Toward interactive visual tools for comparing phenotype profiles
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Monarch Initiative presentation on the phenogrid visualization tool, presented during the 2014 Phenotype Day workshop held by the BioOntologies SIG
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Toward interactive visual tools for comparing phenotype profiles
- 1. Toward interactive visual tools for comparing phenotype profiles Charles Borromeo, Jeremy Espino, Ncole L. Washington, Maryann Martone, Christopher J. Mungall, Melissa A. Haendel, Harry Hochheiser
- 2. Goal: Visually compare patient phenotypes across species 2 ▪ Ontological similarity of phenotype profiles within human and across taxa can inform diagnosis and identify models ! ▪ Challenge: interpret correspondences between input phenotypes and matches within and across species
- 3. How do models recapitulate disease?3 b2b1035Clo (aka Blue Meanie) b2b012Clo (aka Heart Under Glass) Fgfr2 Fuzb2b1273Clo (aka octomouse) Duplex kidney Cleft palate Prenatal growth retardation Tricuspid valve atresia Persistent truncus arteriosis Double outlet right ventricle Anophthalmia Microphthalmia Kidney cysts Pulmonary valve atresia Polycystic kidney Ventricular septal defect Common atrium Atrioventricular septal defect Complete atrioventricular septal defect …… Cleft palate Abnormal sternum morphology Double outlet right ventricle Polydactyly Pulmonary hypoplasia Kidney cysts Duplex kidney Right aortic arch Common atrium Complete atrioventricular septal defect Pulmonary artery atresia
- 4. Why is visualization needed? 4 Human phenotypes! p1! .! .! .! pn Model 1 phenotypes! m1,1! .! .! .! m1,j Model m phenotypes! mm,1! .! .! .! mm,k n input phenotypes! m models! ! O(nm) comparisons! ! O(102) phenotypes ! ! O(103) models Need a dense display! to facilitate comparisons ! and ! access details..
- 5. Questions and Challenges 5 Patient phenotypes Which input phenotypes are well-covered across multiple models? Which phenotypes are not frequently recapitulated? .. and might therefore be particularly useful for diagnosis? Which model diseases are most similar? Models Which models are most similar to an input phenotype profile? Which models are similar to each other? … and how do they differ? How do different types of models compare? Mouse, zebrafish, fly…. Known diseases, other patients? Relationships Why is a given input phenotype similar to a model phenotype?
- 6. PhenoGrid Overview display 6 Top matches for human, mouse, and zebrafish
- 8. Comparison with mouse genes 8
- 9. Demo… 9
- 10. Implementation Details Monarch-app (Middleware) NIF architecture and data services Client Server jQuery D3 HTML5 Phenogrid Widget jQuery widget suitable for integration into 3rd party sites Code:! ! ! ! ! http://www.github.com/monarch-initiative/monarch-app! Deployment instructions:! http://www.monarchinitiative.org/page/phenogrid
- 11. Next steps… 11 Detailed explanation of phenotype similarity results Additional comparisons: phenotype profile against other patients, or all orthologs of a given gene comparing subtypes of a disease Contributions of individual phenotypes? What if I remove the phenotype?
- 12. Additional next steps.. 12 Add other data sources: proteins, pathways, etc. ! Choose profiles to compare ! Hierarchical display of phenotypes.. use ontology structure. ! Integrate other data network views
- 13. Acknowledgements 13 LBNL ¤ Chris Mungall ¤ Suzanna Lewis ¤ Nicole Washington ! OHSU ¤ Melissa Haendel ! NIH – UDP ¤ Neal Boerkoel Charité / HPO ¤ Peter Robinson ¤ Sebastian Kohler ! Sanger / Exomizer ¤ Damian Smedley ! UCSD / NIF ¤ Maryann Martone ! University of Pittsburgh ¤ Becky Boes ¤ Charles Borromeo Funding: NIH Office of Director: 1R24OD011883 NIH-UDP: HHSN268201300036C