Difference between revisions of "Acknowledgments"
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* [http://visionlab.web.unc.edu/ Todd Vision] (Department of Biology) | * [http://visionlab.web.unc.edu/ Todd Vision] (Department of Biology) | ||
* [http://www.mendeley.com/profiles/jim-balhoff/ Jim Balhoff] (Renaissance Computing Institute) | * [http://www.mendeley.com/profiles/jim-balhoff/ Jim Balhoff] (Renaissance Computing Institute) | ||
| + | * Shalki Shrivastava (Renaissance Computing Institute) | ||
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* [https://www.usd.edu/faculty-and-staff/Paula-Mabee Paula Mabee] (Department of Biology) | * [https://www.usd.edu/faculty-and-staff/Paula-Mabee Paula Mabee] (Department of Biology) | ||
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* [[User:Hilmar| Hilmar Lapp]] (Center for Genomic and Computational Biology) | * [[User:Hilmar| Hilmar Lapp]] (Center for Genomic and Computational Biology) | ||
| + | * Amandeep Rathee (M.Sc. Student) | ||
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| − | * [http://www.uyedalab.com/ Josef Uyeda] | + | * [http://www.uyedalab.com/ Josef Uyeda] (Department of Biological Sciences) |
| + | * Diego Sasso Porto (postdoc) | ||
| + | * Sergei Tarasov (now at Finnish Museum of Natural History) | ||
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| − | * | + | * Paul Sereno |
* Nizar Ibrahim | * Nizar Ibrahim | ||
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* David Blackburn | * David Blackburn | ||
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| − | * | + | * Hong Cui |
| − | * | + | * Zilong Chang |
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* Chris Mungall | * Chris Mungall | ||
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'''Meetings''' | '''Meetings''' | ||
* Advisory Board meeting on January 7, 2020, after the SSB 2020 meeting at University of Florida | * Advisory Board meeting on January 7, 2020, after the SSB 2020 meeting at University of Florida | ||
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=== Phenoscape II === | === Phenoscape II === | ||
Latest revision as of 23:44, 16 December 2019
Contents
- 1 Project team
- 2 Advisory Board
- 3 Contributors
- 3.1 Phenoscape Contributors to the Uberon Anatomy Ontology
- 3.2 Teleost Anatomy Ontology (TAO) Contributors
- 3.3 Vertebrate and Teleost Taxonomy Ontology Contributors
- 3.4 Vertebrate Skeletal Anatomy Ontology (VSAO) Contributors
- 3.5 Curators (Data Annotation)
- 3.6 Phenoscape Workshop Participants & Contributors
- 3.7 Software testing
- 3.8 Students
- 3.9 Groups
- 4 Data sources
- 5 Funding
Project team
SCATE Project
| University of North Carolina at Chapel Hill | University of South Dakota | |
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| Duke University | Virginia Tech | |
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Phenoscape II Project
| National Evolutionary Synthesis Center (NESCent) | University of South Dakota | University of Oregon (Zebrafish Information Network) | |
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| Oregon Health & Science University | |||
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| University of Chicago | Mouse Genome Informatics | Cincinnati Children's Hospital Medical Center | |
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| California Academy of Sciences | University of Arizona | Lawrence Berkeley National Labs | |
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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 was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 grant and 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.
