Jensen Philip Musk Mark Benson Kevin Burns Claire Wolfe Anjan Purkayastha UI Dimitri Darras Hannah Stogsdill Sri Kiran Chaparala Ajay Doddapaneni Ming Ying Yizhen Chen Karan Sheth QA Laxmi Lolla Gayatri Radhakrishnan Megan Lewis Integrated Frederick National Lab and Essential Software Inc. Team
  22. 22. Thank you. Frederick National Laboratory for Cancer Research https://cbiit.github.io/bento-docs-sphinx/master/installation/bento-quick-start.html

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