Difference between revisions of "ESA 2020 Data Help Desk"

From iDigBio
Jump to: navigation, search
(Additional Resources)
Line 2: Line 2:
  
 
==About the Data Help Desk==
 
==About the Data Help Desk==
For the third year ecological data repositories and data specialists will collaborate at the [https://www.esa.org/saltlake/ Ecological Society of America's annual meeting] to add a Data Help Desk (DHD) to the virtual conference space. The [https://arcticdata.io Arctic Data Center], [https://www.cuahsi.org Consortium of Universities for the Advancement of Hydrologic Science (CUAHSI)], [https://www.dataone.org DataONE], [https://environmentaldatainitiative.org Environmental Data Initiative (EDI)], [https://www.gbif.org GBIF], [https://www.idigbio.org iDigBio], [https://www.neonscience.org NEON], and [https://www.neotomadb.org Neotoma] will each engage with meeting attendees about questions, comments and concerns using DHD partner data in their own discipline and area of research. The conference is being held virtually due to the COVID-19 pandemic, from August 3 - 6, 2020.
+
For the third year ecological data repositories and data specialists will collaborate at the [https://www.esa.org/saltlake/ Ecological Society of America's annual meeting] to add a Data Help Desk (DHD) to the virtual conference space. The [https://arcticdata.io Arctic Data Center], [https://www.cuahsi.org Consortium of Universities for the Advancement of Hydrologic Science (CUAHSI)], [https://www.dataone.org DataONE], [https://environmentaldatainitiative.org Environmental Data Initiative (EDI)], [https://www.gbif.org GBIF], [https://www.idigbio.org iDigBio], [https://www.data.neonscience.org NEON], the [https://biorepo.neonscience.org/ NEON Biorepository], and [https://www.neotomadb.org Neotoma] will each engage with meeting attendees about questions, comments and concerns using DHD partner data in their own discipline and area of research. The conference is being held virtually due to the COVID-19 pandemic, from August 3 - 6, 2020.
  
 
DHD partners are also contributing talks to the ESA 2020 '''[https://www.esa.org/saltlake/program/career-central/ Career Central]'''. The schedule below summarizes these career fair contributions.
 
DHD partners are also contributing talks to the ESA 2020 '''[https://www.esa.org/saltlake/program/career-central/ Career Central]'''. The schedule below summarizes these career fair contributions.
Line 18: Line 18:
 
|  
 
|  
 
| ''asynchronous''
 
| ''asynchronous''
| Erin McLean (Arctic Data Center), Amber Budden (DataONE), Margaret O'Brien (EDI), Deborah Paul (iDigBio), Erica Krimmel, Julia Masterman (CUASHI), Jack Williams (Neotoma), Marie Faust (NEON), Kelsey Yule (NEON Biorepository), Kyle Copas (GBIF)
+
| Erin McLean (Arctic Data Center), Amber Budden (DataONE), Margaret O'Brien (EDI), Deborah Paul (iDigBio), [mailto:ekrimmel@fsu.edu Erica Krimmel], Julia Masterman (CUASHI), Jack Williams (Neotoma), Marie Faust (NEON), Kelsey Yule (NEON Biorepository), Kyle Copas (GBIF)
 
| [[Media:TBD|Data Help Desk: So much data, so little time!]]
 
| [[Media:TBD|Data Help Desk: So much data, so little time!]]
 
| This session is an introduction to data repositories where you can deposit your datasets to meet funder or publisher requirements, and also retrieve public data to further your research. Representatives from seven repositories will give 3-min presentations highlighting their holdings, approach and services, followed by general Q&A and discussion initiated by the audience.
 
