Difference between revisions of "Acknowledgments"

From phenoscape
(→‎Phenoscape II Project)
 
(96 intermediate revisions by 10 users not shown)
Line 1: Line 1:
−
<h2>Contributors</h2>
+
== Project team ==
−
<p>The following individuals have contributed to Phenoscape ontology development, data curation, workshops, and data entry:</p>
 
−
<h3>Teleost Anatomy Ontology Contributors</h3>
 
−
<ul>
 
−
<li>Gloria Arratia, The University of Kansas</li>
 
−
<li>David Blackburn, University of Kansas</li>
 
−
<li>Miles Coburn, John Carroll University</li>
 
−
<li>Kevin Conway, St. Louis University</li>
 
−
<li>Wasila Dahdul, University of South Dakota</li>
 
−
<li>Mário de Pinna, Universidade de São Paulo</li>
 
−
<li>Alexander Diehl, The Jackson Laboratory</li>
 
−
<li>Jeff Engeman, University of South Dakota</li>
 
−
<li>Terry Grande, Loyola University, Chicago</li>
 
−
<li>Melissa Haendel, Zebrafish Information Network</li>
 
−
<li>Brian Hall, Dalhousie University</li>
 
−
<li>Eric Hilton, Virginia Institute of Marine Science</li>
 
−
<li>John Lundberg, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Paula Mabee, University of South Dakota</li>
 
−
<li>Richard Mayden, St. Louis University</li>
 
−
<li>Martin Ringwald, The Jackson Laboratory</li>
 
−
<li>Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Erik Segerdell, University of Calgary</li>
 
−
<li>Brian Sidlauskas, Oregon State University</li>
 
−
<li>Sandrine Tercerie, Muséum National d'Histoire Naturelle</li>
 
−
<li>Ceri Van Slyke, Zebrafish Information Network</li>
 
−
<li>Richard Vari, National Museum of Natural History, Smithsonian Institution</li>
 
−
<li>Matt Vickaryous, University of Guelph</li>
 
−
<li>Jacqueline Webb, University of Rhode Island</li>
 
−
<li>Edward Wiley, The University of Kansas</li>
 
−
</ul>
 
−
<h3>Teleost Taxonomy Ontology Contributors</h3>
 
−
<ul>
 
−
<li>Nicolas Bailly, WorldFish Center, Philippines</li>
 
−
<li>Stan Blum, California Academy of Sciences</li>
 
−
<li>Miles Coburn, John Carroll University</li>
 
−
<li>Kevin Conway, St. Louis University</li>
 
−
<li>Wasila Dahdul, University of South Dakota</li>
 
−
<li>Bill Eschmeyer, California Academy of Sciences</li>
 
−
<li>Rainer Froese, Leibniz-Institute of Marine Sciences</li>
 
−
<li>Terry Grande, Loyola University, Chicago</li>
 
−
<li>Eric Hilton, Virginia Institute of Marine Science</li>
 
−
<li>John Lundberg, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Richard Mayden, St. Louis University</li>
 
−
</ul>
 
−
<h3>Curators (Data Annotation)</h3>
 
−
<ul>
 
−
<li>Miles Coburn, John Carroll University</li>
 
−
<li>Sonia Crichigno, Centro Regional Universitario Bariloche, (Univ. Nac. del Comahue), Argentina</li>
 
−
<li>Jeff Engeman, University of South Dakota</li>
 
−
<li>Terry Grande, Loyola University, Chicago</li>
 
−
<li>Eric Hilton, Virginia Institute of Marine Science</li>
 
−
<li>John Lundberg, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Paula Mabee, University of South Dakota</li>
 
−
<li>Richard Mayden, St. Louis University</li>
 
−
<li>Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Sandrine Tercerie, Muséum National d'Histoire Naturelle</li>
 
