Acknowledgments

Project team

SCATE Project

University of North Carolina at Chapel Hill	University of South Dakota
Todd Vision (Department of Biology) Jim Balhoff (Renaissance Computing Institute)	Paula Mabee Wasila Dahdul
Duke University	Virginia Tech
Hilmar Lapp (Center for Genomic and Computational Biology)	Josef Uyeda

Phenoscape II Project

National Evolutionary Synthesis Center (NESCent)	University of South Dakota	University of Oregon (Zebrafish Information Network)
Todd Vision (also University of North Carolina at Chapel Hill) Hilmar Lapp (now at Duke University, Center for Genomic and Computational Biology) Jim Balhoff (now at RTI Intl.) Prashanti Manda (now at University of North Carolina at Greensboro)	Paula Mabee Wasila Dahdul Alex Dececchi	Monte Westerfield Yvonne Bradford Ceri Van Slyke
	Oregon Health & Science University
	Melissa Haendel
University of Chicago	Mouse Genome Informatics	Cincinnati Children's Hospital Medical Center
Paul Sereno Nizar Ibrahim	Judith Blake Terry Hayamizu	Aaron Zorn (Xenbase) Christina James-Zorn (Xenbase)
California Academy of Sciences	University of Arizona	Lawrence Berkeley National Labs
David Blackburn	Hong Cui Zilong Chang	Chris Mungall

Phenoscape I Project

• Paula Mabee, University of South Dakota
• Monte Westerfield, Zebrafish Information Network and University of Oregon
• Todd Vision, National Evolutionary Synthesis Center and University of North Carolina at Chapel Hill
• Hilmar Lapp, National Evolutionary Synthesis Center
• Jim Balhoff, National Evolutionary Synthesis Center
• Wasila Dahdul, University of South Dakota
• Peter Midford, National Evolutionary Synthesis Center

Advisory Board

SCATE Project

Members

• Scott Chamberlain (rOpenSci)
• Emily Jane McTavish (University of California, Merced)
• Brian Sidlauskas (Oregon State University)
• Pam Soltis (University of Florida)
• Paul Thomas (University of Southern California)

Meetings

• Advisory Board meeting on January 7, 2020, after the SSB 2020 meeting at University of Florida

Phenoscape II

Members

• John Day-Richter (Google)
• Brian K. Hall (Dalhousie University)
• Cyndy Parr (Encyclopedia of Life) (2012-)
• Paul Schofield (University of Cambridge)
• Peter Vize (University of Calgary)
• Alan Ruttenberg (University of Buffalo)

Meetings

• Advisory Board meeting on Dec. 12, 2013. (by conference call): agenda and notes
• Advisory Board meeting on Dec. 4, 2012. (by conference call): agenda and notes
• Advisory Board meeting (face to face): Friday, April 27, 2012; Phenoscape project meeting will precede this on April 25, 26
• Advisory Board meeting on Nov. 11, 2011 (by conference call): agenda and notes

Contributors

The following groups and individuals have contributed to Phenoscape ontology development, data curation, workshops, and data entry:

Phenoscape Contributors to the Uberon Anatomy Ontology

• Wasila Dahdul, University of South Dakota
• David Blackburn, California Academy of Sciences
• T. Alexander Dececchi, University of South Dakota
• Pasan Chinthana Fernando, University of South Dakota
• Melissa Haendel, Oregon Health Sciences University
• Terry Hayamizu, Mouse Genome Informatics
• Nizar Ibrahim, University of Chicago
• Laura Jackson, University of South Dakota
• Paula Mabee, University of South Dakota
• Chris Mungall, Lawrence Berkeley Labs

Teleost Anatomy Ontology (TAO) Contributors

• Gloria Arratia, The University of Kansas
• David Blackburn, University of Kansas
• Miles Coburn, John Carroll University
• Kevin Conway, St. Louis University
• Wasila Dahdul, University of South Dakota
• Mário de Pinna, Universidade de São Paulo
• Alexander Diehl, University at Buffalo, The State University of New York
• Jeff Engeman, University of South Dakota
• Benjamin Frable, National Museum of Natural History, Smithsonian Institution
• Terry Grande, Loyola University, Chicago
• Melissa Haendel, OHSU
• Brian Hall, Dalhousie University
• Eric Hilton, Virginia Institute of Marine Science
• John Lundberg, The Academy of Natural Sciences, Philadelphia
• Paula Mabee, University of South Dakota
• Richard Mayden, St. Louis University
• Martin Ringwald, The Jackson Laboratory
• Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia
• Erik Segerdell, OHSU
• Brian Sidlauskas, Oregon State University
• Sandrine Tercerie, Muséum National d'Histoire Naturelle
• Ceri Van Slyke, Zebrafish Information Network
• Richard Vari, National Museum of Natural History, Smithsonian Institution
• Matt Vickaryous, University of Guelph
• Jacqueline Webb, University of Rhode Island
• Edward Wiley, The University of Kansas