| This session is an introduction to data repositories where you can deposit your datasets to meet funder or publisher requirements, and also retrieve public data to further your research. Representatives from seven repositories will give 3-min presentations highlighting their holdings, approach and services, followed by general Q&A and discussion initiated by the audience.
Line 25: Line 25:
 
| 12:30-1pm EDT
 
| 12:30-1pm EDT
 
|  
 
|  
| Q&A Session
+
| [https://eco.confex.com/eco/2020/meetingapp.cgi/Session/18668 Q&A Session] - must be logged in to the ESA conference site for Zoom link
 
|  
 
|  
 
|-
 
|-
Line 38: Line 38:
 
|  
 
|  
 
| ''asynchronous''
 
| ''asynchronous''
| Erica Krimmel (iDigBio)
+
| [mailto:ekrimmel@fsu.edu Erica Krimmel] (iDigBio)
 
| [[Media:TBD|Reading data directly into your analysis script: Introduction to APIs]]
 
| [[Media:TBD|Reading data directly into your analysis script: Introduction to APIs]]
 
| Do you write scripts to analyze your data? An Application Programming Interface (API) can provide direct access to data and metadata in online repositories, saving you time and increasing the reproducibility of your analyses. This talk will provide an introduction in R to using APIs from several repositories of ecological data.  
 
| Do you write scripts to analyze your data? An Application Programming Interface (API) can provide direct access to data and metadata in online repositories, saving you time and increasing the reproducibility of your analyses. This talk will provide an introduction in R to using APIs from several repositories of ecological data.  
Line 57: Line 57:
 
| 12:30-1pm EDT
 
| 12:30-1pm EDT
 
|  
 
|  
| Q&A Session
+
| [https://eco.confex.com/eco/2020/meetingapp.cgi/Session/18669 Q&A Session] - must be logged in to the ESA conference site for Zoom link
 
|  
 
|  
 
|-
 
|-
Line 95: Line 95:
 
| 12:30-1pm EDT
 
| 12:30-1pm EDT
 
|  
 
|  
| Q&A Session
+
| [https://eco.confex.com/eco/2020/meetingapp.cgi/Session/18670 Q&A Session] - must be logged in to the ESA conference site for Zoom link
 
|  
 
|  
 
|-
 
|-
 
|}
 
|}
 +
 +
===Got data questions?===
 +
Find us on Twitter using the hashtag [https://twitter.com/hashtag/datahelpdesk?f=live #DataHelpDesk]! Or, if your question relates to a specific Data Help Desk partner, feel free to email them directly:
 +
 +
* [mailto:info@arcticdata.io info@arcticdata.io]
 +
* [mailto:info@environmentaldatainitiative.org info@environmentaldatainitiative.org]
 +
* [mailto:data@idigbio.org data@idigbio.org]
 +
** And/or drop in to the [https://www.idigbio.org/content/open-office-hours-hosted-api-user-group-r-based iDigBio API Open Office Hours], every second and fourth Wednesday of every month at 3:30pm Eastern
  
 
===Additional Resources===
 
===Additional Resources===
Line 104: Line 112:
 
* [https://www.idigbio.org/wiki/index.php/ESA_2019_Data_Help_Desk 2019 ESA Data Help Desk]
 
* [https://www.idigbio.org/wiki/index.php/ESA_2019_Data_Help_Desk 2019 ESA Data Help Desk]
 
* [https://www.idigbio.org/wiki/index.php/ESA_2018_Data_Help_Desk 2018 ESA Data Help Desk]
 
* [https://www.idigbio.org/wiki/index.php/ESA_2018_Data_Help_Desk 2018 ESA Data Help Desk]
 +
 +
====Learning Data Skills and Best Practices====
 
* [http://dmtclearinghouse.esipfed.org/ ESIP Data Management Training Clearinghouse]
 
* [http://dmtclearinghouse.esipfed.org/ ESIP Data Management Training Clearinghouse]
 
* [https://dataoneorg.github.io/Education/ Data Management Skillbuilding Hub]
 