−
</ul>
 
−
<h3>Phenoscape Workshop Participants &amp; Contributors</h3>
 
−
<ul>
 
−
<li>Arhat Abzhanov, Harvard University</li>
 
−
<li>Angel Amores, University of Oregon</li>
 
−
<li>Gloria Arratia, The University of Kansas</li>
 
−
<li>Michael Ashburner, University of Cambridge</li>
 
−
<li>Jim Balhoff, National Evolutionary Synthesis Center</li>
 
−
<li>Susan Bassham, University of Oregon</li>
 
−
<li>Rüdiger Bieler, Field Museum, Chicago</li>
 
−
<li>David Blackburn, University of Kansas</li>
 
−
<li>Judith Blake, The Jackson Laboratory</li>
 
−
<li>Stan Blum, California Academy of Sciences</li>
 
−
<li>Miles Coburn, John Carroll University</li>
 
−
<li>Kevin Conway, St. Louis University</li>
 
−
<li>William Cresko, University of Oregon</li>
 
−
<li>Quentin Cronk, The University of British Columbia</li>
 
−
<li>Wasila Dahdul, University of South Dakota</li>
 
−
<li>Mário de Pinna, Universidade de São Paulo</li>
 
−
<li>Andy Deans, North Carolina State University</li>
 
−
<li>April DeLaurier, University of Oregon</li>
 
−
<li>Alexander Diehl, The Jackson Laboratory</li>
 
−
<li>Torsten Dikow, Field Museum, Chicago</li>
 
−
<li>Jeff Engeman, University of South Dakota</li>
 
−
<li>George Gkoutos, University of Cambridge</li>
 
−
<li>Lance Grande, Field Museum, Chicago</li>
 
−
<li>Terry Grande, Loyola University, Chicago</li>
 
−
<li>Melissa Haendel, Zebrafish Information Network</li>
 
−
<li>Brian Hall, Dalhousie University</li>
 
−
<li>Eric Hilton, Virginia Institute of Marine Science</li>
 
−
<li>Robert Ho, University of Chicago</li>
 
−
<li>Hopi Hoekstra, Harvard University</li>
 
−
<li>Hans Hofmann, University of Texas at Austin</li>
 
−
<li>Elizabeth Jockusch, Univesity of Connecticut</li>
 
−
<li>Elizabeth Kellogg, University of Missouri, St. Louis</li>
 
−
<li>Chuck Kimmel, University of Oregon</li>
 
−
<li>Cartik Kothari, National Evolutionary Synthesis Center</li>
 
−
<li>Hilmar Lapp, National Evolutionary Synthesis Center</li>
 
−
<li>Suzanna Lewis, Berkeley Bioinformatics and Ontology Project</li>
 
−
<li>John Lundberg, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Paula Mabee, University of South Dakota</li>
 
−
<li>Anne Maglia, Missouri University of Science and Technology</li>
 
−
<li>Joanna Mandecki, University of Chicago</li>
 
−
<li>Austin Mast, Florida State University</li>
 
−
<li>Richard Mayden, St. Louis University</li>
 
−
<li>Charlene McCord, University of Chicago</li>
 
−
<li>Peter Midford, National Evolutionary Synthesis Center</li>
 
−
<li>Chris Mungall, Berkeley Bioinformatics and Ontology Project</li>
 
−
<li>Conor O'Brien, University of Oregon</li>
 
−
<li>Vicky Prince, University of Chicago</li>
 
−
<li>Martin Ramirez, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Argentina</li>
 
−
<li>Sue Rhee, Carnegie Institution</li>
 
−
<li>Martin Ringwald, The Jackson Laboratory</li>
 
−
<li>Nelson Rios, Tulane University</li>
 
−
<li>Callum Ross, University of Chicago</li>
 
−
<li>Mark Sabaj Pérez, The Academy of Natural Sciences, Philadelphia</li>
 
−
<li>Erik Segerdell, University of Calgary</li>
 
−
<li>Paul Sereno, University of Chicago</li>
 
−
<li>Brian Sidlauskas, Oregon State University</li>
 
−
<li>Barry Smith, University at Buffalo</li>
 
−
<li>David Stern, Princeton University</li>
 
−
<li>Jared Talbot, University of Oregon</li>
 
−
<li>Margaret Thayer, Field Museum, Chicago</li>
 
−
<li>Tom Titus, University of Oregon</li>
 
−
<li>Ceri Van Slyke, Zebrafish Information Network</li>
 
−
<li>Matt Vickaryous, University of Guelph</li>
 
−
<li>Todd Vision, National Evolutionary Synthesis Center and University of North Carolina at Chapel Hill</li>
 
−
<li>Peter Vize, University of Calgary</li>
 
−
<li>Gunter Wagner, Yale University</li>
 
−
<li>Michael Wallinga, University of South Dakota</li>
 
−
<li>Nicole Washington, Lawrence Berkeley National Lab</li>
 
−
<li>Monte Westerfield, Zebrafish Information Network and University of Oregon</li>
 
