Jonathan Mortensen

Biomedical Informatics

Head of West Coast Data Science
BlueVoyant, San Francisco, California

Doctor of Philosophy, Biomedical Informatics, January 2016
Stanford University, Stanford, California

Bachelor of Science in Engineering, Biomedical Engineering, May 2011
Case Western Reserve University, Cleveland, Ohio

Contact Information

Interests

clinical informatics, knowledge representation, medical terminologies, data integration, VR

Prior Experience

Co-Founder, Gyroscope Software (2017-2018)
Data Scientist, Nuna (2014-2017)
Lister Hill National Center for Biomedical Communications, NLM - Summer 2010 and 2011 (Lab)
DePaul University MedIX NSF Research Experience for Undergraduates - Summer 2009 (Lab)
Cincinnati Children's Hospital Summer Undergraduate Research Fellowship - Summer 2008 (Lab)

Publications

Tomczak, A, Mortensen JM, et al. “Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations” Scientific Reports, Mar 2018.
Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA. “Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology” JBI, Apr 2016.
Mortensen JM, Minty E, Januszyk M, Sweeney T, Rector AL, Noy NF, Musen MA. "Using the Wisdom of Crowds to Find Critical Errors in a Biomedical Ontology". Journal of Americal Medical Informatics. June, 2015.
Winnenburg R, Mortensen JM, Bodenreider O. “Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT” Journal of biomedical semantics. Mar 2015.
Mortensen JM, Musen MA, Noy NF. "An Empirically Derived Taxonomy of Errors in SNOMED CT". Proceedings of the AMIA Annual Symposium, 2014.
Matthew Horridge, Mortensen JM, Bijan Parsia, Ulrike Sattler, Mark Musen. "A Study on the Atomic Decomposition of Ontologies". Proceedings of the International Semantic Web Conference, 2014
Blair DR, Lyttle CS, Mortensen JM, et al. A Non-Degenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk. Cell. 2013.
Mortensen JM, Musen MA, Noy NF. "Crowdsourcing the Verification of Relationships in Biomedical Ontologies". Proceedings of the AMIA Annual Symposium, 2013. -- Best Student Paper Award
Mortensen JM, Musen MA, Noy NF. "Developing Crowdsourced Ontology Engineering Tasks: An iterative process". International Semantic Web Conference, CrowdSem Workshop, 2013.
Mortensen JM. "Crowdsourcing Ontology Verification". International Semantic Web Conference, Doctoral Consortium, 2013.
Mortensen JM, Alexander PR, Musen MA, Noy NF. "Crowdsourcing Ontology Verification". International Conference on Biomedical Ontology, 2013.
Peters L, Mortensen JM, Nguyen T, Bodenreider O. "Enabling complex queries to drug information sources through functional composition". Stud Health Technol Inform (Proc Medinfo) 2013.
LePendu P, Iyer S V, Bauer-Mehren A, Harpaz R, Mortensen JM, Shah NH. Pharmacovigilance using clinical notes. Nature CPT. 2013.
Noy NF, Mortensen JM, Alexander PR, Musen MA. "Mechanical Turk as an Ontology Engineer? Using Microtasks as a Component of an Ontology Engineering Workflow". ACM Web Science Conference. 2013.
Matthew Horridge, Mikel Egaña Aranguren, Mortensen JM, Mark Musen and Natalya Noy. "Ontology Design Pattern Language Expressivity Requirements". Proceedings of the International Semantic Web Conference, 2012
Mortensen JM, Matthew Horridge, Mark A. Musen and Natalya F. Noy. "Modest Use of Ontology Design Patterns in a Repository of Biomedical Ontologies". Proceedings of the International Semantic Web Conference, 2012
Mortensen JM, Matthew Horridge, Mark Musen, Natalya Noy. "Applications of Ontology Design Patterns in Biomedical Ontologies". Proceedings of the AMIA Annual Symposium, 2012.
Mortensen JM, Olivier Bodenreider. “Comparing Pharmacologic Classes in NDF-RT and SNOMED CT”. Proceedings of the Fourth International Symposium on Semantic Mining in Biomedicine, 2010. View
Giannini, Courtney M, Hye K Kim, Mortensen JM, et al. “Culture of Non-Genital Sites Increases the Detection of Gonorrhea in Women”. Journal of Pediatric and Adolescent Gynecology 23.4 (2010): 246-252. View
Mortensen JM, Julia Wu, John Rogers, Jacob Furst, Daniela Raicu. “Effect of Image Linearization on Normalized Compression Distance”. International Symposium on Signal Processing, Image Processing and Pattern Recognition (SIP 2009), Jeju Island, Korea, December 10-12, 2009. View
Mortensen JM, Joel E. Mortensen. “The Power of Capsaicin”. Journal of Continuing Education: Topics & Issues. Volume 11, Number 1, 2009, pg 8-13. View

Presentations

"Using Python to build an AI to play and win SNES Streetfighter II". PyCon 2018.
"A Taxonomy of Errors in SNOMED CT". American Medical Informatics Association Annual Symposium, 2014.
"Crowdsourcing the Verification of Relationships in Biomedical Ontologies". American Medical Informatics Association Annual Symposium, 2013.
"Developing Crowdsourced Ontology Engineering Tasks". CrowdSem Workshop, International Semantic Web Conference, 2013.
"Crowdsourcing Ontology Verification". International Conference on Biomedical Ontology, 2013.
"Modest Use of Ontology Design Patterns in a Repository of Biomedical Ontologies". Workshop on Ontology Design Patterns (WOP), International Semantic Web Conference, 2012
"Applications of Ontology Design Patterns in Biomedical Ontologies". AMIA Annual Symposium, 2012.
"Comparing Pharmacologic Classes in NDF-RT and SNOMED CT". The Fourth International Symposium on Semantic Mining in Biomedicine, October 2010.
"The Power of Capsaicin". American Medical Technologists: Ohio State Society, Spring Seminar, 2010.

Posters and Abstracts

Mortensen JM, Mark Musen, Natalya Noy. "Prospective Expert and Crowd Verification of SNOMED CT". AMIA Annual Summits: Clinical Research Informatics, 2014.
Mortensen JM, Mark Musen, Natalya Noy. "Crowdsourcing Ontology Verification". Conference on Human Computation and Crowdsourcing (HComp), 2013.
Mortensen JM, Mark Musen, Natalya Noy. "Crowdsourcing Ontologies". National Library of Medicine Informatics Training Conference, 2013.
Mortensen JM,Matthew Horridge, Mark Musen, Natalya Noy. "Adoption of Ontology Design Patterns in Biomedical Ontologies" NCBC Showcase, 2012.
Giannini, Courtney M, Hye K Kim, Jonathan Mortensen, et al. “Culture of Non-Genital Sites Increases Detection of Gonorrhea in Adult but not Adolescent Women.” Journal of Pediatric and Adolescent Gynecology 22.2 (2009): e14.
Mortensen JM, Keith Marsolo, et al. “i2b2 and You- A Step Toward Personalized Medicine” Cincinnati Children’s Hospital Medical Center, Summer Undergraduate Research Fellowship, Poster Session, 2008.