Difference between revisions of "Marine Invertebrate Digitization Workshop 2019"

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{| class="wikitable" style="float:right; margin-left: 10px;"
 
{| class="wikitable" style="float:right; margin-left: 10px;"
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Quick Links for DigIn: Marine Invertebrate Digitization Workshop 2018
+
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | DigIn: Marine Invertebrate Digitization Workshop 2018
 
|-
 
|-
 
| colspan="2" style="text-align:center;font-size:7pt" |  
 
| colspan="2" style="text-align:center;font-size:7pt" |  
 
|-
 
|-
!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt |[[File:Anisogammarus_pugettensis_dFHL_03419a.jpg|center|300px]]
+
!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt |[[File:Anisogammarus_pugettensis_dFHL_03419a.jpg|center|350px]]
 
|-  
 
|-  
 
|[[Marine_Invertebrate_Digitization_Workshop_2019#Agenda|Agenda]]
 
|[[Marine_Invertebrate_Digitization_Workshop_2019#Agenda|Agenda]]
 
|-  
 
|-  
 +
|[https://www.idigbio.org/content/understand-ocean-we-need-get-wet To understand the ocean - we need to get wet]
 +
|-
 
|}
 
|}
  
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|-
 
|-
 
| 8:20-8:40
 
| 8:20-8:40
| Logistics
+
| Logistics<br/>Intro to ADBC and iDigBio
 
| Gustav and Deb
 
| Gustav and Deb
| Welcome, logistics, agenda, round of introductions
+
| Welcome, logistics, agenda<br/>
 +
[[Media:IntroiDigBioSlidesDeb_DigIn.pdf|Intro to ADBC and iDigBio]]
 
* https://bit.ly/DigInFolder
 
* https://bit.ly/DigInFolder
 
* https://bit.ly/DigInWiki [this wiki page]
 
* https://bit.ly/DigInWiki [this wiki page]
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| Intro & overview
 
| Intro & overview
 
| Gustav Paulay
 
| Gustav Paulay
| Introduction presentation
+
| [[Media:DigIn_intro.pdf|Introduction]] presentation
 
|-
 
|-
 
|  
 
|  
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| Collection Overviews
 
| Collection Overviews
 
| Adam Baldinger<br/>Deborah Paul
 
| Adam Baldinger<br/>Deborah Paul
| Collection presentations
+
| Collection presentations<br/>
 +
:[[Media:Collection Overview AMNH.pdf|AMNH]] Chris Johnson, Lily Berniker
 +
:Alabama MNH Kevin Kocot
 +
:[[Media:ANSP general invertebrates_iDigBio.pdf|ANSP]] Gary Rosenberg
 +
:[[Media:AUMNH.pdf|AUMNH]] Briane Varnerin
 +
:[[Media:CASIZ Colln_Piotrowski.pdf|CASIZ]] Christina Piotrowski
 +
:[[Media:CMN_Marine Invert Digitization_iDigBIO-Feb 2019.pdf|CMN]] Jean-Marc Gagnon
 +
:[[Media:FLMNH - IZ Intro.pdf|FLMNH]] Amanda Bemis
 +
:[[Media:FMNH inverts intro.pdf|FMNH]] Rudiger Bieler
 +
:[[Media:FWRI_SIS.pdf|FWRI]] Paul Larson
 +
:[[Media:Baldinger_iDigBio_Feb 2019.pdf|MCZ]] Adam Baldinger
 +
:[[Media:NCMNS collections.pdf|NCMNS]] Megan McCuller
 +
:[[Media:NHMLA intro.pdf|NHMLA]] Trina Roberts, Libby Ellwood
 +
:[[Media:NMNH-IZcollections_WEM.pdf|NMNH]] William Moser
 +
:[[Media:HC.Jan.2019.RBCM.Coll.Summary.pdf|RBCM]] Henry Choong
 +
:Scripps Greg Rouse
 +
:[[Media:TAMU Collections.pdf|TAMU]] Mary Wicksten
 +
:[[Media:VIMS Invertebrate Collection_J.Dreyer.pdf|VIMS]] Jennifer Dreyer
 
|-
 
|-
 
|  
 
|  
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|-
 
|-
 
| 10:45-11:15
 
| 10:45-11:15
| Goals part 1
+
| Goals Inspiration<br/>Goals part 1
| Chris Johnson
+
| Jim Carlton<br/>Chris Johnson
| Goals and general discussion
+
| [[Media:Carlton.Epibiota Museum Collections.pdf|Consider Epibiota]]<br/>[https://docs.google.com/document/d/1YWvuhB7BX9Bthrjs87qUGWs7CfYwRh1dcxtYOxf9sVM/edit?usp=sharing Goals] and general discussion
 