* [https://dataoneorg.github.io/Education/ Data Management Skillbuilding Hub]
* [https://dmptool.org Data Management Planning Tool - DMPTool]
+
* [https://learn.canvas.net/courses/ Research Data Management Librarian Academy]
* [https://www.idigbio.org/content/open-office-hours-hosted-api-user-group-r-based iDigBio API Open Office Hours], every second and fourth Wednesday of every month at 3:30pm Eastern
+
* [https://carpentries.org/ The Carpentries]
 +
* [https://qubeshub.org/community/groups/neon/educational_resources NEON teaching modules]
 +
* [https://www.neonscience.org/resources/data-tutorials NEON data tutorials]
 
* [https://biodiversity-specimen-data.github.io/specimen-data-use-case/ GitHub repo with specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions]
 
* [https://biodiversity-specimen-data.github.io/specimen-data-use-case/ GitHub repo with specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions]
* About the '''Intersection across Ecology + Collections + COVID-19''' (or host-pathogen relationships in general), please see:
+
 
** The [https://www.idigbio.org/wiki/index.php/ViralMuse_Task_Force ViralMuse Task Force]: In response to the 2020 COVID-19 pandemic, natural history museum faculty and staff recognized the need to organize a task force to coalesce needed responses to the current SARS-Cov-2 virus "spillover" event. Goals of the group include producing recommendations for the COVID-19 situation that leverage the biodiversity infrastructure (e.g., specimens and informatics) of natural history museums and draw attention to the changes in standards of practice seen as critical by this group for preventing and mitigating future emerging zoonotic events. Members of this group note that much of what is needed is known. Questions center on how to ensure everyone (i.e. scientific, government, individuals) can move forward to implement recommended changes.
+
====Planning for Data Management====
*** [https://doi.org/10.1093/biosci/biaa064 Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases], BioScience, https://doi.org/10.1093/biosci/biaa064 ''by'' Joseph A Cook, Satoru Arai, Blas Armién, John Bates, Carlos A Carrion Bonilla, Maria Beatriz de Souza Cortez, Jonathan L Dunnum, Adam W Ferguson, Karl M Johnson, Faisal Ali Anwarali Khan, Deborah L Paul, DeeAnn M Reeder, Marcia A Revelez, Nancy B Simmons, Barbara M Thiers, Cody W Thompson, Nathan S Upham, Maarten P M Vanhove, Paul W Webala, Marcelo Weksler, Richard Yanagihara, Pamela S Soltis ''on'' 24 June 2020  
+
* [https://dmptool.org Data Management Planning Tool - DMPTool]
*** '''[https://theconversation.com/museums-preserve-clues-that-can-help-scientists-predict-and-analyze-future-pandemics-141175 Museums preserve clues that can help scientists predict and analyze future pandemics'''], ''by'' Soltis P, Cook J, Yanagihara R. ''in'' The Conversation June 24, 2020
+
* [https://www.re3data.org/ Registry of Research Data Repositories]
*** And note a new NSF grant (Sept 2020 to August 2022) to support further development of an '''Infrastructure for Predicting, Understanding, and Mitigating Zoonotic Disease Outbreaks.''' Contact Pamela Soltis at University of Florida for more information. NSF Grant Number 2037937
+
* [https://zenodo.org/record/1475430#.XymT9C2ZNTZ Data Repository Selection Decision Tree for Researchers in the Earth, Space, and Environmental Sciences]
** The [https://cetaf.org/covid19-taf-communities-taking-action CETAF-DiSSCo COVID-19 Task Force]
+
 
