Cyberinfrastructure Working Group: Difference between revisions
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==About== | |||
The Cyberinfrastructure Working Group (CYWG) was established as an outcome of the [http://www.idigbio.org/content/idigbio-it-standards-workshop iDigBio IT Standards Workshop] held in Gainesville, FL on March 28-30, 2012. In line with the iDigBio roadmap, the focus of the initial group will be on the iDigBio data ingestion procedures related to API (Application Programming Interface) or appliance specification, implementation and test. | The Cyberinfrastructure Working Group (CYWG) was established as an outcome of the [http://www.idigbio.org/content/idigbio-it-standards-workshop iDigBio IT Standards Workshop] held in Gainesville, FL on March 28-30, 2012. In line with the iDigBio roadmap, the focus of the initial group will be on the iDigBio data ingestion procedures related to API (Application Programming Interface) or appliance specification, implementation and test. | ||
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The working group will produce material with concrete data ingestion use cases from [[TCNs]], provide input about the existing cyberinfrastructure, produce data ingestion requirements, and help evaluate iDigBio services and appliances implementations. | The working group will produce material with concrete data ingestion use cases from [[TCNs]], provide input about the existing cyberinfrastructure, produce data ingestion requirements, and help evaluate iDigBio services and appliances implementations. | ||
To express an interest in joining the working group, please contact [ | |||
==Members== | |||
To express an interest in joining the working group, please contact [https://www.idigbio.org/contact/Dr._Renato_J._Figueiredo Renato Figueiredo]. | |||
Current members: | Current members: | ||
*[http://www.idigbio.org/contact/ | *[http://www.idigbio.org/contact/Renato_J._Figueiredo Renato Figueiredo] (Co-Lead), iDigBio IT | ||
*[http://www.idigbio.org/contact/Joanna_McCaffrey Joanna McCaffrey] (Co-Lead), iDigBio Biodiversity Informatics Manager | *[http://www.idigbio.org/contact/Joanna_McCaffrey Joanna McCaffrey] (Co-Lead), iDigBio Biodiversity Informatics Manager | ||
*[http://www.idigbio.org/contact/Dan_Stoner Dan Stoner], iDigBio IT | *[http://www.idigbio.org/contact/Dan_Stoner Dan Stoner], iDigBio IT | ||
*[http://www.idigbio.org/contact/Kevin_Love Kevin Love], iDigBio IT | *[http://www.idigbio.org/contact/Kevin_Love Kevin Love], iDigBio IT | ||
*[mailto:ranglin@wisc.edu Robert Anglin] [[Documenting the Occurrence through Space and Time of Aquatic Non-indigenous Fish, Mollusks, Algae, and Plants Threatening North_America's Great Lakes| Great Lakes Invasives]] TCNs IT | *[mailto:ranglin@wisc.edu Robert Anglin] [[Documenting the Occurrence through Space and Time of Aquatic Non-indigenous Fish, Mollusks, Algae, and Plants Threatening North_America's Great Lakes| Great Lakes Invasives]] TCNs IT | ||
*[mailto:beach@ku.edu James Beach], [[Creating A PALEONICHES| Paleoniches TCN]] IT/Co-PI, University of Kansas | *[mailto:beach@ku.edu James Beach], [[Creating A PALEONICHES| Paleoniches TCN]] IT/Co-PI, University of Kansas | ||
*[mailto:rbeaman@nsf.gov Reed Beaman] | *[mailto:rbeaman@nsf.gov Reed Beaman] | ||
*[mailto:jeb0037@auburn.edu Jason Bond], [[InvertEBase: Reaching Back to See the Future: Species-rich Invertebrate Faunas Document Causes and Consequences of Biodiversity Shifts| InvertEBase]] | *[mailto:jeb0037@auburn.edu Jason Bond], [[InvertEBase: Reaching Back to See the Future: Species-rich Invertebrate Faunas Document Causes and Consequences of Biodiversity Shifts| InvertEBase]] | ||
*[mailto:andrew.brown@kesoftware.com Andrew Brown] | *[mailto:andrew.brown@kesoftware.com Andrew Brown] Axiell Software / EMu | ||
