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Georeferencing for Research Use

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Georeferencing for Research Use, a short course
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Quick Links for GWG Second Train the Trainers Workshop
Georeferencing for Research Use - link to agenda
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Georeferencing for Research Use, short course report

iDigBio - CCBER GWG Georeferencing for Research Use, a short course

 
hotel and NCEAS map

October 4 - 7, 2016 at (https://www.nceas.ucsb.edu/) NCEAS, Santa Barbara California

We welcome you to this short course, with a focus on research use of georeferenced natural history collections data. We will include activities and discussions about best practices and tools for georeferencing, capturing locality data in the field, and using georeferenced specimen locality data in research. Attendees must have a basic level of experience with georeferencing techniques and tools and be researchers or directly involved with researchers.

After the workshop, we will encourage our participants to share use cases, any training materials developed, and to offer workshops, webinars, talks, or other events aimed at increasing use of best practices for georeferencing legacy locality data, best practices for capturing the locality data from future biological and paleontological collecting and sampling events, and best practices for using the data in research.

Some anticipated course content includes discussion and activities about georeferencing integration, georeferenced data visualization, and georeferences for modeling and research. Detailed agenda in development.

Logistics:

Meet the Participants:

  • Participant list

Bring your Datasets and Laptops:

Participants are strongly encouraged to bring representative datasets from their collections that need georeferencing to expose everyone to the variety of locality data georeferencing issues and give the experts and participants a chance to work together to address any challenges.

Participants must bring their own laptops and everyone will have wired access to facilitate the best possible workshop experience.

Pre-Workshop Assignments

  1. Attend pre-workshop online meeting. Two options, choose one.
    1. Thursday September 15th - two times to choose from:
      1. 11am EDT (10am CDT, 9am MDT, 8am PDT)
      2. 3pm EDT (2pm CDT, 1pm MDT, 12pm PDT)
    2. Sign Up Here: https://goo.gl/forms/WmJO6z79rx5nHlv32
    3. Meet: http://idigbio.adobeconnect.com/geotrain
  2. Please watch the following videos - before the workshop. (flipped-classroom). Be sure to note any questions / insights to share with the group.
    1. Collaboration to Automation: https://vimeo.com/53006304 (25 min lecture, 10 min discussion)
    2. Geographical Concepts: https://vimeo.com/53008556 (4 min lecture, 2 min discussion)
      1. https://vimeo.com/album/2163673/video/63692461 (4 min lecture only)
    3. Point Radius Method and Best Practices: https://vimeo.com/53006303 (20 min lecture, 5 min discussion)
    4. OPTIONAL video: BITC Global Online Seminar #25: Simple Workflow for Data Cleaning (1 hour)
  3. Please install the following software
    1. QGIS and QGIS Plugins
      1. QGIS: http://qgis.org/en/site/forusers/download.html
      2. QGIS Plug-ins:
        1. Lifemapper
    2. Open Refine: (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, - should work fine (Explorer not recommended). You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer. (Use these resources Open Refine Install or Install Open Refine for more help if you run into any Open Refine install issues).
      1. Windows
        1. Go to the OpenRefine download page.
        2. Click on Windows kit to download the install file
        3. To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
        4. OpenRefine will then open in your web browser.
        5. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
      2. MacOS
        1. Go to the OpenRefine download page.
        2. Click on Mac kit to download the install file
        3. Open the downloaded .dmg file
        4. Drag the icon in to the Applications folder
        5. Double click on the icon and Google Refine will then open in your web browser.
        6. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
      3. Linux
        1. Go to the OpenRefine download page.
        2. Click on Linux kit to download the install file
        3. Download and extract
        4. Type ./refine in your terminal and Google Refine will then open in your web browser.
        5. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
    3. Spreadsheet software (your choice, Libre Office, Excel, etc.,)
      1. We'll be using a spreadsheet program. If you already have a spreadsheet program installed, like LibreOffice, Excel or OpenOffice, you can use whatever you already have. If you don't have a spreadsheet program, please download and install LibreOffice from http://www.libreoffice.org/download/libreoffice-fresh/
    4. Java: Please make sure you have Java installed (needed for Open Refine to work).
  4. OPTIONAL software install and tutorials - if you are interested in the R section we will offer at the workshop.
    1. R: R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
      1. Windows
        1. Video Tutorial
        2. Install R by downloading and running this .exe file from CRAN (http://cran.r-project.org/index.html).
        3. Also, please install the RStudio IDE.
      2. Mac OS X
        1. Video Tutorial
        2. Install R by downloading and running this .pkg file from CRAN (http://cran.r-project.org/index.html).
        3. Also, please install the RStudio IDE.
      3. Linux
        1. You can download the binary files for your distribution from CRAN. Or you can use your package manager
          1. e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R.
        2. Also, please install the RStudio IDE.
    2. Then install packages:
    3. R Tutorials. OPTIONAL take a short course in R. If you are a novice, take a beginner course. We don't expect you know know R well, but we do need you be familiar enough to follow along with one of our optional hands-on sessions. There are several good options:
      1. Try R (Code School course)
      2. Beginner Course: Up and Running with R with Barton Poulson (course at lynda.com)
      3. Intermediate Course: R Statistics Essential Training with Barton Poulson(course at lynda.com)
      4. For the future you could take a Coursera class. intro to R(Coursera course started August 22nd).