 +
====Addressing the intersection of Ecology + Collections + COVID-19 (or host-pathogen relationships in general)====
 +
* The [https://www.idigbio.org/wiki/index.php/ViralMuse_Task_Force ViralMuse Task Force]: In response to the 2020 COVID-19 pandemic, natural history museum faculty and staff recognized the need to organize a task force to coalesce needed responses to the current SARS-Cov-2 virus "spillover" event. Goals of the group include producing recommendations for the COVID-19 situation that leverage the biodiversity infrastructure (e.g., specimens and informatics) of natural history museums and draw attention to the changes in standards of practice seen as critical by this group for preventing and mitigating future emerging zoonotic events. Members of this group note that much of what is needed is known. Questions center on how to ensure everyone (i.e. scientific, government, individuals) can move forward to implement recommended changes.
 +
** [https://doi.org/10.1093/biosci/biaa064 Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases], BioScience, https://doi.org/10.1093/biosci/biaa064 ''by'' Joseph A Cook, Satoru Arai, Blas Armién, John Bates, Carlos A Carrion Bonilla, Maria Beatriz de Souza Cortez, Jonathan L Dunnum, Adam W Ferguson, Karl M Johnson, Faisal Ali Anwarali Khan, Deborah L Paul, DeeAnn M Reeder, Marcia A Revelez, Nancy B Simmons, Barbara M Thiers, Cody W Thompson, Nathan S Upham, Maarten P M Vanhove, Paul W Webala, Marcelo Weksler, Richard Yanagihara, Pamela S Soltis ''on'' 24 June 2020  
 +
** '''[https://theconversation.com/museums-preserve-clues-that-can-help-scientists-predict-and-analyze-future-pandemics-141175 Museums preserve clues that can help scientists predict and analyze future pandemics'''], ''by'' Soltis P, Cook J, Yanagihara R. ''in'' The Conversation June 24, 2020
 +
** And note a new NSF grant (Sept 2020 to August 2022) to support further development of an '''Infrastructure for Predicting, Understanding, and Mitigating Zoonotic Disease Outbreaks.''' Contact Pamela Soltis at University of Florida for more information. NSF Grant Number 2037937
 +
* The [https://cetaf.org/covid19-taf-communities-taking-action CETAF-DiSSCo COVID-19 Task Force]

Revision as of 12:29, 4 August 2020

DataHelpDesk_image_w_logos.png

About the Data Help Desk

For the third year ecological data repositories and data specialists will collaborate at the Ecological Society of America's annual meeting to add a Data Help Desk (DHD) to the virtual conference space. The Arctic Data Center, Consortium of Universities for the Advancement of Hydrologic Science (CUAHSI), DataONE, Environmental Data Initiative (EDI), GBIF, iDigBio, NEON, the NEON Biorepository, and Neotoma will each engage with meeting attendees about questions, comments and concerns using DHD partner data in their own discipline and area of research. The conference is being held virtually due to the COVID-19 pandemic, from August 3 - 6, 2020.

DHD partners are also contributing talks to the ESA 2020 Career Central. The schedule below summarizes these career fair contributions.