−
<li>Mark Westneat, Field Museum, Chicago</li>
 
−
<li>Edward Wiley, The University of Kansas</li>
 
−
<li>Matt Yoder, North Carolina State University</li>
 
−
</ul>
 
−
<h3>Software testing</h3>
 
−
<ul>
 
−
<li>Carole Baldwin, Smithsonian National Museum of Natural History</li>
 
−
<li>Julie Mounts, Smithsonian National Museum of Natural History</li>
 
−
<li>Lynne Parenti, Smithsonian National Museum of Natural History</li>
 
−
<li>Jiakun Song, Smithsonian National Museum of Natural History</li>
 
−
<li>Daniel Lumbantobing, George Washington University</li>
 
−
</ul>
 
−
<h3>Students</h3>
 
−
<ul>
 
−
<li>Alex Ahearn, Duke University</li>
 
−
<li>Alyssa Block, University of South Dakota</li>
 
−
<li>Sonia Crichigno, Centro Regional Universitario Bariloche, (Univ. Nac. del Comahue), Argentina</li>
 
−
<li>Jeff Engeman, University of South Dakota</li>
 
−
<li>Ericka Grey, University of South Dakota</li>
 
−
<li>Jonathan Lee, Duke University</li>
 
−
<li>Leah Mabee, University of South Dakota</li>
 
−
<li>Mtakai Ngara, International Institute of Tropical Agriculture, Nairobi, Kenya</li>
 
−
<li>Carla Perez, Duke University</li>
 
−
<li>Carin Rambow, University of South Dakota</li>
 
−
<li>Du Rui, University of South Dakota</li>
 
−
<li>Brad Schanche, University of South Dakota</li>
 
−
<li>Michael Wallinga, University of South Dakota</li>
 
−
</ul>
 
  
−
<h2>Project team</h2>
+
=== SCATE Project ===
−
<ul>
 
−
<li>Paula Mabee, University of South Dakota</li>
 
−
<li>Monte Westerfield, Zebrafish Information Network and University of Oregon</li>
 
−
<li>Todd Vision, National Evolutionary Synthesis Center and University of North Carolina at Chapel Hill</li>
 
−
<li>Hilmar Lapp, National Evolutionary Synthesis Center</li>
 
−
<li>Jim Balhoff, National Evolutionary Synthesis Center</li>
 
−
<li>Wasila Dahdul, University of South Dakota</li>
 
−
<li>Peter Midford, National Evolutionary Synthesis Center</li>
 
−
</ul>
 
  
−
<h2>Data sources</h2>
+
{| width="90%"
−
<ul>
+
|- align="left" valign="top" style="font-weight: bold;"
−
<li>[http://zfin.org ZFIN] - mutant and morpholino zebrafish genes and phenotypes</li>
+
| style="width: 48%;" | University of North Carolina at Chapel Hill
−
<li>[http://research.calacademy.org/ichthyology/catalog Catalog of Fishes] - fish taxonomy</li>
+
| style="width: 48%;" | University of South Dakota
−
<li>[http://www.fishbase.org/ Fishbase] - fish common names</li>
+
|- valign="top"
−
</ul>
+
|
 +
* [http://visionlab.web.unc.edu/ Todd Vision] (Department of Biology)
 +
* [http://www.mendeley.com/profiles/jim-balhoff/ Jim Balhoff] (Renaissance Computing Institute)
 +
* Shalki Shrivastava (Renaissance Computing Institute)
 +
|
 +
* [https://www.usd.edu/faculty-and-staff/Paula-Mabee Paula Mabee] (Department of Biology)
 +
* [https://orcid.org/0000-0003-3162-7490 Wasila Dahdul] (Department of Biology)
 +
|
 +
|- style="height: 5px;"
 +
|
 +
|- align="left" style="font-weight: bold; "
 +
| Duke University
 +
| Virginia Tech
 +
|- valign="top"
 +
|
 +
* [[User:Hilmar| Hilmar Lapp]] (Center for Genomic and Computational Biology)
 +
* Amandeep Rathee (M.Sc. Student)
 +
|
 +
* [http://www.uyedalab.com/ Josef Uyeda] (Department of Biological Sciences)
 +
* Diego Sasso Porto (postdoc)
 +
* Sergei Tarasov (now at Finnish Museum of Natural History)
 +
|}
  
−
<h2>Funding</h2>
+
=== Phenoscape II Project ===
−
<p>The Phenoscape project is funded by NSF grant BDI-0641025, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0423641.</p>
+
 
