Dr. Melissa Anne Haendel
725 Amelia Ave., Brownsville, OR, 97327
haendel@ohsu.edu
503-407-5970
Education
Ph.D. Neuroscience, University of Wisconsin, 1999
B.A. Chemistry, Reed College, 1991
Positions
Assistant Professor and department head
2009-present
Ontology Development Group, Oregon Health and Science University, Library and
Department of Medical Informatics and Epidemiology, 2009-present
Development of ontologies and best practices for representation and query of
biomedical resources, model organisms, clinical specimens and related data; content
management; end-user requirements and user interface design and testing;
management of data curation team; data standards development and outreach.
Ontologist and Scientific Curator
2004-2009
University of Oregon, Dr. Westerfield
Development of anatomical ontologies and syntax for phenotype ontologies; genetic
nomenclature coordinator; curation of genomic, gene expression and phenotype data
from the zebrafish literature; and development of data standards.
Post-doctoral fellow
2002-2004
Oregon State University, Dr. Bailey and Dr. Tanguay
Effects of biocides on zebrafish development and microarray analysis. Set up a new
laboratory.
Post-doctoral fellow
2000-2002
University of Oregon, Dr. Eisen and Dr. Darimont
Involvement of thyroid hormone during early neural development in the zebrafish.
Ph. D. dissertation
1993-1999
University of Wisconsin, Dr. Gary Lyons
Identification and knock-out of a novel gene important for neural development in
mice.
Laboratory technician
Oregon State University, 1993, Dr. David Barnes
Maintenance of zebrafish stocks and cell culture lines.
Undergraduate thesis
1993
1990-1991
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Dr. Melissa Haendel
Reed college, 1990-1991, Dr. Alan Shusterman
Utilization of chemical modeling programs to analyze drug-receptor interactions.
Teaching Experience
Guest Lecturer: Research Methods, 2013
Guest lectured on problem analysis and use of public data for an upper-level
informatics course.
Information Science Workshop, 2013
Co-organized and taught a workshop on information management to graduate
students in naturopathic medicine.
Inter-model organism workshop, 2013
Organized workshop on unification of data models for representation of model
organism data.
Neural crest workshop, 2012
Organized workshop on representation of anatomical structures pertaining to neural
crest development for evolutionary and biomedical purposes
Anatomy ontology course instructor, National Evolutionary Synthesis Center, 2012 and
2013.
Co-organized a week-long course on ontology development best practices.
Skeletal ontology workshop, 2011
Organized workshop on representation of skeletal structures for evolutionary and
biomedical purposes.
Informatics Fellows mentor, Oregon Health and Science University, 2010-present
Mentored two student projects to model reagents, cell lines, and observational clinical
studies with ontologies for the purposes of resource discovery, experimental inference,
and development of new data standards.
Workshop coordinator, International Conference on Biomedical Ontology, 2011
Co-organized a workshop to disseminate best practices in anatomy ontology
development.
Undergraduate mentor, University of Oregon, 2008
Mentored student project to model the zebrafish brain with ontologies.
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Dr. Melissa Haendel
Meeting facilitator, National Evolutionary Synthesis Center, 2008
Taught principles of ontology construction and interoperability to evolutionary
biologists.
Meeting facilitator, National Center for Biomedical Ontology, 2006
Lead group of anatomists in developing good ontology principles for representing
anatomy and homology.
Instructor for Biochemistry: Writing in the discipline, University of Oregon, 2002
Formulated and taught a writing course for undergraduates in the biological sciences,
utilizing peer review and editorial skills.
Guest Lecturer: Developmental neurobiology, 2001-2002
Guest lectured on neurogenesis and fate specification for an upper-level neuroscience
course.
Molecular biology rotation student mentor, University of Oregon, 2001
Taught the student basic molecular and embryological techniques, bioinformatics
analysis, and presentation skills.
Instructor at the Center for Talented Youth, Johns Hopkins University, 1999 and 2000
Designed and taught an accelerated introductory course in neuroscience for high
school students. This included teaching the students how to find, read, interpret and
write scientific literature.
