Photo of Melissa A. Haendel, Ph.D.

Melissa A. Haendel Ph.D.

  •      (503) 407-5970
    • Associate Professor of Medical Informatics and Clinical Epidemiology School of Medicine
    • Co-Director, OHSU Library Library
    • Director of the Ontology Development Group Library
    • Biomedical Informatics Graduate Program School of Medicine

Melissa is co-director of the OHSU Library and the director of the Ontology Development Group and an Associate Professor in the Library and the Department of Medical Informatics and Clinical Epidemiology.

Major Responsibilities

Interim Co-Director of the Library Director of the Ontology Development Research Laboratory within the OHSU Library and Department of Medical Informatics and Epidemiology

Principal investigator of: 

The Monarch Initiative
The NCATS Data Translator
PCORI "Realization of a Standard of Care for Rare Diseases Using Patient-Engaged Phenotyping”

Development of ontologies and data standards

End-user requirements and user interface design and testing

Science of Science

Promotion of research reproducibility

Development of open science policies and practices

Areas of interest

  • When not working, Melissa is usually planting, harvesting, cooking, or eating food.


  • B.A., Reed College, Portland Oregon United States 1991
  • Ph.D., University of Wisconsin, Madison Wisconsin United States 1999


Selected publications

  • Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, LaRocca GM, Haendel MA. (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature.PeerJ 1:e148      

  • Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. (2013) Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30;14(1):263.

  • Haendel MA, Chesler EJ. Lost and found in behavioral informatics. (2012) Int Rev Neurobiol. 2012;103:1-18. doi:10.1016/B978-0-12-388408-4.00001-0.     

  • Nicole Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson and Melissa Haendel (2012) Research resources: curating the new eagle-i discovery system. Database Vol. 2012, bar067.            

  • Torniai, C., Brush, M., Vasilevsky, N., Segerdell, E., Wison, M., Johnson, T., Corday, K., Shaffer, C., and Haendel, M. (2011) Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.   

  • Mungall CJ, Anderson D, Bandrowski A, Canada B, Chatyr-Aryamontri A, Cheng K, Conn PM, Dolinski K, Ellisman M, Eppig J, Grethe JS, Kemnitz J, Iadonato S, Larson SD, Magness C, Martone ME, Tyers M, Torniai C, Troyanskaya O, Turner J, Westerfield M, Haendel MA. (2011) An ontology-based approach to linking model organisms and resources to human diseases. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.        

  • Mitchell S, Torniai C, Lowe, B, Corson-Rikert J, Wilson M, Ahmed M, Chen S, Ding Y, Rejack N, Haendel MA. (2011) Aligning research resource and researcher representation: the eagle-i and VIVO use case. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

  • Brush MH, Vasilevsky N, Torniai C, Johnson T, Shaffer C, Haendel MA. (2011) Developing a reagent application ontology within the OBO Foundry Framework. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

  • Mungall, C.J., Gkoutos, G.V., Smith, C.L., Haendel, M.A., Lewis, S.E., and Ashburner, M. (2010) Integrating Phenotype Ontologies across Multiple Species. Genome Biol. 2010 Jan 8;11(1):R2.        

  • Washington, N.L.*, Haendel, M.A.*, Mungall, C.J., Ashburner, M., Westerfield, M., and Lewis, S.L. (2009) Linking human disease to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov;7(11):e1000247. Epub 2009 Nov 24.                                                                     *These authors contributed equally to this manuscript.       


