Peter E. Midford



Department of Ecology and Evolutionary Biology

University of Kansas

2041 Haworth Hall

1200 Sunnyside Avenue

Lawrence, KS 66045

Telephone: 785-864-1768



PhD Zoology, 1999
University of Wisconsin, Madison, WI
Advisor: Jack P. Hailman


MS Computer Science, 1987
Yale University, New Haven, CT
Advisor: Roger C. Schank


BS Mathematics, 1983
Harvey Mudd College, Claremont, CA


Professional and Research Experience

2007-present:        Adjunct Research Associate University of Kansas. 
Conducting research in phylogenetics and ontology construction.

2007-present:        Ontology curator, Phenoscape project
Construct, extend and maintain ontologies of teleost taxonomy and specimen collections.

2006-2007:            Research Associate University of British Columbia. 
Conducted research in phylogenetics.

2005:                        Contract Bioinformatics Programmer. 
Designed and implemented enhancements for the Mesquite Phylogeny package.

2004-2005:            Short-term Bioinformatics Programmer, University of Michigan Zoology Museum.
Designed and implemented web-interfaces to two biological specimen databases and several utility programs for molecular evolution at the University of Michigan.

2003:                        Staff Programmer Cycorp, Austin TX.
Developed prototype of a trainable natural language parser and contributed to construction of the Cyc knowledge base.

2001-2002:            NSF Bioinformatics Postdoctoral Fellow, University of Arizona.
Developed ontologies for behavior and phylogenetic comparative methods using Mesquite.

2000:                        Post doctoral position, Ruhr Universität Bochum.
Conducted experiments, and developed software related to pigeon courtship and perception of biological motion.

1993-1999:            Graduate student programmer, University of Wisconsin - Madison.
Designed, implemented and extended "Phenotypic Diversity Analysis Programs" for phylogenetic comparative methods along with several data acquisition and editing programs.

1990-1999:            Doctoral student, University of Wisconsin – Madison.
Conducted dissertation research on social learning in Florida scrub jays at the Archbold Biological Station, Lake Placid FL.  Funded by fellowship, teaching assistantship, and research assistantship.

1986-1990:            Software Engineer, Hughes Simulation Systems, West Covina CA.
Implemented and lead enhancement effort on graphical front end for an automated computer software generation tool.

1984-1985:            Graduate student, Yale University.
Contributed to group research projects in models of human learning and automatic generation of explanations by computer.

1983:                        Undergraduate senior research, Harvey Mudd College.
Built simulation model of early visual processing.

1982-1983:            Undergraduate research assistant in linguistics, Pitzer College.
Assisted in data analysis and. development of a model of human understanding of linguistic understanding of terms for social roles.



Maddison, W. P., Midford, P. E., and Otto, S. P. 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56:701-710.

Ramirez, M. J., Coddington, J. A., Maddison, W. P., Midford P. E., Prendini, L., Miller, J., Griswold, C. E., Hormiga, G., Sierwald, P., Scharff, N., Benjamin, S. P., and Wheeler, W. C. 2007. Linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology 56:283-294.

Ives, A. R., Midford P. E., and Garland, T., Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252-270.

Midford, P. E., 2004. Ontologies for Behavior. Bioinformatics 20:3700-3701.

Midford, P. E., 2002. Robots aren't the only physical models. Behavioral and Brain Sciences 24:1069-1070.

Midford, P. E., Hailman, J. P., and Woolfenden, G. E. 2000. Social learning of a novel foraging patch in families of free-living Florida scrub-jays. Animal Behaviour 59:1199-1027.

Garland, T., Jr, Midford, P. E., and Ives, A. R., 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. American Zoologist 39:374-388.

Midford, P. E., 1998. High–Level social learning in apes: imitation or observation–assisted planning? Behavioral and Brain Sciences 21:698-699.

Midford, P. E., 1993. Cultural transmission is more than cultural learning. Behavioral and Brain Sciences 16:529-530.


Publications in Preparation

Midford, P. E., Balhoff, J. and Vision, T. in prep.  TTO: An ontology for teleost taxonomy.

Midford, P. E., and Hailman, J. P., in prep. Juvenile Florida Scrub-jays fail to retain.

Midford, P. E., Maddison, W. P., and Otto, S. P. in prep. Detecting and distinguishing biases in character change, speciation and extinction using the BiSSE method.


Software Publications

"PDAP:PDTREE"  package for Mesquite, Version 1.15 November 2008. P. E. Midford, T. Garland, Jr. and W. Maddison. Available at: This package has been cited over 130 times in publications listed in Web of Scicnce

“OwlWatcher” 0.036, May 2008.  P. E. Midford.

 “Diverse” module for Mesquite, September 2007.  P. E. Midford, and W Maddison.

 “Correl” module for Mesquite, May 2006. Included in Mesquite 1.1 and later versions. This package has been cited in a publication listed in Web of Science

“EKB” demonstration ontology for behavior.  Available at

"Phenotypic Diversity Analysis Programs” (PDAP) Distributed privately and Version 6.0 Copyright  25 September 2001 by T. Garland, Jr., J. A. Jones, A. W. Dickerman, P. E. Midford, and R. Díaz-Uriarte. Available from T. Garland (


Published Abstracts

Garland, T., Ives, A. R., Midford, P. E. 2004. Within-species variation and measurement error in phylogenetic comparative methods. Integrative and Comparative Biology, 44:556.

Midford, P. E. 2002. Ontology as ethogram: Knowledge representation for behavior. Measuring Behavior 2002 (Amsterdam, The Netherlands), p.176.  Poster Abstract.

Jokisch, D., Midford, P. E., & Troje, N. F. 2001. Biological motion as a cue for the perception of absolute size. Journal of Vision, 1(3), 357a.