|-
 
|-
 
|  
 
|  
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10 min x 6
 
10 min x 6
 
|-
 
|-
| rowspan="6" colspan="3" |  
+
| rowspan="4" colspan="3" |  
 
| Mandy Bemis (UF)
 
| Mandy Bemis (UF)
 +
:[[Media:FLMNH_-_IZ_Workflow-Mandy_s_edits.pdf|FLMNH IZ Digitization Workflow]]
 
|-
 
|-
 
| Bill Moser (Smithsonian)
 
| Bill Moser (Smithsonian)
 +
:[[Media:DigitizationWorkflows_WEM.pdf|Digitization: Various Workflows and Challenges]]
 
|-
 
|-
 
| Jean-Marc Gagnon (CMN)
 
| Jean-Marc Gagnon (CMN)
 +
:[[Media:CMN_Marine_Invert_Digitization_iDigBIO-_CMN_Digit_Procedures_Feb_2019.pdf|Digitization and Data Capture at CMN]]
 
|-
 
|-
| Henry Choong (RBCM) – Specify Workbench issues
+
| Henry Choong (RBCM) adding Specify Workbench issues<br>
|-
+
Libby Ellwood (LACM LaBrea Tar Pits) adding CitSci data capture pros and cons
| Ed Gilbert (Symbiota) – Symbiota bulk uploads
+
|-
+
| Libby et al (LACM) citizen science pros & cons
+
 
|-
 
|-
 
| style="background-color:#ffffc7;" | 12:30-1:30
 
| style="background-color:#ffffc7;" | 12:30-1:30
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| Georeferencing
 
| Georeferencing
 
| Nelson Rios
 
| Nelson Rios
| Georeferencing overview & discussion
+
| [[Media:Rios_iDigBio_Dig_In_2019.pdf|Georeferencing overview]] & discussion
 
|-
 
|-
 
|  
 
|  
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| Ed Gilbert
 
| Ed Gilbert
 
| Symbiota
 
| Symbiota
 +
:[[Media:Symbiota_2019-02-03.pdf|SYMBIOTA: specimen-based platform to support digitization, publication, and public outreach]]
 +
:[[Media:SymbiotaWorkflows_2015-07-26.pdf|Symbiota and Specimen Label Digitization Workflows]]
 
|-
 
|-
 
|  
 
|  
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| rowspan="4" colspan="2" |  
 
| rowspan="4" colspan="2" |  
 
| (self select)
 
| (self select)
| [https://docs.google.com/document/d/1pntODxEPj4jGfaxyheS6bonqge3M3H0deY9Qy3RkYxo/edit GROUP 1] - what taxa, areas, scientific goals
+
| [https://docs.google.com/document/d/1pntODxEPj4jGfaxyheS6bonqge3M3H0deY9Qy3RkYxo/edit?usp=sharing GROUP 1] - what taxa, areas, scientific goals
 
|-
 
|-
 
|  
 
|  
| GROUP 2 - how much data to capture and how?
+
| [https://docs.google.com/document/d/1prUAuCSX-dZ47O4qnTTGMORZO9t5BDo4PRzT8Q9a_8U/edit?usp=sharing GROUP 2] - how much data to capture and how?
 
|-
 
|-
 
|  
 
|  
| GROUP 3 - estimating effort & cost
+
| [https://docs.google.com/document/d/1LQQm5AxwYTAMIfzOSY3Xwzk82HuZahlGWYpy0tdC4sQ/edit?usp=sharing GROUP 3] - estimating effort & cost
 
|-
 
|-
 
|  
 
|  
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| 3:45-4:15
 
| 3:45-4:15
 
| Imaging
 
| Imaging
| Zach Randall?
+
| Zach Randall
| Imaging – presentation & discussion
+
| [[Media:Imaging_Digin_2019_Randall.pdf|Digitization in Museums: 2D Imaging]]
 
|-
 
|-
 
|  
 
|  
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| Genetics
 
| Genetics
 
| Regina Wetzer
 
| Regina Wetzer
| Genetic collections
+
| [[Media:Copy_of_Genetic_Collections_-_LACM_Wetzer.pdf|Genetic collections]]
 
|-
 
|-
 
|  
 
|  
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|-
 
|-
 
| 8:30-9:00
 
| 8:30-9:00
| Sequence data
+
| Vouchering sequence data: BOLD, GenBank
 
| Adriana Radulovici
 
| Adriana Radulovici
Ed Gilbert
+
| [[Media:Radulovici_FL_2019.pdf|Linking Specimens and DNA Sequences through BOLD]]
| Vouchering sequence data: BOLD, GenBank
+
 
