Melissa Haendel

Lead Ontologist

Assistant Professor
OHSU Library
Department of Medical Informatics & Clinical Epidemiology

LinkedIn profile

Major Responsibilities

  • Director of the Ontology Development Group within the OHSU Library and Department of Medical Informatics and Epidemiology
  • Principal investigator of the Monarch Initiative (monarchinitiative.org)
  • Development of ontologies and data standards
  • End-user requirements and user interface design and testing
  • Management of Data Curation team
  • Research profiling
  • Promotion of research reproducibility



Ph.D. Neuroscience (1999) University of Wisconsin, Madison, WI
B.A. Chemistry (1991) Reed College, Portland, OR

Research experience

•  Ontologist and Scientific Curator (2004-2009) Dr. Monte Westerfield, University of Oregon, Eugene, OR
•  Post-doctoral fellow (2002-2004) Dr. George Bailey and Dr. Robert Tanguay, Oregon State University, Corvalis, OR
•  Post-doctoral fellow (2000-2002) Dr. Judith Eisen and Dr. Beatrice Darimont, University of Oregon, Eugene, OR
•  Graduate Research Assistant (1993-1999) Dr. Gary Lyons, University of Wisconsin, Madison, WI
•  Laboratory technician (1993) Dr. David Barnes, Oregon State University, Corvalis, OR
•  Undergraduate Research Assistant (1990-1991) Dr. Alan Shusterman, Reed College, Portland, OR

Select Teaching Experience

•  Anatomy ontology course instructor, National Evolutionary Synthesis Center (2012 and 2013)
Co-organized a week-long course on ontology development best practices.
•  Workshop coordinator, International Conference on Biomedical Ontology (2011) Co-organized a workshop to disseminate best practices in anatomy ontology development.
•  Informatics Fellow mentor, Oregon Health and Science University (2010-present) Mentored student project to model reagents and cell lines with ontologies for the purposes of resource discovery and experimental inference.
•  Undergraduate mentor, University of Oregon (2008) Mentored student project to model the zebrafish brain with ontologies.

Select Publications and Presentations

•  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.                                                                         

•  Haendel, M.A., F. Neuhaus, D.S. Osumi-Sutherland, P.M. Mabee, J.L.V. Mejino, C.J. Mungall and B. Smith. (2008) CARO - The Common Anatomy Reference Ontology. In: Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).


Outside of work:

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