cabig: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-ken-buetow.pdf ·...
TRANSCRIPT
![Page 1: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/1.jpg)
caBIG: the cancer Biomedical
Informatics GridKen Buetow
NCICB/NCI/NIH/DHHS
![Page 2: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/2.jpg)
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
![Page 3: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/3.jpg)
•Trials•Animal Models
states
context•pathways•ontologies
agents•therapeutics•probes
components•genes•genotypes•geneexpression•proteins•proteinexpression
etiology,treatment,prevention
![Page 4: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/4.jpg)
MolecularPathology
ClinicalTrials
caCORE
accessportals
participatinggroup nodes
CancerGenomicsMouse
Models
building common architecture, common tools, and common standards
![Page 5: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/5.jpg)
Interoperability
SemanticSemanticinteroperabilityinteroperability
SyntacticSyntacticinteroperabilityinteroperability
Courtesy: Charlie Mead
! in·ter·op·er·a·bil·i·ty- ability of a system...to use the parts or equipment of another systemSource: Merriam-Webster web site
! interoperability- ability of two or more systems or components to exchange information and to use the information that has been exchanged.Source: IEEE Standard Computer Dictionary: A Compilation of IEEE Standard Computer Glossaries, IEEE, 1990]
![Page 6: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/6.jpg)
! Information integration
! Cross-discipline reasoning
caCORE – common ontologicrepresentation environment
biomedical objects
common data elements
controlled vocabulary
![Page 7: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/7.jpg)
Enterprise Vocabulary! NCI Meta-Thesaurus
(Cross-map standard vocabularies/ontologies,e.g. SNOMED, MEDRA, ICD)
- Semantic integration, inter-vocabulary mapping
- UMLS Metathesaurus extended with cancer-oriented vocabularies
• 800,000 Concepts, 2,000,000 terms and phrases
• Mappings among over 50 vocabularies
! NCI Thesaurus- Description logic-based- 18,000 “Concepts”
• Concept is the semantic unit• One or more terms describe a Concept
– synonymy• Semantic relationships between
Concepts
biomedical objects
common data elements
controlled vocabulary
![Page 8: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/8.jpg)
Common Data Elements
! Structured data reporting elements(e.g. LOINC)
! ISO11179 compliant
biomedical objects
common data elements
controlled vocabulary
![Page 9: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/9.jpg)
Biomedical Information Objects
! Computer model of a biomedical object –“Plato’s Forms”- capture properties of object- can be joined together to make
complex systems- isolate data from data source- isolate applications from data
! Examples:- HL7-RIM- MAGE-OM
biomedical objects
common data elements
controlled vocabulary
![Page 10: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/10.jpg)
Standards Supporting Infrastructure
! Enterprise Vocabulary Services (EVS)! cancer Data Standards Repository
(caDSR)! cancer Bioinformatics Infrastructure
Objects (caBIO)
![Page 11: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/11.jpg)
Data AccessObjects
Object Managers
DomainObjects
RMI
Web Server
TomcatServlets
JSPsSOAP
UI BeanXML
XSL/XSLT
HTML/XML Clients
(Browsers)
SOAP Clients
Java Applications
DataObjectPresentationClient
NCI
Files
Other Data Others [caBIG]
UCSC
architecture
![Page 12: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/12.jpg)
Prototype GRID Core architecture extension
caBIO server
caBIO client
OGSA-DAI +Globus
Globus
OGSA-DAI caGRID extension(metadata)
caGRID extension (caBIO adapter)
caGRID extension(query)
Client
Grid
Data Source
caGRID extension (Concept Discovery)
caGRID extension (Federated Query)
caGRID Extension (Integration of Discovery and Query Services)
![Page 13: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/13.jpg)
NCICB applications:• clincial trials support - C3DS• molecular pathology - caArray• cancer images - caImage• pre-clinical models - caModelsDb• laboratory support - caLIMS
![Page 14: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/14.jpg)
• Data System for the conduct of clinical trials in CCR that is generalizable to academic environments.
