NCI efforts to build a foundation for in-silico cancer research - - PowerPoint PPT Presentation

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NCI efforts to build a foundation for in-silico cancer research - - PowerPoint PPT Presentation

Jul 03, 2023 287 likes •675 views

NCI efforts to build a foundation for in-silico cancer research Ken Buetow NCICB/NCI/NIH/DHHS Incredible developments in biomedical information generation Biomedical information tsunami overwhelming volume of data multitude of

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NCI efforts to build a foundation for in-silico cancer research

Ken Buetow NCICB/NCI/NIH/DHHS

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Incredible developments in biomedical information generation

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Biomedical information tsunami

  • overwhelming

volume of data

  • multitude of

sources

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Informatics tower of Babel

  • Each cancer

research community and institution:

– Speaks its own scientific “dialect” – Builds its own infrastructure and applications

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NCI biomedical informatics

  • Goal: A virtual web of interconnected

data, individuals, and organizations redefines how research is conducted, care is provided, and patients/participants interact with the biomedical research enterprise

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Molecular Signatures Clinical Trials

NCI Core

access portals participating group nodes Cancer Genomics

TGI GAI

CCAP

Mouse Models

Center for Bioinformatics

building common architecture, common tools, and common standards

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  • Information

integration

  • Cross-discipline

reasoning

caCORE – common ontologic representation environment

biomedical objects common data elements controlled vocabulary

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…a sharing architecture

Data Sources

External Apps

Clients Presentation Layer Object Layer

Browsers Other Apps HTML /HTTP XML/ HTTP RDF Internal Java Apps Web Server URLs

Flat Files

Databases Agents SOAP Genes Expression Trials Tissues Agents Models Diseases Other

Domain Objects

  • open

source

  • open

development

  • open

access

  • federated
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NCICB applications:

  • clincial trials support - C3DS
  • molecular pathology - caArray
  • cancer images - caImage
  • pre-clinical models - caModelsDb
  • laboratory support - caLIMS
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electronic data capture for Clinical Trials

  • WWW

accessible

  • Reusable

eCRF library built using NCI CDEs

  • CTMS and

CDUS reporting

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http://caarray.nci.nih.gov/

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Image Portal

  • The NCICB has

developed an image portal to allow researchers to search for mouse and human images and annotations

– Human and mouse images and annotations were provided by the MMHCC

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Cancer (A) to Normal (B) Expression Ratio for breast on Chromosome 17

ERBB2

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Cancer Biomedical Informatics Grid (caBIG)

  • Common, widely distributed infrastructure

permits cancer research community to focus on innovation

  • Shared vocabulary, data elements, data

models facilitate information exchange

  • Collection of interoperable applications

developed to common standard

  • Raw published cancer research data is

available for mining and integration

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Within a group, extended NCICB caCORE and local infrastructure join diverse data and connect it to public data sources

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Cancer Biomedical Informatics Grid (caBIG)

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caBIG principles

  • Open source
  • Open access
  • Open development
  • Federated
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caBIG action plan

  • Establish pilot network of Cancer Centers

– Groups agreeing to caBIG principles – Mixture of capabilities – Mixture of contributions

  • Expanding collection of participants
  • Establish consortium development process

– Collecting and sharing expertise – Identifying and prioritizing community needs – Expanding development efforts

  • Moving at the speed of the internet…
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Three Domain Workspaces and two Cross Cutting Workspaces will be launched during the Pilot phase

DOMAIN WORKSPACE 3 Tissue Banks & Pathology Tools Will provide for the integration, development, and implementation of tissue and pathology tools. DOMAIN WORKSPACE 2 Integrative Cancer Research Will provide tools and systems to enable integration and sharing of information. DOMAIN WORKSPACE 1 Clinical Trial Management Systems Will address the need for consistent, open and comprehensive tools for clinical trials management. CROSS CUTTING WORKSPACE 2 Architecture Will develop architectural standards and provide architectural assistance as necessary to other workspaces. CROSS CUTTING WORKSPACE 1 Vocabularies & Common Data Elements Will be responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software systems for content delivery

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acknowledgements

  • NCICB

– Peter Covitz – Sue Dubman – Carl Schaefer – Mervi Heiskanen – Denise Hise – Kotien Wu – Frank Hartel – Sheri De Coronado – Gilberto Fragoso

  • LPG/CCR

– Michael Edmundson – Bob Clifford – Cu Nguyen

http://ncicb.nci.nih.gov http://cmap.nci.nih.gov http://caBIG.nci.nih.gov