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![Page 1: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/1.jpg)
Stanford Centerfor Biomedical Informatics Research
Representing, Querying and Mining Knowledge about Autism Phenotypes
Amar K. Das, MD, PhDDepartments of Medicine and
of Psychiatry and Behavioral Sciences
![Page 2: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/2.jpg)
NDAR Ontology SIGJune 28, 2010
Outline Prior work NDAR project Phenologue project Future directions
![Page 3: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/3.jpg)
NDAR Ontology SIGJune 28, 2010
Hasler G,et al. Toward constructing an endophenotype strategy for bipolar disorders. Biological Psychiatry (2006)
Represent findings and their links using structured knowledge
![Page 4: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/4.jpg)
NDAR Ontology SIGJune 28, 2010
Phenomics
“A primary task for the new field of phenomics will be to clarify what, in practical terms, constitutes a phenotype and then to delineate the different phenotypic components that compose the phenome.”
Freimer & Sabatti, Nature Genetics (2003)
![Page 5: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/5.jpg)
NDAR Ontology SIGJune 28, 2010
Phenotypes in Psychiatry
‘The observable structural and functional characteristics of an organism determined by its genotype and modulated by its environment’
Diagnostic component Intermediate phenotype Quantitative phenotype Covariates
![Page 6: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/6.jpg)
NDAR Ontology SIGJune 28, 2010
OMIM
![Page 7: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/7.jpg)
NDAR Ontology SIGJune 28, 2010
dbGaP
Mailman, M.D. Nature Genetics (2007)
![Page 8: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/8.jpg)
NDAR Ontology SIGJune 28, 2010
PhenoWiki
![Page 9: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/9.jpg)
NDAR Ontology SIGJune 28, 2010
PhenoWiki
![Page 10: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/10.jpg)
NDAR Ontology SIGJune 28, 2010
Current Approaches Lack of standardization Lack of organization Lack of computability
![Page 11: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/11.jpg)
NDAR Ontology SIGJune 28, 2010
NDAR Project Systematic review Extension to NIFSTD ontology Rulebase development
![Page 12: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/12.jpg)
NDAR Ontology SIGJune 28, 2010
Systematic Review “(ADI-R or ADOS or Vineland) and
(genes or genetics) and autism” 26/43 papers relevant
156 unique phenotypes found Mean # phenotypes 4.1, range 0-13 Three basic types (1:1, sum, cutoff score)
![Page 13: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/13.jpg)
NDAR Ontology SIGJune 28, 2010
Systematic Review Different terms
e.g., ‘age of first phrases’ and ‘age of onset of phrase speech’
Different cutoff scorese.g., ‘delayed word’
Different definitionse.g., ‘regression’e.g., use of different instruments
![Page 14: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/14.jpg)
NDAR Ontology SIGJune 28, 2010
SWRL: Semantic Web Rule Language Rules in SWRL can be used to deduce
new knowledge about an existing OWL ontology
Specification can be extended through the use of built ins
![Page 15: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/15.jpg)
NDAR Ontology SIGJune 28, 2010
NDAR Codebook
![Page 16: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/16.jpg)
NDAR Ontology SIGJune 28, 2010
Extension to NIFSTD
![Page 17: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/17.jpg)
NDAR Ontology SIGJune 28, 2010
Phenologue Project (R01 MH877)
Develop a knowledge base that maps phenotypes to brain connectivity, neural deficits, and genetic markers
Develop logic-based methods to encode and classify phenotypes based on multi-scale measurements
Create tools to acquire new phenotypes and annotate phenotype-genotype findings in online resources such as published literature
Develop query-elicitation methods that can evaluate hypotheses about the phenotypes using deductive inference
![Page 18: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/18.jpg)
NDAR Ontology SIGJune 28, 2010
Phenologue Project
Database
Phenotype Definitions
New Associations
Query
Catalog Analysis
![Page 19: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/19.jpg)
NDAR Ontology SIGJune 28, 2010
Axiomé Rule Management Tool Rule paraphrasing Rule elicitation Rulebase visualization Knowledge mining using rules
Hassanpour. S., et al. RuleML (2009)
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NDAR Ontology SIGJune 28, 2010
Computational Phenomics Develop methods to
Apply machine learning methods to discover groups of rules with common semantics
Use natural language processing method to discover phenotype rules in published text
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NDAR Ontology SIGJune 28, 2010
Semantic Similarity
![Page 22: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/22.jpg)
NDAR Ontology SIGJune 28, 2010
Semantic Clustering Use vector space model and k-
means clustering
![Page 23: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/23.jpg)
NDAR Ontology SIGJune 28, 2010
Semantic Clustering Found 17 phenotype clusters Example cluster
ConcludePositiveHistoryofRegressionConcludeNegativeHistoryofRegressionConcludeQuestionableHistoryofRegression1ConcludePositiveHistoryofRegression2ConcludePositiveHistoryofRegression1ConcludeQuestionableHistoryofRegression2ConcludeNoPhrasesConcludePhrasesConcludeNegativeHistoryofRegression
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NDAR Ontology SIGJune 28, 2010
Text Mining
Hassanpour. S., et al. ACM IHI (submitted)
![Page 25: Stanford Center for Biomedical Informatics Research Representing, Querying and Mining Knowledge about Autism Phenotypes Amar K. Das, MD, PhD Departments.](https://reader034.fdocuments.us/reader034/viewer/2022050714/56649e555503460f94b4c56e/html5/thumbnails/25.jpg)
NDAR Ontology SIGJune 28, 2010
Evaluation of Precision
Level of Semantics Precision
Only rules 62%
Only ontology hierarchies 73%
Both rules and ontology hierarchies 76%
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NDAR Ontology SIGJune 28, 2010
Future Directions Develop rule management
technologies to support grouping Expand ontology to capture multi-
scale representation of endophenotypes