Summer Research Program in Biology mentor, University of Wisconsin, 1998-1999
Taught the student molecular and histological techniques, bioinformatics analysis,
experiment design, literature analysis, and presentation skills.
Teaching Assistant, Cell and Molecular Biology, Biocore program, University of
Wisconsin, 1998
Led discussion sections, graded and wrote homework and exams.
Volunteer at OMSI science museum, Neuroscience exhibit, 2001
Participation in Brain Awareness Week at local high schools, 1993-1999
Course in Teaching College Biology, 1999
Mentor, High School Honors in Science Program, Madison, WI, 1994
Teaching Assistant, Organic chemistry Laboratory, Reed College, 1989
Teaching areas:
Ontology design and knowledge engineering, Information management, data standards
and management, biomedical writing, developmental biology, anatomy and
physiology, genetics and molecular biology, neuroscience, introductory biology.
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Dr. Melissa Haendel
Professional honors and memberships
International/national committees and memberships
International Conference of Biomedical Ontologies Scientific Program Committee 2014
Conference on Semantics in Healthcare and Life Sciences Scientific Program Committee
2014
International Conference of Biomedical Ontologies Scientific Program Committee 2013
American Medical Informatics Association Scientific Program Committee of the 2013
Annual meeting
American Medical Informatics Association Scientific Program Committee of the 2013
Summit on Translational Bioinformatics (TBI)
American Society of Human Genetics member 2013- present
Force 11 member, 2012 - present
American Medical Informatics Association, 2011- present
Open Biomedical Ontology Coordinating Board 2010-present
Phenotype Resource Coordination Network Vertebrate Working Group Lead 2010present
International Biocuration Society member, 2006 - present
American Association of Cancer Research Pathobiology Workshop participant, 2003
Instructor at the Center for Talented Youth, Johns Hopkins University 1998-1999
Society for Developmental Biology, 1996-99
Commended for Excellence in Scholarship, Reed College, 1991
Institutional committees
OHSU School of Medicine Research Roadmap committee, 2012- present
OHSU Cloud computing taskforce, 2013
OHSU Data stewardship taskforce, 2011-present
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Dr. Melissa Haendel
Post-doctoral committee, University of Oregon, 2000-02
Graduate representative to the University of Wisconsin Medical School, 1998-9
Awards
Beyond the PDF 2 1K challenge award, 2013, “Starting at Ground Zero” – promoting
development of library capabilities to support research data management and
publication. http://www.force11.org/1Kchallenge#1k2
Monarch Initiative grant, Office of the Director, NIH, PI – 2010-2016 Program to
develop software and standardize data to enable cross-species genotype to
phenotype analysis and promote publication of data standards. (4 yrs) NIH
1R24OD011883 http://www.monarchinitiative.org
CTSAconnect NIH NCATs contract 2011-2013 – development and integration of data
standards for research profiling (1.5 yrs) CTSA 10-001: 100928SB23
PROJECT #: 00921-0001. http://www.ctsaconnect.org
Medical Research Foundation of Oregon New Investigator Award, 2011-2012 (1yr)
“Indexing and retrieval of biospecimen Infonnatlon within the Oregon Health &
Science University Biolibrary.”
RJ Reynolds Post-doctoral Research award, 2002-2004 (2 yrs)
Individual Post-doctoral National Research Service Award, NIH, 2000-2003 (3 yrs)
“Differentiation factor receptors and neural cell fate” NIH 5F32NS011170
Individual Pre-doctoral National Research Service Award, NIH, 1997-1999 (3 yrs)
“Trapping novel genes involved in neural development” NIH 5F31MH011560
Publications
Torniai C, Essaid S, Barnes C, Conlon M, Williams S, Hajagos JG, Bremer E, Corson-Rikert J,
Haendel M. (2013) From EHRs to Linked Data: representing and mining encounter data for clinical
expertise evaluation. AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:165. PMID:24303330
Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP,
Liu K, Hernandez P. (2013) An ontology-based method for secondary use of electronic dental record
data. AMIA Summits Transl Sci Proc. Mar 18;2013:234-8. PMID:24303273
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno
M, Campbell J, Fitzpatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J,
Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH,
Park SM, Riggs ER, Scott RH, Sisodiya S, Vooren SV, Wapner RJ, Wilkie AO, Wright CF, Vulto-van
Silfhout AT, Leeuw Nd, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef
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Dr. Melissa Haendel
BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. (2013) The Human Phenotype
Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res.