*[mailto:BrownH@dnr.sc.gov Herrick Brown] [[The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot| SERNEC TCN]] | *[mailto:BrownH@dnr.sc.gov Herrick Brown] [[The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot| SERNEC TCN]] | ||
*[mailto:bruhnrp@yahoo.com Robert Bruhn] Biospex, IT expert, FSU | *[mailto:bruhnrp@yahoo.com Robert Bruhn] Biospex, IT expert, FSU | ||
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*[mailto:Paul.Heinrich@nau.edu Paul L Heinrich], [[Southwest Collections of Arthropods Network (SCAN)| SCAN TCN]] | *[mailto:Paul.Heinrich@nau.edu Paul L Heinrich], [[Southwest Collections of Arthropods Network (SCAN)| SCAN TCN]] | ||
*[mailto:chris_h@BERKELEY.EDU Chris Hoffman] University of California, Berkeley | *[mailto:chris_h@BERKELEY.EDU Chris Hoffman] University of California, Berkeley | ||
*[mailto:dmasaki@usgs.gov Derek Masaki], BISON | *[mailto:dmasaki@usgs.gov Derek Masaki], BISON | ||
*[mailto:garymotz@INDIANA.EDU Gary Motz] Indiana University | *[mailto:garymotz@INDIANA.EDU Gary Motz] Indiana University | ||
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*[mailto:kseltmann@amnh.org Katja Seltmann], [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] IT, AMNH | *[mailto:kseltmann@amnh.org Katja Seltmann], [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] IT, AMNH | ||
*[mailto:psierwald@fieldmuseum.org Petra Sierwald] [[InvertEBase: Reaching Back to See the Future: Species-rich Invertebrate Faunas Document Causes and Consequences of Biodiversity Shifts| InvertEBase]] | *[mailto:psierwald@fieldmuseum.org Petra Sierwald] [[InvertEBase: Reaching Back to See the Future: Species-rich Invertebrate Faunas Document Causes and Consequences of Biodiversity Shifts| InvertEBase]] | ||
*[mailto:mtulig@nybg.org Melissa Tulig] [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] NYBG | *[mailto:mtulig@nybg.org Melissa Tulig] [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] NYBG | ||
*[mailto:kwatson@nybg.org Kim Watson] [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] NYBG | *[mailto:kwatson@nybg.org Kim Watson] [[Thematic Focus: Collaborative Research - Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations| Tri-trophic TCN]] NYBG | ||
*Ex Officio: [http://www.idigbio.org/contact/Dr.%20Jose%20Fortes José Fortes], iDigBio Director for Computational Activities | *Ex Officio: [http://www.idigbio.org/contact/Dr.%20Jose%20Fortes José Fortes], iDigBio Director for Computational Activities | ||
==CYWG Meetings== | ==CYWG Meetings== | ||
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Meeting with external participation: | Meeting with external participation: | ||
*Friday, April 23, 2015 - 4PM EDT ([http://idigbio.adobeconnect.com/p893lqq26wj/ Data quality, usage, and issue tracking using GitHub], by John Wieczorek, et al at VertNet), in conjunction with the [[Data Management Interest Group]]. | *Friday, April 23, 2015 - 4PM EDT ([http://idigbio.adobeconnect.com/p893lqq26wj/ Data quality, usage, and issue tracking using GitHub], by John Wieczorek, et al at VertNet), in conjunction with the [[Data Management Interest Group]]. | ||
*Thursday, May 28, 2015 2:00 PM-4:00 PM ([ | *Thursday, May 28, 2015 2:00 PM-4:00 PM ([http://idigbio.adobeconnect.com/p7ht0zf5i7p/ Towards user-definable, semi-automated workflows for curating biodiversity data], by Bob Morris, Paul Morris et al. at Filtered PUSH, Kepler Kurator, and *Akka), in conjunction with the [[Data Management Interest Group]]. Webinar announcement [https://www.idigbio.org/content/webinar-towards-user-definable-semi-automated-workflows-curating-biodiversity-data here]. | ||