Invited talks

2008:                        “Ontologies and the Rebirth of the Ethogram” Department of Biology, University of South Dakota

2008:                        “Names, Ranks, Clades, and Taxonomy Ontologies” Workshop on Ontologies in Evolutionary Biology, Evolution 2008, Minneapolis MN

2007:                        “The two trees: Phylogeny meets ontology” Department of Zoology, Southern Illinois University, Carbondale IL

2003:                        “Representing and analyzing behavior using ontologies” Rat Genome Database project, Medical College of Wisconsin, Milwaukee WI


Presented Papers

2009:                        “Do optimization issues limit the power of BiSSE analyses: A preliminary comparison” Evolution 2009 Moscow ID

2008:                        “Taxonomic ontologies: Bridging phylogenetic and taxonomic history” TDWG 2008, Fremantle, Western Australia

2007:                        “Using ontologies to answer comparative behavior questions: Three approaches” Animal Behavior Society, Burlington, VT

2004:                        “Ontologies and the comparative method” Evolution 2004, Fort Collins, CO

2002:                        “Ontology as an ethogram: A case study using jumping spider courtship” Animal Behavior Society, Bloomington, IN

2002:                        “Representing behavior: A case study using Habronattus courtship” American Arachnology Society, Riverside, CA

2002:                        “The ethogram as an ontology” Gene Ontology Users Group, Tucson, AZ

1998:                        “Training and retention of a simple foraging task by the Florida scrub-jay” Animal Behavior Society, Carbondale, IL

1998:                        “Training and retention of a simple foraging task by the Florida scrub-jay” North American Ornithological Conference, St. Louis, MO

1996:                        “Social learning and tradition in the Florida scrub-jay” American Ornithological Union 114th stated meeting, Boise, ID

1996:                        “Social learning and tradition in the Florida scrub-jay” Animal Behavior Society, Flagstaff, AZ

1994:                        “Tradition and social learning in the Florida scrub-jay” Midwest Animal Behavior Conference, Carbondale, IL


Conference Posters

2008:                        “Ontology patterns for behavior: From counting to annotating” Congress of the International Society for Behavioral Ecology 2008, Ithaca, NY.

2008:                        “Linking evolutionary morphology to genomics using ontologies” Evolution 2008, Minneapolis, MN (with multiple co-authors)

2008:                        “Using context dependent methods and ontologies to address comparative questions in Animal Behavior” Evolution 2008, Minneapolis, MN

2007:                        “Linking evolution to genomics using phenotype ontologies” Biocurator meeting 2007, San Jose CA (with multiple co-authors)

2006:                        “Owlwatcher: An ontology-based tool for collecting behavior data” Animal Behavior Society,  Snowbird UT

2001:                        “Ontologies for the study of behavior” Animal Behavior Society, Corvalis OR

2001:                        “The development of an ontology for behavior and its application to comparative studies” Evolution 2001, Knoxville, TN

1998:                        “Social learning the Florida scrub-jay: A field study” Napoli Social Learning Conference, Naples Italy

1996:                        “Do Florida scrub-jays learn the concept center-of” Symposium on animal cognition preceding the Animal Behavior Society meeting, Flagstaff, AZ


Invited Workshops

2008:                        OBO (Open Biomedical Ontologies) relations meeting, Denver CO.

2007:                        Evoinformatics working group, NESCent, Durham NC.

2006:                        Second Fish Evolution Database Workgroup meeting, NESCent, Durham NC.

2005:                        Behavior MetaData II, Ithaca, NY

2004:                        Behavior MetaData I, Ithaca, NY

2002:                        Ethoinformatics, Bloomington, IN

2001:                        Evolution Synthesis Center I, Arlington, VA (rapporteur)


Teaching Experience

2004:                        Designed and taught computer literacy courses (e.g., Introduction to the Internet, Power Point) to adult students in Austin TX.

2001-2002:            Tutored and taught adult students in GED math course in Tucson AZ.

1991-1999:            As graduate student served as teaching assistant and guest lecturer in courses including Evolution (3x), Animal Behavior, Animal Behavior Lab, Ornithology Lab, Non-majors Ecology, Introductory Zoology, Introductory Zoology Lab (3x).


Mentoring Experience

2009:                        Google summer of code – Mentored Kasia Hayden in development and initial release of a Mesquite-based viewer for ontology-based annotations of cells in character matrices

2008:                        Google summer of code – Mentored Mathew Ackermann in development and initial release of PDSIM, an implementation of PDSIMUL (part of PDAP) for Mesquite


Reviewer for

Evolution (2009,2008x2,2007,2002,2001)

Integrative and Comparative Biology (2008)

Journal of Theoretical Biology (2008)

Systematic Biology (2009x2,2007)

IEEE-BIBE (International Conference on BioInformatics and BioEngineering) (2007)

American Naturalist (2007)

Evolution and Development (2007)

Journal of Comparative Psychology (1999,1998,1996)


Awards and Fellowships

2001-2002:            National Science Foundation Bioinformatics Postdoctoral Fellowship

1996:                        John Emlen Memorial Award, Department of Zoology, University of Wisconsin – Madison

1993:                        John Jefferson Davis summer fellowship, Department of Zoology, University of Wisconsin – Madison

1990-1991:            University Fellowship, University of Wisconsin – Madison

1990:                        Hughes Simulation Systems Technical Excellence award for “Model Builder Debugger” software project

1983-1985:            Departmental Fellowship, Department of Computer Science, Yale University


Professional and Honor Society Memberships

Sigma Xi, Animal Behavior Society, Society for Integrative and Comparative Biology, TDWG, American Association for Artificial Intelligence


Other Service

2008-2009:            Ethosource advisory board