2014 Jan 1;42(1):D966-74. doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11. PMID:24217912
Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE,
Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. (2014) Improved
exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014
Jan 2. PMID:24162188
Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. What is an anatomy ontology? (2013)Anat Rec
(Hoboken). 2013 Dec;296(12):1797-9. doi: 10.1002/ar.22805. Epub 2013 Oct 11. No abstract
available. PMID:24127438
Tenenbaum JD, Sansone SA, Haendel M. (2013)A sea of standards for omics data: sink or swim? J Am
Med Inform Assoc. 2013 Oct 4. doi: 10.1136/amiajnl-2013-002066. PMID:24076747
On the reproducibility of science: unique identification of research resources in the biomedical literature.
Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA. PeerJ.
2013 Sep 5;1:e148. doi: 10.7717/peerj.148. PMID:24032093
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;14:263. doi: 10.1186/1471-2105-14-263. PMID:24004649
Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE,
Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K,
Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K,
Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K,
Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. An overview of the BioCreative 2012
Workshop Track III: interactive text mining task. (2013) Database (Oxford). 2013 Jan 17;2013:bas056.
doi: 10.1093/database/bas056. Print 2013. PMID:23327936
Haendel M.A., J.P. Balhoff , Bastian F.B., Blackburn D.C., Blake J.A., Bradford Y., Comte A., Dahdul
W.M., Dececchi T.A., R.E. Druzinsky, T.F. Hayamizu, N. Ibrahim, S.E. Lewis, P.M. Mabee, A.
Niknejad, M. Robinson-Rechavi, P.C. Sereno, C.J. Mungall.. (2013) Unification of multi-species
vertebrate anatomy ontologies for comparative biology in Uberon. Submitted to Journal of Biomedical
Semantics.
Dahdul W.M., Cui H., Mabee P.M., Mungall C.J., Osumi-Sutherland D., Walls R., Haendel M.A. (2013)
The Biological Spatial Ontology: spatial descriptors for phenotypic diversity. Submitted to Journal of
Biomedical Semantics.
Van Slyke C. E., Yvonne M Bradford Y.M., Westerfield M., Haendel M.A. (2013) The Zebrafish
Anatomy and Stage Ontologies: Representing the Anatomy and Development of Danio rerio.
Submitted to Journal of Biomedical Semantics.
Brush M., Mungall C.J., Washington N., and Haendel M. (2013) What’s in a Genotype?: An Ontological
Characterization for Integration of Genetic Variation Data. International Conference on Biomedical
Ontology proceedings. July 7-9; Montreal.
Essaid E., Torniai C., and Haendel, M. (2013) Enabling semantic search in a bio-specimen repository.
International Conference on Biomedical Ontology proceedings. July 7-9; Montreal.
Haendel M.A. and Chesler E.J. (2012) Lost and found in behavioral informatics, in Int Rev Neurobiol.
103:1-18. doi: 10.1016/B978-0-12-388408-4.00001-0.
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Dr. Melissa Haendel
Arighi C.N., Carterette B., Cohen K.B., Krallinger M., Wilbur W.J., Fey P., Dodson R., Cooper L., Van
Slyke C.E., Dahdul W., Mabee P., Li D., Harris B., Gillespe M., Jimenez S., Roberts P., Mathews L.,
Becker, K., Drabkin, H., Bellow S., Licata L., Chatr-Aryamontri A., Schaeffer M.L., Park, J., Haendel
M., Van Auken K., Li Y., Chan J., Muller, H., Cui H., Balhoff J.P., Chi-Yang Wu J., Lu Z., Wei C.,
Tudor C.O., Raja K., Subramani S., Natarajan J., Cejuela J.M., Dubey P., Wu C. (2013) An overview
of the BioCreative 2012 Workshop Track III: interactive text mining task. Database, The Journal of
Biological Databases and Curation 01/2013; 2013:bas056.