**Part 1: [https://www.idigbio.org/sites/default/files/working-groups/dm/FP-Akka-iDigBio-webinar3.pdf Kurator presentation (pdf)] | **Part 1: [https://www.idigbio.org/sites/default/files/working-groups/dm/FP-Akka-iDigBio-webinar3.pdf Kurator presentation (pdf)] | ||
**Part 2: designed for IT-oriented folks wanting to install and test. Full workflow described at: http://wiki.datakurator.net/web/iDigBioWebinar_May2015 | **Part 2: designed for IT-oriented folks wanting to install and test. Full workflow described at: http://wiki.datakurator.net/web/iDigBioWebinar_May2015 | ||
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*[[iDigBio Virtual Appliances]] (November 2013) | *[[iDigBio Virtual Appliances]] (November 2013) | ||
*[[iDigBio APIs]] (November, 2013) | *[[iDigBio APIs]] (November, 2013) | ||
*iDigBio APIs v2 webinar (April 28, 2015) | |||
** [https://www.idigbio.org//sites/default/files/workshop-images/ApiHackathon2015/HackathonWebinarIntro.pptx Presentation slides]: | |||
*** Introduction, by Matt Collins | |||
*** Search, Spatial Mapping, and Summary APIs, by Alex Thompson | |||
*** Examples of iDigBio API uses, by Greg Traub | |||
*** General hackathon resources and process, by Dan Stoner | |||
** [http://idigbio.adobeconnect.com/p7o6pl2m7t5/ AdobeConnect session, includes Q/A session] | |||
** [https://vimeo.com/126388360 Vimeo video without Q/A] | |||
* iDigBio API Hackathon (June 3-5, 2015): | |||
** [https://github.com/idigbio-api-hackathon/HackathonCentral/wiki Hackathon wiki] | |||
** [https://www.idigbio.org/content/idigbio-api-hackathon-report Hackathon reports] | |||
*[http://www.idigbio.org/content/idigbio-intellectual-property-policy Intellectual Property Policy] (April 17, 2012) | *[http://www.idigbio.org/content/idigbio-intellectual-property-policy Intellectual Property Policy] (April 17, 2012) | ||
* View the overall [[Data Ingestion Report|count and distribution of datasets ingested into the portal]] | * View the overall [[Data Ingestion Report|count and distribution of datasets ingested into the portal]] | ||
Latest revision as of 20:31, 24 June 2018
About
The Cyberinfrastructure Working Group (CYWG) was established as an outcome of the iDigBio IT Standards Workshop held in Gainesville, FL on March 28-30, 2012. In line with the iDigBio roadmap, the focus of the initial group will be on the iDigBio data ingestion procedures related to API (Application Programming Interface) or appliance specification, implementation and test.
The working group will produce material with concrete data ingestion use cases from TCNs, provide input about the existing cyberinfrastructure, produce data ingestion requirements, and help evaluate iDigBio services and appliances implementations.
Members
To express an interest in joining the working group, please contact Renato Figueiredo.
Current members:
- Renato Figueiredo (Co-Lead), iDigBio IT
- Joanna McCaffrey (Co-Lead), iDigBio Biodiversity Informatics Manager
- Dan Stoner, iDigBio IT
- Kevin Love, iDigBio IT
- Robert Anglin Great Lakes Invasives TCNs IT
- James Beach, Paleoniches TCN IT/Co-PI, University of Kansas
- Reed Beaman
- Jason Bond, InvertEBase
- Andrew Brown Axiell Software / EMu
- Herrick Brown SERNEC TCN
- Robert Bruhn Biospex, IT expert, FSU
- Nico Franz Great Lakes Invasives TCNs IT
- Larry Gall Yale Peabody
- Edward Gilbert, Lichens & Bryophytes, SCAN and Great Lakes Invasives TCNs IT, Symbiota
- Corinna Gries, Lichens & Bryophytes, PI
- Paul L Heinrich, SCAN TCN
- Chris Hoffman University of California, Berkeley
- Derek Masaki, BISON
- Gary Motz Indiana University
- Ben Norton, North Carolina Museum of Natural Sciences
- Katja Seltmann, Tri-trophic TCN IT, AMNH
- Petra Sierwald InvertEBase
- Melissa Tulig Tri-trophic TCN NYBG
- Kim Watson Tri-trophic TCN NYBG
- Ex Officio: José Fortes, iDigBio Director for Computational Activities
CYWG Meetings
Presentations from iDigBio IT:
- Wed, January 23rd, 2013 - 1:00pm EST (iDigBio DwC-A Pull Ingestion)
- Tue, February 19th, 2013 - 1:00pm EST (iDigBio Image Ingestion Appliance - presentation slides)
- Mon, September 9th, 2013 - 10:00am EDT (CYWG iDigBio v3 Preview - presentation slides) - release of v3 APIs as described in this document has been delayed.