• Components:– C3D (Cancer Central Clinical Database)
• Primary data capture by protocol – C3PR (Cancer Central Clinical Participant Registry)
• Central registration of participants across protocols – C3PA (Cancer Central Clinical Protocol Administration)
• Scientific management system for clinical protocols – C3TR (Cancer Central Clinical Tissue Repository)
• Tissue repository – C3DW (Cancer Central Clinical Data Warehouse)
• De-identified patient information accessed via caBIO
![Page 15: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/15.jpg)
C3DS Data Flow
C3D(Clinical DataManagement)
C3D(Clinical DataManagement)
C3PA(ProtocolAdmin)
C3PA(ProtocolAdmin)
C3TR(Tissue
Repository)
C3TR(Tissue
Repository)
C3DW(Clinical DataWarehouse)
C3DW(Clinical DataWarehouse)
Adverse EventReporting
System
Adverse EventReporting
System
Legacy DBs
AEDetails
ProtocolReporting
Requirements
ProtocolAccruals/Approvals
Active ProtocolData
PatientSpecimens
Non-AccruingProtocol Data
PeriodicUpdates
Source DBs
Batch LoadClinical (Lab) Data
PeriodicDownloads
EnrollPatients
FDA
PatientDetails
AEReports
PeriodicUpdates
Patient Demographics
C3PR(ParticipantRegistry)
C3PR(ParticipantRegistry)
PatientSpecimens
De-Identified Patient Details
SponsorsSponsors
![Page 16: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/16.jpg)
electronic data capture for clinical research• WWW
accessible• Reusable
eCRFlibrary built using NCI CDEs
• Electronic Regulatory reporting
![Page 17: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/17.jpg)
![Page 18: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/18.jpg)
![Page 19: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/19.jpg)
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
![Page 20: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/20.jpg)
Pathway Database • Enhance value of imperfect, but
available, pathway knowledge• Make biological assumptions
explicit• Combine sources of data (e.g.
KEGG, BioCarta, ...)• Merge data from separate
pathways• Build a causal framework to
support (future) quantitative simulation/analysis
![Page 21: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/21.jpg)
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
![Page 22: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/22.jpg)
caBIG will facilitate sharing of infrastructure, applications, and data
![Page 23: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/23.jpg)
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…
![Page 24: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/24.jpg)
Three Domain Workspaces and two Cross Cutting Workspaces have been launched during the Pilot phase
DOMAIN WORKSPACE 3Tissue Banks & Pathology Tools
provides for the integration, development, and implementation of tissue and pathology tools.
DOMAIN WORKSPACE 2Integrative Cancer Research
provides tools and systems to enable integration and sharing of information.
DOMAIN WORKSPACE 1Clinical Trial Management Systems
addresses the need for consistent, open and comprehensive tools for clinical trials management.
CROSS CUTTING WORKSPACE 2Architecture
developing architectural standards and architecture necessary for other workspaces.
CROSS CUTTING WORKSPACE 1Vocabularies & Common
Data Elements
responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software systems for content delivery
![Page 25: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/25.jpg)
caBIG deliverables! Componentized, standards-based Clinical Trials
Management System- e-IND filing/regulatory reporting with FDA- Electronic management of trials- Integration of diverse trials
! Tissue Management System- Systematic description and characterization of tissue
resources- Ability to link tissue resources to clinical and
molecular correlative descriptions! “Plug and Play” analytic tool set! Diverse library of raw, structured data
![Page 26: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/26.jpg)
Cancer Molecular Analysis Project (CMAP)- a prototypic biomedical data integration effort
biomedical objects
common data elements
controlled vocabulary
Profiles, Targets, Agents, Clinical Trials
CGAPNCBIUCSC
(via DAS)
BioCartaKEGGGene
Ontologies
CTEP clinical trialsCGAP gene expression
NCI drug screening
NCI drug screening
![Page 27: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/27.jpg)
![Page 28: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/28.jpg)
![Page 29: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/29.jpg)
![Page 30: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/30.jpg)
![Page 31: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/31.jpg)
![Page 32: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/32.jpg)
![Page 33: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/33.jpg)
![Page 34: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/34.jpg)
![Page 35: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/35.jpg)
![Page 36: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/36.jpg)
![Page 37: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/37.jpg)
![Page 38: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/38.jpg)
![Page 39: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/39.jpg)
caBIG community contributions! Infrastructure
- Ontologies- Databases
! Applications- Clinical trials
support- Analytic tools- Data mining
! Data- Trials- Experimental
outcomes• Genomic• Microarray• Proteomic
![Page 40: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/40.jpg)
![Page 41: caBIG: the cancer - prismeforum.orgprismeforum.org/wp-content/uploads/2015/03/3.-Ken-Buetow.pdf · caGRID extension (Concept Discovery) caGRID extension (Federated Query) caGRID Extension](https://reader031.vdocuments.site/reader031/viewer/2022022421/5a8e2cdb7f8b9afe568cf07b/html5/thumbnails/41.jpg)
acknowledgements! NCICB
- Peter Covitz- Sue Dubman- Carl Schaefer- Mervi Heiskanen- Denise Hise- Kotien Wu- Fei Xu- Ulli Wagner- Frank Hartel- Sheri De Coronado- Gilberto Fragoso
! LPG/CCR- Michael Edmundson- Bob Clifford- Cu Nguyen
http://ncicb.nci.nih.govhttp://cmap.nci.nih.govhttp://caBIG.nci.nih.gov