Vertebrate and Teleost Taxonomy Ontology Contributors

• John Alroy, Paleobiology Database
• Nicolas Bailly, WorldFish Center, Philippines
• Stan Blum, California Academy of Sciences
• Miles Coburn, John Carroll University
• Kevin Conway, St. Louis University
• Wasila Dahdul, University of South Dakota
• T. Alexander Dececchi, University of South Dakota
• Bill Eschmeyer, California Academy of Sciences
• Rainer Froese, Leibniz-Institute of Marine Sciences
• Terry Grande, Loyola University, Chicago
• Eric Hilton, Virginia Institute of Marine Science
• Nizar Ibrahim, University of Chicago
• John Lundberg, The Academy of Natural Sciences, Philadelphia
• Richard Mayden, St. Louis University
• Paul Sereno, University of Chicago

Vertebrate Skeletal Anatomy Ontology (VSAO) Contributors

• James P. Balhoff, National Evolutionary Synthesis Center
• David C. Blackburn, California Academy of Sciences
• Wasila Dahdul, University of South Dakota
• Alexander D. Diehl, University at Buffalo, The State University of New York
• Melissa A. Haendel, Oregon Health & Science University
• Brian K. Hall, Dalhousie University
• Terry Hayamizu, The Jackson Laboratory
• Nizar Ibrahim, University of Chicago
• Hilmar Lapp, National Evolutionary Synthesis Center
• John G. Lundberg, The Academy of Natural Sciences
• Paula M. Mabee, University of South Dakota
• Christopher J. Mungall, Lawrence Berkeley National Laboratory
• Martin Ringwald, The Jackson Laboratory
• Erik Segerdell, Oregon Health & Science University
• Paul Sereno, University of Chicago
• Ceri E. Van Slyke, Zebrafish Information Network
• Matthew K. Vickaryous, University of Guelph
• Monte Westerfield, Zebrafish Information Network and University of Oregon
• Christina James Zorn, Xenbase

Curators (Data Annotation)

• Bruno Chanet, Muséum National d'Histoire Naturelle
• Miles Coburn, John Carroll University
• Sonia Crichigno, Centro Regional Universitario Bariloche, (Univ. Nac. del Comahue), Argentina
• Wasila Dahdul, University of South Dakota
• T. Alexander Dececchi, University of South Dakota
• Pasan Chinthana Fernando, University of South Dakota
• Jeff Engeman, University of South Dakota
• Benjamin Frable, National Museum of Natural History, Smithsonian Institution
• Terry Grande, Loyola University, Chicago
• Eric Hilton, Virginia Institute of Marine Science
• Nizar Ibrahim, University of Chicago
• Laura Jackson, University of South Dakota
• Tova Just, Bryn Mawr College
• John Lundberg, The Academy of Natural Sciences, Philadelphia
• Paula Mabee, University of South Dakota
• Richard Mayden, St. Louis University
• Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia
• Sandrine Tercerie, Muséum National d'Histoire Naturelle

Phenoscape Workshop Participants & Contributors

• Arhat Abzhanov, Harvard University
• Gloria Arratia, The University of Kansas
• Michael Ashburner, University of Cambridge
• Jim Balhoff, National Evolutionary Synthesis Center
• Rüdiger Bieler, Field Museum, Chicago
• David Blackburn, University of Kansas
• Judith Blake, The Jackson Laboratory
• Stan Blum, California Academy of Sciences
• Miles Coburn, John Carroll University
• Kevin Conway, St. Louis University
• Quentin Cronk, The University of British Columbia
• Wasila Dahdul, University of South Dakota
• Mário de Pinna, Universidade de São Paulo
• Andy Deans, North Carolina State University
• Alexander Diehl, University at Buffalo, The State University of New York
• Torsten Dikow, Field Museum, Chicago
• Jeff Engeman, University of South Dakota
• George Gkoutos, University of Cambridge
• Lance Grande, Field Museum, Chicago
• Terry Grande, Loyola University, Chicago
• Melissa Haendel, Zebrafish Information Network
• Brian Hall, Dalhousie University
• Eric Hilton, Virginia Institute of Marine Science
• Robert Ho, University of Chicago
• Hopi Hoekstra, Harvard University
• Hans Hofmann, University of Texas at Austin
• Elizabeth Jockusch, Univesity of Connecticut
• Elizabeth Kellogg, University of Missouri, St. Louis
• Chuck Kimmel, University of Oregon
• Cartik Kothari, National Evolutionary Synthesis Center
• Hilmar Lapp, National Evolutionary Synthesis Center
• Suzanna Lewis, Berkeley Bioinformatics and Ontology Project
• John Lundberg, The Academy of Natural Sciences, Philadelphia
• Paula Mabee, University of South Dakota
• Anne Maglia, Missouri University of Science and Technology
• Joanna Mandecki, University of Chicago
• Austin Mast, Florida State University
• Richard Mayden, St. Louis University
• Charlene McCord, University of Chicago
• Peter Midford, National Evolutionary Synthesis Center
• Chris Mungall, Berkeley Bioinformatics and Ontology Project
• Vicky Prince, University of Chicago
• Martin Ramirez, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Argentina
• Sue Rhee, Carnegie Institution
• Martin Ringwald, The Jackson Laboratory
• Nelson Rios, Tulane University
• Callum Ross, University of Chicago
• Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia
• Erik Segerdell, University of Calgary
• Paul Sereno, University of Chicago
• Brian Sidlauskas, Oregon State University
• Barry Smith, University at Buffalo
• David Stern, Princeton University
• Margaret Thayer, Field Museum, Chicago
• Ceri Van Slyke, Zebrafish Information Network
• Matt Vickaryous, University of Guelph
• Todd Vision, National Evolutionary Synthesis Center and University of North Carolina at Chapel Hill
• Peter Vize, University of Calgary
• Gunter Wagner, Yale University
• Michael Wallinga, University of South Dakota
• Nicole Washington, Lawrence Berkeley National Lab
• Monte Westerfield, Zebrafish Information Network and University of Oregon
• Mark Westneat, Field Museum, Chicago
• Edward Wiley, The University of Kansas
• Matt Yoder, North Carolina State University