Dahdul W.M., Balhoff J.P., Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg
J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M.,
Mabee P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One.
2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10. PMID: 23251424
Haendel, M.A., Vasilevsky N.A. and Wirz, J.A. (2012) Dealing with Data: A Case Study on Information
and Data Management Literacy. Plos Biology 10(5): e1001339. doi:10.1371/journal.pbio.1001339
Vasilevsky N., Johnson T., Corday K, Torniai C., Brush M. Segerdell E. Wilson M., Shaffer C., Robinson
D., Haendel M. (2012) Research resources: curating the new eagle-i discovery system.
Database Vol. 2012 published online March 20, 2012, doi:10.1093/database/bar067.
Mungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E., and Haendel, M.A. (2012) Uberon, an integrative
multi-species anatomy ontology”, Genome Biology 13, R5. http://genomebiology.com/2012/13/1/R5
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, Haendel MA, Ireland A, Manzoor S, Meehan T, Osumi-Sutherland D, Torniai C, and Diehl
A. (2011) Modularization for the Cell Ontology. International Conference on Biomedical Ontology;
July 26–30; 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.
Dahdul, W.M., Mabee, P.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel,
M.A., Westerfield, M. (2009) The Teleost Anatomy Ontology: Anatomical Representation for the
Genomics Age. Systematic Biology, 59(4):369-383.
Sprague, J., Bayraktaroglu, L.,Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M.,
Howe, D., Mani, P., Moxon, S., Pich, C., Ramachandran, S., Schaper, K., Shao, X., Singer, A., Song,
P., Sprunger, B., Van Slyke, C., Westerfield, M. (2008) The Zebrafish Information Network: the
zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic
Acids Research. Jan;36(Database issue):D768-72.
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).
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Dr. Melissa Haendel
Takayama, S., Hostick, U., Haendel, M., Eisen, J., and Darimont, B. (2008) An F-domain introduced by
alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha. Gen. Comp.
Endocrinol. Jan 1;155(1):176-89.
N. Washington, M. Gibson, Mungall C., Ashburner M., Gkoutos G.V., Westerfield M., Haendel M., Lewis
S.E. (2008) In proceeding of: Ontologies and Text Mining for Life Sciences: Current Status and Future
Perspectives, 24.03. - 28.03.2008
Day-Richter, J., Harris, M.A., Haendel, M.A., The Gene Ontology OBO-Edit Working Group and Lewis,
S. (2007). OBO-Edit - An Ontology Editor for Biologists. Bioinformatics. 23(16):2198-2200.
Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N.,
and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case
study from Cypriniformes including zebrafish. J. Exp. Zoolog. B Mol. Dev. Evol. 308B(5):655-668.
Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C., and
Westerfield, M. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends
Ecol. Evol. 22(7):345-350.
Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe,
D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van
Slyke, C.E., and Westerfield, M. (2006) The Zebrafish Information Network: the zebrafish model
organism database. Nucleic Acids Res. 34:D581-585.
Metcalfe S.M., Muthukumarana P.A., Thompson H.L., Haendel M.A., Lyons G.E. (2005) Leukaemia
inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to
regulatory immune tolerance. FEBS Lett. 579(3):609-14.
Haendel, M.A., Tilton, F., Bailey, G.S., and Tanguay, R.L. (2004) Developmental Toxicity of the
Dithiocarbamate Pesticide Sodium Metam in Zebrafish. Toxicol. Sci. 81(2):390-400.
Reyes, R., Haendel, M., Grant, D., Melançon, E., and Eisen, J.S. (2004) Slow degeneration of zebrafish
Rohon-Beard neurons during programmed cell death. Dev. Dyn. 229(1):30-41.
Haendel, M.A., (1999) In vitro preselection and characterization of the novel gene, axotrophin, University
of Wisconsin Ph.D. Thesis.
Lyons, G.E., Swanson, B.J., Haendel, M.A., and Daniels, J. (2000) Gene trapping in embryonic stem cells
in vitro to identify novel developmentally regulated genes in the mouse. Methods Mol Biol. 136:297307.