|-
 
|-
 
|  
 
|  
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|  
 
|  
 
|-
 
|-
|  
+
| 9:00-9:15
|  
+
| Linking Genetic Resources
|  
+
| Warren Brown
|  
+
| [[Media:GRR-Sync.pdf|Connecting a Genetic Resource Repository to Specify]]
 
|-
 
|-
| 9:00-9:30
+
| 9:15-9:45
 
| WoRMS
 
| WoRMS
 
| Bart Vanhoorne
 
| Bart Vanhoorne
| [http://www.marinespecies.org/index.php WoRMS]
+
| [[Media:DigIn_WoRMS_Vanhoorne_2018-02-05.pdf|World Register of Marine Species (WoRMS)]]
 +
:[http://www.marinespecies.org/index.php WoRMS] (website)
 
|-
 
|-
 
|  
 
|  
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|  
 
|  
 
|-
 
|-
| 9:30-10:00
+
| 9:45-10:00
 
| Nomenclature
 
| Nomenclature
 
| Rudiger Bieler
 
| Rudiger Bieler
| Nomenclature –discussion
+
| [https://drive.google.com/open?id=1yDSspoungoh909AJW6ArOR7mECy6dKYsV_VXkbeivSY Nomenclature] discussion
 
|-
 
|-
 
|  
 
|  
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| Breakout Groups
 
| Breakout Groups
 
| Leads
 
| Leads
| Ancillary data & nomenclature –breakout discussions
+
| Ancillary data & nomenclature breakout discussions
 
|-
 
|-
 
| rowspan="4" colspan="2" |  
 
| rowspan="4" colspan="2" |  
 
| (self select)
 
| (self select)
| GROUP 1 – imaging
+
| [https://docs.google.com/document/d/1BVeVhSHUaXZBs5v9CLOHleZ3ydx6ry1KAbAEq7NAt80/edit?usp=sharing GROUP 1 workflows including georeferencing]
 
|-
 
|-
 
|  
 
|  
| GROUP 2 – genetics
+
| [https://docs.google.com/document/d/1w9eXb8V_VGubPXFoTyisr2idQpTsP4jYXzb_PIoFEL0/edit?usp=sharing GROUP 2 genetics]
 
|-
 
|-
 
|  
 
|  
| GROUP 3 – nomenclature
+
| [https://docs.google.com/document/d/14Eh2dWKgSwqAL0Ix708Nbky_KFVcpOMOnTE-VF2OGhc/edit?usp=sharing GROUP 3 nomenclature]<br/>Rudiger's [https://drive.google.com/open?id=1yDSspoungoh909AJW6ArOR7mECy6dKYsV_VXkbeivSY Nomenclature] discussion notes
 
|-
 
|-
 
|  
 
|  
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|-
 
|-
 
| 11:15-11:35
 
| 11:15-11:35
| Digitization Overview
+
| Digitization Overview<br/>Symbiota live demo
 
| Deb Paul <br/>Edward Gilbert
 
| Deb Paul <br/>Edward Gilbert
| Digitization Overview
+
| [[Media:DigitizationOverview_DigIn_short.pdf|Digitization Overview]]<br/>
 +
[http://hasbrouck.asu.edu/sandbox/ Symbiota Sandbox]
 
|-
 
|-
 
|  
 
|  
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| Data Mobilization
 
| Data Mobilization
 
| Kevin Love
 
| Kevin Love
| Data Mobilization
+
| [[Media:Love-iDigBio_Data_Mobilization_Presentation-1.pdf|Data Mobilization]]
 
|-
 
|-
 
|  
 
|  
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| Jean-Marc Gagnon
 
| Jean-Marc Gagnon
 
Henry Choong
 
Henry Choong
| Specimen storage & collection organization - presentation & discussion
+
| [[Media:CMN_Marine_Invert_Digitization_iDigBIO-_CMN_%26_RBCM_Storage_Best_Practices_2019.pdf|Specimen storage & collection organization]] presentation & discussion
 
|-
 
|-
 
|  
 
|  
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|-
 
|-
 
| 1:30-2:30
 
| 1:30-2:30
| Dream Big: Science with IZ data
+
|Dream Big: Science with IZ data
 
| Jean-Marc Gagnon
 
| Jean-Marc Gagnon
| Scientific goals
+
| Scientific goals<br/>
 +
[[Media:Marine_Invert_Digitization_iDigBIO_Science_with_IZ_Data_2019.pdf|Dream Big: Science with IZ data]]
 
