Presented in the life sciences panel at the 1st U.S. SEMANTIC TECHNOLOGIES SYMPOSIUM 2018. http://us2ts.org/

1. Semantics for rare disease phenotyping,
diagnostics, and discovery
Melissa Haendel, PhD
@ontowonka
@monarchinit

2. Prevailing clinical diagnostic pipelines leverage only
a tiny fraction of the available data

3. Prevailing clinical diagnostic pipelines leverage only
a tiny fraction of the available data
Under-utilized data à
Loss of discriminatory power
?

4. The (translational)
chasm of semantic despair
CD2H

5. The Human Phenotype Ontology
§ 11,813
phenotype
terms
§ 217,351 disease
-phenotype
annotations
bit.ly/hpo-paper
https://monarchinitiative.org/

6. Fuzzy (semantic similarity) phenotype
matching
DOI: 10.1126/scitranslmed.3009262

7. OMIM
(brown)
MESH
(grey)
ORDO/Orphanet
(yellow)
SubClassOf
(solid line)
Xref
(dashed grey line)
Hemolytic anemia
mappings across
resources
The ontologies inconsistently map to each other, leading to
poor interoperability and computability

9. New integrated ontology
Bayesian OWL Ontology Merging (kBOOM)
Mungall et al. http://bit.ly/k-BOOM
http://bit.ly/mondo-repo
http://purl.obolibrary.org/obo/mondo.owl

10. Patients can and should be empowered
to help with all of this.

11. Plain language synonyms for computable
phenotypes

12. Global patient matchmaking
Computational matching of rare disease patients across clinical & public sources
Find models and experts for functional validation
bit.ly/mme-matchbox
patientarchive.org
bit.ly/exomiser-2017

13. With many thanks
Lawrence Berkeley
Chris Mungall
Suzanna Lewis
Jeremy Nguyen
Seth Carbon
Nicole Washington
Charite
Sebastian Kohler
Ga rv a n
Tudor Groza
Craig McNamara
RENCI
Jim Balhoff
Boston Children’s
Ingrid Holm
Catherine Brownstein
John Brownstein
E BI
Helen Parkinson
David Osumi-Sutherland
OH SU
Matt Brush
Kent Shefchek
Julie McMurry
Tom Conlin
Nicole Vasilevsky
Dan Keith
Maureen Hoatlin
Tim Putman
JP Gourdine
David Ellison
Gen omi cs E n gland/Queen
M a ry
Damian Smedley
Jules Jacobson
Tomasz Konopka
Pilar Cacheiro
J a ckson La boratory
Peter Robinson
Leigh Carmody
Hannah Blau
With special thanks to Julie McMurry for excellent graphic design
Johns Hopkins
Chris Chute
Casey Overby
Ada Hamosh
Scripps
Andrew Su
Ben Good
Chunlei Wu
Gregg Stupp
Sanford Health Imagenetics
Neal Boerkoel
Kayli Rageth
Murat Sincan
ClinGen
Heidi Rehm
Larry Babb
Harindra Arachchi