Hunter, P.J., Swanson, B.S., Haendel, M.A., Lyons, G.E., and Cross, J.C. (1999) Mrj encodes a DnaJrelated chaperone that is essential for murine placental development. Development. 126:1247-1258.
Yamakawa, K., Huo, Y.K. Haendel, M. A., Huber., R., Cehn, X.N., Lyons, G.E., and Korenburg, J. R.
(1998) DS-CAM: A novel member of the immunoglobulin superfamily maps in a Down Syndrome
region and is involved in the development of the nervous system. Hum Mol Genet. 7(2):227-37.
Baker*, R.K., Haendel*, M.A., Swanson*, B.J., Shcambaugh, J.C., Micales, B.K., and Lyons, G.E. (1997)
In vitro preselection of gene-trapped embryonic stem cell clones for characterizing novel
developmentally regulated genes in the mouse. Dev Biol. 185(2):201-214.
*These authors contributed equally to this manuscript.
Haendel, M.A., Bollinger, K.E., and Baas, P.W. (1996) Cytoskeletal changes during neurogenesis in
cultures of avian neural crest cells. J Neurocytol. 25:289-301.
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Dr. Melissa Haendel
Haendel, M.A. (1991) Designing drugs: A new method using MEPs in constructing QSARs. Reed College
Undergraduate Thesis.
Edited volumes
Bioinformatics of Behavior. Int Rev Neurobiol. (2012) Vol 103 and Vol 104. doi: 10.1016/B978-0-12388408-4.00001-0. Haendel, M.A. and Chesler, E.J. Editors. Elsevier.
Recent selected talks
Haendel, M.A. (2013) ISCB Rocky Bioinformatics keynote: Tales from the Crypt: Do You Know Where
Your Data Has Been?
Haendel M. The integrated cross-species phenome as a tool for understanding disease. Intrafrontier IMPCIKMC, Rome, Italy, December 2013.
E Bremer, J Corson-Rikert, M Haendel, J Hajagos, B Lowe. (2013) Integrated Semantic Framework:
launching the next generation VIVO ontology. VIVO conference St Louis, MO. August 2013.
http://www.slideshare.net/mhaendel/isf-vivo2013
Haendel, M.A. (2013) On the reproducibility of science. Beyond the PDF2, March 19-20th, Amsterdam,
Netherlands. Invited speaker. http://www.slideshare.net/mhaendel/reproducibility-ofscience-final
Haendel, M.A. (2013) National Center for Biomedical Ontology Seminar series. “Removing Roadblocks:
Leveraging ontologies for data aggregation and computation.”
http://www.slideshare.net/mhaendel/ncb-ohaendel2013
Haendel, M.A. Ontolog Ontology Evaluation Forum. (2013) “Intrinsic ontology evaluation from a
biologist’s perspective.”
Haendel, M.A. (2012) “CTSAconnect: A Linked Open Data approach to represent clinical and research
expertise, activities, and resources” and “Panel – Building better teams: innovative approaches to the
design and deployment of researcher recommendation systems.”
http://www.vivoweb.com/files/Schedule%20At%20A%20Glance%2020120730%20v5.pdf
Haendel, M.A. (2013) “A merger of multi-species anatomy ontologies. Society for Biocuration 2013.
http://www.slideshare.net/mhaendel/haendelbiocurator2013-uberonv2
Haendel, M.A. (2013) “Biocurator: Add equal parts biologist, librarian, philosopher, and engineer.”
Science Beyond the Ivory Tower Seminar Series, Information Careers in the Biosciences, City of
Hope.
Haendel, M.A., (2013) “The eagle-i Network: enabling research resource discovery.” At the eScience
Workshop: The Research Lifecycle: Partnering for Success, University of Utah.
http://nnlm.gov/2013escience/
Haendel, M.A. CTSA tool shop Webinar series. CTSAconnect presentation, 2012.
https://www.ctsacentral.org/sites/default/files/documents/CTSAconnect_FactSheet_MH.pdf
Full list of presentations available upon request.