|-
 
|-
 
|  
 
|  
 
|  
 
|  
| Breakout groups?
+
| Breakout groups<br/>google docs
 
|  
 
|  
 +
:[https://docs.google.com/document/d/1oM_lck8_dNWEL7i8DB3KQ3VoqxJD7mrbdsyZ7LZKsiw/edit?usp=sharing What does NSF want?]
 +
:[https://docs.google.com/document/d/1bo0XGhLZiBWqE12IzPBC3LrwzWLEFs_P96rMdVrE9Lk/edit?usp=sharing Marine Resource]
 +
:[https://docs.google.com/document/d/1GnJpcFiOn281c5pns05Joivxak8ue6ckIc76BdXvzYA/edit?usp=sharing Dream Big: Scientific Goals]
 
|-
 
|-
 
| 2:30-3:15
 
| 2:30-3:15
 
| Broader Impacts
 
| Broader Impacts
 
| Libby Ellwood<br/>Molly Phillips
 
| Libby Ellwood<br/>Molly Phillips
| Broader impacts
+
|[[Media:BroaderImpacts.pdf|DigIn Broader Impacts]]
 
|-
 
|-
 
|  
 
|  
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| 3:30-4:00
 
| 3:30-4:00
 
| Management
 
| Management
| Chris Johnson
+
| Chris Johnson<br/>Edward Gilbert<br/>Nelson Rios
 
| Project and Data Management
 
| Project and Data Management
 
|-
 
|-
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| 4:00-4:30
 
| 4:00-4:30
 
| Wrap up
 
| Wrap up
|  
+
| Gustav Paulay
 
|  
 
|  
 
|-
 
|-
 
| 4:30-4:45
 
| 4:30-4:45
 
| Survey
 
| Survey
|  
+
| Everyone
 
| iDigBio exit survey for participants
 
| iDigBio exit survey for participants
 
|}
 
|}
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* [https://www.idigbio.org/content/workflow-modules-and-task-lists Workflow Modules and Task Lists]
 
* [https://www.idigbio.org/content/workflow-modules-and-task-lists Workflow Modules and Task Lists]
 
* Broader Impacts
 
* Broader Impacts
 +
*[https://sketchfab.com/USF_digital/collections/biological-specimens 3D Images - FWRI]
 +
 +
[[Category:Symposium]][[Category:Workshop]][[Category: Biodiversity informatics]][[Category:Imaging]][[Category:Project management]][[Category:Data use]]

Latest revision as of 15:58, 15 February 2019

DigIn: Marine Invertebrate Digitization Workshop 2018
Anisogammarus pugettensis dFHL 03419a.jpg
Agenda
To understand the ocean - we need to get wet


General Information

When: 4-5 February 2019
Where: iDigBio, Gainesville, Florida

Directions Google Map Link: https://goo.gl/maps/Q4DMRDP2MRT2 from Holiday Inn University Center to Dickinson Hall

Overview

In this 2 day workshop, collection personnel from all major and most medium-sized IZ collections in the US will share information about their collections and curatorial and digitization workflows. Participants will discuss best practices and consider ways to improve on existing methods to improve efficiency and speed of data mobilization. These will include discussing citizen-enabled data capture such as Notes from Nature, handling labels in fluid collections, imaging methods, assembling, sharing, and digitization of station data from major expeditions, etc. We will also discuss standardizing nomenclature through the World Register of Marine Species (WoRMS), linking tissue collections through Global Genome Biodiversity Network (GGBN), and DNA sequence/barcode data through Barcode of Life Data System (BOLD).

Agenda

Agenda below may change as we desire or need.

Online abbreviated version
Online annotated version


Sunday 3 February 2019
Informal Collection Tours 5-630 PM, Dickinson Hall, 1659 Museum Road
Informal Dinner at Piesano's Restaurant 7 PM (restaurant located in the Holiday Inn University Center, Gainesville)

Monday
4 Feb 2019
TIME THEME WHO / comments TOPICS TO COVER
8-8:20 Arrival Coffee – Tea – Sign-in – Log-on Demographics
8:20-8:40 Logistics
Intro to ADBC and iDigBio
Gustav and Deb Welcome, logistics, agenda