  • "ClinGen advancing genomic data-sharing standards as a GA4GH driver project." Human mutation  In: , Vol. 39, No. 11, 01.11.2018, p. 1686-1689.
  • "Classification, ontology, and precision medicine." New England Journal of Medicine  In: , Vol. 379, No. 15, 11.10.2018, p. 1452-1462.
  • "A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative." Genetics in Medicine  In: , 15.06.2018, p. 1-12.
  • "Plain-language medical vocabulary for precision diagnosis /692/700/478 /631/208/1516 correspondence." Nature Genetics  In: , Vol. 50, No. 4, 01.04.2018, p. 474-476.
  • "Looking beyond the exome : A phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases." Genetics in Medicine  In: , Vol. 20, No. 4, 01.04.2018, p. 464-469.
  • "Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder." American Journal of Human Genetics  In: , Vol. 102, No. 3, 01.03.2018, p. 494-504.
  • "matchbox : An open-source tool for patient matching via the Matchmaker Exchange." Human mutation  In: , 01.01.2018.
  • "PDX-MI : Minimal information for patient-derived tumor xenograft models." Cancer Research  In: , Vol. 77, No. 21, 01.11.2017, p. e62-e66.
  • "Matchmaker Exchange." Current Protocols in Human Genetics  In: , Vol. 95, 18.10.2017, p. 9.31.1-9.31.15.
  • "Disease model discovery from 3,328 gene knockouts by the International Mouse Phenotyping Consortium." Nature Genetics  In: , Vol. 49, No. 8, 01.08.2017, p. 1231-1238.
  • "Identifiers for the 21st century : How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data." PLoS Biology  In: , Vol. 15, No. 6, e2001414, 29.06.2017.
  • "MARRVEL : Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome." American Journal of Human Genetics  In: , Vol. 100, No. 6, 01.06.2017, p. 843-853.
  • "Bedside Back to Bench : Building Bridges between Basic and Clinical Genomic Research." Cell  In: , Vol. 169, No. 1, 23.03.2017, p. 6-12.
  • "A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3." American Journal of Human Genetics  In: , Vol. 100, No. 1, 05.01.2017, p. 128-137.
  • "The Monarch Initiative : An integrative data and analytic platform connecting phenotypes to genotypes across species." Nucleic Acids Research  In: , Vol. 45, No. D1, 01.01.2017, p. D712-D722.
  • "The human phenotype ontology in 2017." Nucleic Acids Research  In: , Vol. 45, No. D1, 01.01.2017, p. D865-D876.
  • "Improved diagnosis and care for rare diseases through implementation of precision public health framework."   Advances in Experimental Medicine and Biology. Vol. 1031 Springer New York LLC, 2017. p. 55-94 (Advances in Experimental Medicine and Biology; Vol. 1031).
  • "Aligning the human phenotype and mammalian phenotype ontology using dead simple ontology design patterns." CEUR Workshop Proceedings  In: , Vol. 2137, 01.01.2017.
  • "Reproducible and reusable research : Are journal data sharing policies meeting the mark?" PeerJ  In: , Vol. 2017, No. 4, e3208, 2017.
  • "Tools for exploring mouse models of human disease." Drug Discovery Today: Disease Models  In: , 2017.
  • "Model organisms facilitate rare disease diagnosis and therapeutic research." Genetics  In: , Vol. 207, No. 1, 2017, p. 9-27.
  • "Navigating the phenotype frontier : The monarch initiative." Genetics  In: , Vol. 203, No. 4, 01.08.2016, p. 1491-1495.
  • "Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency." Genetics in Medicine  In: , Vol. 18, No. 6, 01.06.2016, p. 608-617.
  • "A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease." American Journal of Human Genetics  In: , 04.04.2016.
  • "The Ontology for Biomedical Investigations." PLoS One  In: , Vol. 11, No. 4, e0154556, 01.04.2016.
  • "Reproducibility and conflicts in immune epitope data." Immunology  In: , Vol. 147, No. 3, 01.03.2016, p. 349-354.
  • "Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease." Applied and Translational Genomics  In: , 01.03.2016.
  • "Muscle logic : New knowledge resource for anatomy enables comprehensive searches of the literature on the feeding muscles of mammals." PLoS One  In: , Vol. 11, No. 2, e0149102, 01.02.2016.
  • "The Resource Identification Initiative : A cultural shift in publishing." Journal of Comparative Neurology  In: , Vol. 524, No. 1, 01.01.2016, p. 8-22.
  • "The Resource Identification Initiative : A cultural shift in publishing." Brain and Behavior  In: , Vol. 6, No. 1, 01.01.2016, p. 1-14.

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