Genetics Plan

1
Modeling Cytogenetic Information in the
Cliniical Bioinformatics Ontology (CBO) Mark
Hoffman, Ph.D. Maki Moussavi, MS Catherine Arnoldi
APIII - 2005
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Cytogenetics and informatics

• Molecular pathology is often complemented by
  cytogenetic analysis
• Boundary between cytogenetics and molecular
  genetics is becoming increasingly blurred
• Both constitutional and somatic cytogenetics use
  a common vocabulary and standard ISCN
• Controlled medical vocabularies generally lack
  discrete terms capable of describing detailed
  elements found in a cytogenetics report
• Cytogenetics labs have requirement of ability to
  search for cases with common findings, a
  difficult task without standardized vocabulary
• Associating molecular genetic information with
  cytogenetics observations currently requires
  multiple layered searches

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SNOMED
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Example report
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Complex report

• Compound based on multiple observations
• Highly variable set of result options

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FISH results

• FISH results Discrete response
• Determination of which probes to use for a
  patient is non-standardized

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Evolution of Reporting
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The Clinical Bioinformatics Ontology (CBO)

• Address gaps in existing clinical vocabularies
  and bioinformatics resources
• SNOMED-CT
• LOINC
• OMIM
• Scope
• Molecular pathology
• Clinical Genetics
• Infectious disease
• Current state (August 2005)
• 5,872 approved concepts
• 13,030 Relationships 
• 2,602 Terms 
• 3,118 Facets  
• Available at www.clinbioinformatics.org

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Philadelphia Cytogenetic and molecular
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Definitional relationships
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Band resolution Chromosome 9
(gDNA).ABL1
(gDNA).ABL1
(gDNA).ABL1
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Band relationships in semantic format
q
400
550
850
9p
400.9q34
550.9q34.1
850.9q34.11
850.9q34.12
850.9q34.13
Band_of
550.9q34.2
550.9q34.2
550.9q34.3
550.9q34.3
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(No Transcript)
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Karyotype in a semantic network
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Millennium Helix and the CBO

• Blood Center of Wisconsin
• VCU
• ARUP

Proprietary Designed to leverage
semantic network of the CBO
Millennium Helix for the Laboratory
CBO
Open content
NCI Metathesaurus Users from 11 countries, 24
states
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Concept browser in Cerner Millennium
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Summary

• A semantic model that uses a defined set of
  definitional relationships can be built that
  supports the description of complex cytogenetic
  observations
• The CBO supports the integration of molecular and
  cytogenetic findings in a common platform
• Applications enabled to use the CBO position the
  users for improved operational and analytical
  capabilities
• Millennium Helix for the Laboratory
• NCI is incorporating the CBO into their
  Metathesaurus
• Anticipated by end of 2005
• The CBO is available at www.clinbioinformatics.org
  

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www.clinbioinformatics.org

• Mark Hoffman, Ph.D.
• Cerner Corporation
• [phone]
• mhoffman1_at_cerner.com

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Content Process
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CBO Scientific Advisory Board

• David Aronow, Ph.D., MD Ardais
• Yves Lussier, MD, Ph.D. Columbia University
• Joyce Mitchell, Ph.D. University of Utah
• Jonathan Uy, MD University of Illinois, Chicago