Schedule of Career Central Activities

Day Time Speakers Title Description
CC 5 - Data Help Desk: So Much Data, So Little Time!
asynchronous Erin McLean (Arctic Data Center), Amber Budden (DataONE), Margaret O'Brien (EDI), Deborah Paul (iDigBio), Erica Krimmel, Julia Masterman (CUASHI), Jack Williams (Neotoma), Marie Faust (NEON), Kelsey Yule (NEON Biorepository), Kyle Copas (GBIF) Data Help Desk: So much data, so little time! This session is an introduction to data repositories where you can deposit your datasets to meet funder or publisher requirements, and also retrieve public data to further your research. Representatives from seven repositories will give 3-min presentations highlighting their holdings, approach and services, followed by general Q&A and discussion initiated by the audience.
Tuesday, 7/4 12:30-1pm EDT Q&A Session - must be logged in to the ESA conference site for Zoom link
CC 6 - Data Help Desk: Using Data
asynchronous Deborah Paul (iDigBio), Jeanette Clark (Arctic Data Center) Cleaning data and creating tidy data structures to facilitate reproducible research Join us to learn how tidy data concepts can make your analysis easier and improve reproducibility. This session describes how to deal with inconsistencies, missing values, entry errors, multiple values in single columns, and many other data issues. Demonstrations will use R and Open Refine.
asynchronous Erica Krimmel (iDigBio) Reading data directly into your analysis script: Introduction to APIs Do you write scripts to analyze your data? An Application Programming Interface (API) can provide direct access to data and metadata in online repositories, saving you time and increasing the reproducibility of your analyses. This talk will provide an introduction in R to using APIs from several repositories of ecological data.
asynchronous Donal O’Leary (NEON) From our servers to your research: tutorials and resources for loading NEON data into your preferred computing environment When it comes to analyzing 'Big Data,' using Application Programming Interfaces (APIs) will improve your workflow and your efficiency, but they may change depending on your preferred programming language. In this talk, we will use APIs in R, Python, and the command line to download National Ecological Observatory Network (NEON) data into any working environment.
asynchronous Julia Masterman (CUASHI) Cloud-based data tools for research, collaboration, and workflow documentation in the aquatic sciences: Jupyter Hub and HydroShare Cloud-based tools for data analysis and modeling can expedite workflow documentation, aiding in the reproducibility of your science and enabling collaboration. This demo will provide instruction on how to use Jupyter notebooks to operate on HydroShare data resources for research and collaboration in aquatic sciences.
Wednesday, 7/5 12:30-1pm EDT Q&A Session - must be logged in to the ESA conference site for Zoom link
CC 7 - Data Help Desk: Sharing Data
asynchronous Amber Budden (DataONE), Bill Michener (DataONE) 10 simple rules for creating a data management plan A comprehensive plan that describes how your data will be effectively managed during the life of the project and beyond is a valuable research tool in addition to a funder requirement. Learn the critical components of effective data management plans and explore tools that can support you in writing DMPs.
asynchronous Margaret O'Brien (EDI), Amber Budden (DataONE) Data citation – why and how Creating a dataset can be a fair amount of work, and you deserve credit for it. A mechanism now taking hold is data citation. This session will describe current recommendations, plus progress linking datasets to published papers and major search engines.
asynchronous Kyle Copas (GBIF), Abby Benson (US-OBIS) Introduction to publishing ecology data to GBIF GBIF supports the publication of four classes of datasets: resource metadata, plus data from checklists, occurrences, and sampling events. GBIF uses widely accepted biodiversity data standards, and offers free open source software tools to publish and share biodiversity datasets through its network.
asynchronous Jeanette Clark (Arctic Data Center) How to create a comprehensive metadata record Quality metadata enhances the discovery of your data and facilitates reproducible research. Learn the principles of creating a comprehensive metadata record.
asynchronous Jack Williams (Neotoma) Community curation: data stewards and constituent databases The Neotoma Paleoecology Database houses data from the recent fossil record for many taxonomic groups: plus geochemistry and isotopes. To manage this high diversity of scientific disciplines, Neotoma utilizes their own data stewards, and trains others within the community. This presentation outlines their curation process and training opportunities for contributors.
Thursday, 7/6 12:30-1pm EDT Q&A Session - must be logged in to the ESA conference site for Zoom link

Got data questions?

Find us on Twitter using the hashtag #DataHelpDesk! Or, if your question relates to a specific Data Help Desk partner, feel free to email them directly:

Additional Resources

Learning Data Skills and Best Practices

Planning for Data Management

Addressing the intersection of Ecology + Collections + COVID-19 (or host-pathogen relationships in general)

  • The ViralMuse Task Force: In response to the 2020 COVID-19 pandemic, natural history museum faculty and staff recognized the need to organize a task force to coalesce needed responses to the current SARS-Cov-2 virus "spillover" event. Goals of the group include producing recommendations for the COVID-19 situation that leverage the biodiversity infrastructure (e.g., specimens and informatics) of natural history museums and draw attention to the changes in standards of practice seen as critical by this group for preventing and mitigating future emerging zoonotic events. Members of this group note that much of what is needed is known. Questions center on how to ensure everyone (i.e. scientific, government, individuals) can move forward to implement recommended changes.
  • The CETAF-DiSSCo COVID-19 Task Force