- Friday, October 10, 2014 - 11:00am EDT (List of all links to ppt and other useful resources):
- iDigBio Search Portal (queries and GUI features), by Greg Traub (watch)
- iDigBio Data Ingestion (formats, process, etc.), by Dan Stoner (watch)
- iDigBio Architecture, by Alex Thompson (watch)
- iDigBio Infrastructure, by Matt Collins (watch)
- iDigBio Research Tools, Andréa Matsunaga (watch)
- iDigBio Appliances update, by Renato Figueiredo (watch)
Meetings with individual TCNs:
- Wed, September 04, 2013 3:00 PM-3:30 PM (NEVP)
- Wed, September 04, 2013 2:00 PM-2:30 PM (Paleoniches)
- Tue, August 20, 2013 1:00 PM-1:30 PM (SCAN)
- Mon, May 13, 2013 - 2:00pm EST (InvertNet)
- Tue, June 26th, 2013 - 10:00am EST (TTD-AMNH Data ingestion)
- Tue, July 3rd, 2013 - 10:00am EST (TTD-AMNH Image ingestion)
Meeting with external participation:
- Friday, April 23, 2015 - 4PM EDT (Data quality, usage, and issue tracking using GitHub, by John Wieczorek, et al at VertNet), in conjunction with the Data Management Interest Group.
- Thursday, May 28, 2015 2:00 PM-4:00 PM (Towards user-definable, semi-automated workflows for curating biodiversity data, by Bob Morris, Paul Morris et al. at Filtered PUSH, Kepler Kurator, and *Akka), in conjunction with the Data Management Interest Group. Webinar announcement here.
- Part 1: Kurator presentation (pdf)
- Part 2: designed for IT-oriented folks wanting to install and test. Full workflow described at: http://wiki.datakurator.net/web/iDigBioWebinar_May2015
Documentation
Related documentation from iDigBio:
- Data Ingestion Guidance
- GUID Guide (June 26, 2013)
- Data Ingestion Requirements and Guidelines (May 2013)
- Image Format Requirements and Recommendations (September 21, 2012)
- iDigBio Virtual Appliances (November 2013)
- iDigBio APIs (November, 2013)
- iDigBio APIs v2 webinar (April 28, 2015)
- Presentation slides:
- Introduction, by Matt Collins
- Search, Spatial Mapping, and Summary APIs, by Alex Thompson
- Examples of iDigBio API uses, by Greg Traub
- General hackathon resources and process, by Dan Stoner
- AdobeConnect session, includes Q/A session
- Vimeo video without Q/A
- Presentation slides:
- iDigBio API Hackathon (June 3-5, 2015):
- Intellectual Property Policy (April 17, 2012)
- View the overall count and distribution of datasets ingested into the portal
- iDigBio Nuts and Bolts - Data Integration and Ingestion
Miscellaneous documentation:
- Example of trivial transformations on INHS fish dataset
- Example of transformations on InvertNet image metadata dataset
Join us via AdobeConnect: http://idigbio.adobeconnect.com/it
Cyberinfrastructure Working Group listserv idigbio-cywg-l@lists.ufl.edu
Ex Officio: José Fortes, iDigBio Director for Computational Activities
Please feel welcome to explore other working groups.