 +
{| width="90%"
 +
|- align="left" valign="top" style="font-weight: bold;"
 +
| style="width: 33%;" | National Evolutionary Synthesis Center (NESCent)
 +
| style="width: 33%;" | University of South Dakota
 +
| style="width: 33%;" | University of Oregon (Zebrafish Information Network)
 +
|- valign="top"
 +
| rowspan="4" |
 +
* [http://visionlab.web.unc.edu/ Todd Vision] (also University of North Carolina at Chapel Hill)
 +
* [[User:Hilmar| Hilmar Lapp]] (now at Duke University, Center for Genomic and Computational Biology)
 +
* [http://www.mendeley.com/profiles/jim-balhoff/ Jim Balhoff] (now at RTI Intl.)
 +
* Prashanti Manda (now at University of North Carolina at Greensboro)
 +
|
 +
* Paula Mabee
 +
* Wasila Dahdul
 +
* Alex Dececchi
 +
| rowspan="4" |
 +
* [http://zfin.org/cgi-bin/webdriver?MIval=aa-persview.apg&OID=ZDB-PERS-960805-676 Monte Westerfield]
 +
* Yvonne Bradford
 +
* Ceri Van Slyke
 +
|- style="height: 1px;"
 +
|
 +
|- align="left" style="font-weight: bold; "
 +
| Oregon Health & Science University
 +
|- valign="top"
 +
|
 +
* Melissa Haendel
 +
|- style="height: 10px;"
 +
|
 +
|- align="left" style="font-weight: bold; "
 +
| University of Chicago || Mouse Genome Informatics || Cincinnati Children's Hospital Medical Center
 +
|- valign="top"
 +
|
 +
* Paul Sereno
 +
* Nizar Ibrahim
 +
|
 +
* Judith Blake
 +
* Terry Hayamizu
 +
|
 +
* Aaron Zorn (Xenbase)
 +
* Christina James-Zorn (Xenbase)
 +
|- style="height: 10px;"
 +
|
 +
|- align="left" style="font-weight: bold; "
 +
| California Academy of Sciences || University of Arizona || Lawrence Berkeley National Labs ||
 +
|- valign="top"
 +
|
 +
* 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'''
 +
*  [[WG:Advisory Board Meeting 2013-12-12| Advisory Board meeting on Dec. 12, 2013]]. (by conference call): [[Media:Phenoscape_Dec_2013_AB_notes.pdf| agenda and notes]]
 +
* [[WG:Advisory Board Meeting 2012-12-04| Advisory Board meeting on Dec. 4, 2012]]. (by conference call): [[Media:Phenoscape_AB_Dec2012_minutes.pdf| agenda and notes]]
 +
* Advisory Board meeting (face to face): Friday, April 27, 2012; Phenoscape project meeting will precede this on April 25, 26
 +
* [[WG:All-Hands_Meeting_2011-11-11| Advisory Board meeting on Nov. 11, 2011]] (by conference call):  [http://docs.google.com/document/d/1oE9Mp-UVu6r-Ci7G3EHTRaBuXsapyqm7DQ-Q0FjwCyo/edit?hl=en_US agenda] and [[Media:ABmeeting 2011-11-11 notes.pdf| 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 &amp; 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===
 +
* [http://http://www.deepfin.org/ DeepFin Research Coordination Network] - support for training and participation of ichthyology students and researchers
 +
 
 +
==Data sources==
 +
* [https://monarchinitiative.org Monarch Initiative] - aggregated and semantically harmonized model organism and human genes and phenotypes
 +
* [http://zfin.org ZFIN] - mutant and morpholino zebrafish genes and phenotypes
 +
* [http://research.calacademy.org/ichthyology/catalog Catalog of Fishes] - fish taxonomy, list of collections
 +
* [http://www.fishbase.org/ Fishbase] - fish common names
 +
* [http://amphibiaweb.org/ Amphibiaweb] - amphibian taxonomy
 +
* [http://paleodb.org The Paleobiology Database] - taxonomy of extinct chordate taxa
 +
* [http://www.worldbirdnames.org/index.html IOC World Bird Names] - taxonomy of extant birds
 +
* [http://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI taxonomy] - taxonomy for groups not otherwise covered
 +
* [http://www.catalogueoflife.org/ Catalogue of Life] - source of taxonomic synonyms
 +
 
 +
==Funding==
 +
The [http://scate.phenoscape.org 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.
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Community]]
 
[[Category:Community]]

Latest revision as of 23:44, 16 December 2019

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)
  • Shalki Shrivastava (Renaissance Computing Institute)
Duke University Virginia Tech
  • Hilmar Lapp (Center for Genomic and Computational Biology)
  • Amandeep Rathee (M.Sc. Student)
  • Josef Uyeda (Department of Biological Sciences)
  • Diego Sasso Porto (postdoc)
  • Sergei Tarasov (now at Finnish Museum of Natural History)

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
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

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

Data sources

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.

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Acknowledgments&oldid=12140"