Intro to ADBC and iDigBio

8:40-9:00 Intro & overview Gustav Paulay Introduction presentation
9:00-10:30 Collection Overviews Adam Baldinger
Deborah Paul
Collection presentations
AMNH Chris Johnson, Lily Berniker
Alabama MNH Kevin Kocot
ANSP Gary Rosenberg
AUMNH Briane Varnerin
CASIZ Christina Piotrowski
CMN Jean-Marc Gagnon
FLMNH Amanda Bemis
FMNH Rudiger Bieler
FWRI Paul Larson
MCZ Adam Baldinger
NCMNS Megan McCuller
NHMLA Trina Roberts, Libby Ellwood
NMNH William Moser
RBCM Henry Choong
Scripps Greg Rouse
TAMU Mary Wicksten
VIMS Jennifer Dreyer
10:30-10:45 Coffee break
10:45-11:15 Goals Inspiration
Goals part 1
Jim Carlton
Chris Johnson
Consider Epibiota
Goals and general discussion
11:15-12:30 Data Capture Workflows Deb Paul Data capture workflows - presentations
Overview

10 min x 6

Mandy Bemis (UF)
FLMNH IZ Digitization Workflow
Bill Moser (Smithsonian)
Digitization: Various Workflows and Challenges
Jean-Marc Gagnon (CMN)
Digitization and Data Capture at CMN
Henry Choong (RBCM) adding Specify Workbench issues

Libby Ellwood (LACM LaBrea Tar Pits) adding CitSci data capture pros and cons

12:30-1:30 Lunch (provided)
1:30-2:15 Georeferencing Nelson Rios Georeferencing overview & discussion
2:15-2:45 Symbiota Ed Gilbert Symbiota
SYMBIOTA: specimen-based platform to support digitization, publication, and public outreach
Symbiota and Specimen Label Digitization Workflows
2:45-3:15 Breakout Groups Leads Goals & workflow – breakout discussions
(self select) GROUP 1 - what taxa, areas, scientific goals
GROUP 2 - how much data to capture and how?
GROUP 3 - estimating effort & cost
3:15-3:30 Coffee break Coffee – Tea – Log on
3:30-3:45 REPORTS backs from groups Group Leads Take notes and summarize main points w/ Google docs
3:45-4:15 Imaging Zach Randall Digitization in Museums: 2D Imaging
4:15-4:45 Genetics Regina Wetzer Genetic collections
5:00-6:30 Social & IZ tour
7:00 Dinner The Swamp and Map to The Swamp
1642 W University Ave, Gainesville, FL
Tuesday
5 Feb 2019
TIME THEME WHO / comments TOPICS TO COVER
8-8:30 Arrival Coffee – Tea – Log on
8:30-9:00 Vouchering sequence data: BOLD, GenBank Adriana Radulovici Linking Specimens and DNA Sequences through BOLD
9:00-9:15 Linking Genetic Resources Warren Brown Connecting a Genetic Resource Repository to Specify
9:15-9:45 WoRMS Bart Vanhoorne World Register of Marine Species (WoRMS)
WoRMS (website)
9:45-10:00 Nomenclature Rudiger Bieler Nomenclature discussion
10:00-10:15 Coffee break
10:15-10:45 Breakout Groups Leads Ancillary data & nomenclature breakout discussions
(self select) GROUP 1 workflows including georeferencing
GROUP 2 genetics
GROUP 3 nomenclature
Rudiger's Nomenclature discussion notes
10:45-11:15 REPORTS from groups Group Leads Take notes and summarize main points w/ Google docs
11:15-11:35 Digitization Overview
Symbiota live demo
Deb Paul
Edward Gilbert
Digitization Overview

Symbiota Sandbox

11:35-12:00 Data Mobilization Kevin Love Data Mobilization
Ed Gilbert
12:00-1:00 Lunch (provided)
1:00-1:30 Physical infrastructure Jean-Marc Gagnon

Henry Choong

Specimen storage & collection organization presentation & discussion
1:30-2:30 Dream Big: Science with IZ data Jean-Marc Gagnon Scientific goals

Dream Big: Science with IZ data

Breakout groups
google docs
What does NSF want?
Marine Resource
Dream Big: Scientific Goals
2:30-3:15 Broader Impacts Libby Ellwood
Molly Phillips
DigIn Broader Impacts
3:15-3:30 Coffee break
3:30-4:00 Management Chris Johnson
Edward Gilbert
Nelson Rios
Project and Data Management
4:00-4:30 Wrap up Gustav Paulay
4:30-4:45 Survey Everyone iDigBio exit survey for participants

Logistics

  • Logistics for Workshop (pdf) In this document you will find information about:
    • hotel location: Holiday Inn University Center, Gainesville, FL
    • Workshop Location information
    • hotel-airport shuttle information
    • workshop links for uploading talks, connecting to wifi, etc

Group Notes

Taking group notes together.

Workshop Resources