Software testing

• Angel Amores, University of Oregon
• Carole Baldwin, Smithsonian National Museum of Natural History
• Susan Bassham, University of Oregon
• Judith Blake, The Jackson Laboratory
• Miles Coburn, John Carroll University
• William Cresko, University of Oregon
• April DeLaurier, University of Oregon
• Jeff Engeman, University of South Dakota
• Vladimir Gapeyev, National Evolutionary Synthesis Center
• Terry Grande, Loyola University, Chicago
• Melissa Haendel, Zebrafish Information Network
• Eric Hilton, Virginia Institute of Marine Science
• Ryan Kerney, Dalhousie University
• Suzanna Lewis, Berkeley Bioinformatics and Ontology Project
• Daniel Lumbantobing, George Washington University
• John Lundberg, The Academy of Natural Sciences, Philadelphia
• Anne Maglia, Missouri University of Science and Technology
• Richard Mayden, St. Louis University
• Julie Mounts, Smithsonian National Museum of Natural History
• Conor O'Brien, University of Oregon
• Lynne Parenti, Smithsonian National Museum of Natural History
• Rafael de Sá, University of Richmond
• Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia
• Brian Sidlauskas, Oregon State University
• Jiakun Song, Smithsonian National Museum of Natural History
• Jared Talbot, University of Oregon
• Sandrine Tercerie, Muséum National d'Histoire Naturelle
• Tom Titus, University of Oregon
• Linda Trueb, University of Kansas
• Ceri Van Slyke, Zebrafish Information Network
• David Wake, University of California, Berkeley
• Marvalee Wake, University of California, Berkeley
• Matt Yoder, North Carolina State University

Students

• Alex Ahearn, Duke University
• Alyssa Block, University of South Dakota
• Jordan Catlett, University of South Dakota
• Sonia Crichigno, Centro Regional Universitario Bariloche, (Univ. Nac. del Comahue), Argentina
• Jeff Engeman, University of South Dakota
• Pasan Chinthana Fernando, University of South Dakota
• Benjamin Frable, National Museum of Natural History, Smithsonian Institution
• Char Green, University of South Dakota
• Ericka Grey, University of South Dakota
• Laura Jackson, University of South Dakota
• Tova Just, Bryn Mawr College
• Jun Hong Kim, Duke University
• Jonathan Lee, Duke University
• Leah Mabee, University of South Dakota
• Callie Mao, Duke University
• Mtakai Ngara, International Institute of Tropical Agriculture, Nairobi, Kenya
• Carla Perez, Duke University
• Carin Rambow, University of South Dakota
• Du Rui, University of South Dakota
• Brad Schanche, University of South Dakota
• Michael Wallinga, University of South Dakota
• Hong Xu, Duke University
• Lucy Zhang, Duke University

Groups

• DeepFin Research Coordination Network - support for training and participation of ichthyology students and researchers

Data sources

• Monarch Initiative - aggregated and semantically harmonized model organism and human genes and phenotypes
• ZFIN - mutant and morpholino zebrafish genes and phenotypes
• Catalog of Fishes - fish taxonomy, list of collections
• Fishbase - fish common names
• Amphibiaweb - amphibian taxonomy
• The Paleobiology Database - taxonomy of extinct chordate taxa
• IOC World Bird Names - taxonomy of extant birds
• NCBI taxonomy - taxonomy for groups not otherwise covered
• Catalogue of Life - source of taxonomic synonyms

Funding

The SCATE project is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI). The Phenoscape II project is funded by NSF collaborative grants DBI-1062404 and DBI-1062542 grant, and is supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. Its predecessor, the Phenoscape I project, was funded by NSF grant BDI-0641025, and supported by NESCent, NSF #EF-0423641.