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Dr. Melissa Haendel
Other scholarly products
Major Ontologies:
Zebrafish anatomy http://purl.obolibrary.org/obo/zfa.owl
Biological spatial ontology http://purl.obolibrary.org/obo/bspo.owl
eagle-i resource ontology http://purl.obolibrary.org/obo/ero.owl
Integrated semantic framework https://code.google.com/p/connect-isf/
Uberon uberon.org
Ontology of biomedical investigations http://obi-ontology.org/
Reagent ontology https://code.google.com/p/reagent-ontology/
Genotype ontology https://code.google.com/p/monarch-ontology/
Cell ontology http://purl.obolibrary.org/obo/cl.owl
Common anatomy reference ontology http://purl.obolibrary.org/obo/caro.owl
Ontology for oral health and disease https://code.google.com/p/ohd-ontology/
Database contributions:
Zebrafish information Network http://zfin.org
Neuroscience Information Framework http://neuinfo.org (currently housing Monarch
Initiative, though see http://monarchinitiative.org for informational site)
eagle-i http://eagle-i.net
Genbank submissions:
1. Mus musculus estrogen related receptor, beta (Esrrb), transcript variant 2, mRNA
4,309 bp linear mRNA
NM_001159500.1 GI:226958366
2. Mus musculus estrogen related receptor, beta (Esrrb), transcript variant 1, mRNA
4,208 bp linear mRNA
NM_011934.4 GI:226958364
3. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 1, mRNA
4,170 bp linear mRNA
NM_001170744.1 GI:282721028
4. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 2, mRNA
3,047 bp linear mRNA
NM_009980.4 GI:144922610
5. Mus musculus glial cells missing homolog 1 (Drosophila) (Gcm1), mRNA
2,034 bp linear mRNA
NM_008103.3 GI:118130983
6. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 1, mRNA
2,708 bp linear mRNA
NM_001037940.4 GI:188219639
7. Mus musculus glial cells missing homolog 2 (Drosophila) (Gcm2), mRNA
2,879 bp linear mRNA
NM_008104.2 GI:113680508
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Dr. Melissa Haendel
8. Homo sapiens membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase (MARCH7),
mRNA
3,484 bp linear mRNA
NM_022826.2 GI:53828927
9. Danio rerio family with sequence similarity 32, member A, like (fam32al), mRNA
780 bp linear mRNA
NM_001002203.1 GI:50345059
10. Danio rerio nuclear receptor coactivator 2 (ncoa2), mRNA
4,958 bp linear mRNA
NM_131777.1 GI:18859480
11. Mus musculus membrane-associated ring finger (C3HC4) 7 (March7), mRNA
2,719 bp linear mRNA
NM_020575.2 GI:118130502
12. Danio rerio thyroid hormone receptor beta (thrb), mRNA
2,198 bp linear mRNA
NM_131340.1 GI:18859510
13. Mus musculus ring finger protein 4 (Rnf4), mRNA
2,936 bp linear mRNA
NM_011278.4 GI:158508477
14. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 4, mRNA
1,642 bp linear mRNA
NM_001127367.1 GI:188219643
15. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 2, mRNA
1,120 bp linear mRNA
NM_001037941.3 GI:188219641
16. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 3, mRNA
1,645 bp linear mRNA
NM_011847.4 GI:188219640
17. Danio rerio thyroid hormone receptor alpha B (thraB) mRNA, partial cds
653 bp linear mRNA
DQ991962.1 GI:118162028
18. Danio rerio thyroid hormone receptor alpha A 1-2 (thraA) mRNA, partial cds
651 bp linear mRNA
DQ991961.1 GI:118162026
19. Mus musculus axotrophin mRNA, complete cds
2,720 bp linear mRNA
AF155739.1 GI:5052030
20. Homo sapiens CHD2-52 Down syndrome cell adhesion molecule (DSCAM) mRNA, complete cds
6,413 bp linear mRNA
AF023450.1 GI:3169767
21. Mus musculus MRJ (Mrj) mRNA, complete cds
1,546 bp linear mRNA
AF035962.1 GI:3142371
11
Dr. Melissa Haendel
22. Homo sapiens CHD2-42 Down syndrome cell adhesion molecule (DSCAM) mRNA, partial cds
6,110 bp linear mRNA
AF023449.1 GI:3169765
12