Reading Materials and Resources:

  1. Georeferencing.Org
  2. Georeferencing Quick Reference Guide
    version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto
  3. Guide to Best Practices for Georeferencing - Chapman, A.D. and J. Wieczorek (eds). 2006
  4. Georeferencing Working Group Training Videos
  5. Georeferencing Incidents from Locality Descriptions and its Applications: a Case Study from Yosemite National Park Search and Rescue Transactions in GIS, 2011, 15(6): 775–793 Authors: Doherty, Guo, Liu, Wieczorek, Doke
  6. iDigBio Georeferencing Wiki http://tinyurl.com/idbgeowiki
  7. HerpNET Georeferencing Resources
  8. Take Workshop Notes Together Here
  9. Post - Workshop Survey Questions
  10. Got a Georeferencing Question? Post it on the iDigBio Georeferencing List Serve
  11. BITC Global Online Seminar #25: Simple Workflow for Data Cleaning

Wireless / Wired Access Issues:

Both wired and wireless access provided to workshop participants. Connectivity instructions will be provided at the workshop.

Overview:

Goals of the Workshop:

Workshop Objectives:

Desired Outcomes:

Schedule of Events - Agenda

Breakfast every day is on our own.

Day 1, Tuesday October 4th

Time
Activity
 Presenter
8:45
 Pick up Name Tags, Wireless Log-In, Wired Setup
9:00
 Welcome by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER
 Katja Seltmann, Debbie Paul, (NCEAS person)
9:15
 Why This Workshop? What tools do you use? What would you like to be able to do? (georeferencing-wise)
10:00
 Workshop Overview, Introduction to Georeferencing, and Researcher Considerations
 Katja Seltmann, Shelley James,
10:20

10:35
 Break
11:00
 Georeferencing Introduction: Collaboration to Automation
11:30
 Geographical Concepts
11:50
 Point-Radius Method and Best Practices

12:10
 Darwin Core Standard, Key Terminology
iDigBio Recommended fields
12:30
 Lunch (Provided)
13:30
 Georeferencing Quick Reference Guide, Locality Types, and Georeferencing Template
14:40
 Georeferencing Calculator, Calculator Manual
15:30
 Break
16:00
 Georeferencing Calculator Example and Exercises, MaNIS/HerpNET/ORNIS Georeferencing Guidelines
17:00
 Day in Review
Trivia Question of the Day
17:30
 End


Dinner on our own - See list of local restaurants. Optional Evening Activity is: TBA

Day 2, Wednesday October 5th

Time
 		Activity
 		Presenter
9:00
 Review and Questions
 All
9:10
 Group Photo
9:30
 Internet Resources - Where to Begin?
10:00
 Exercises: Internet Resources
 All
10:30
 Break
11:00
 Exercises: Internet Resources (continued)
 All
12:15
 More Online Resources (resources used by/requested by participants)
12:30
 Lunch (Provided)
13:30
 GPS Exercise Introduction
13:45
 GPS Exercises (outside)
 All
15:15
 Break
 All
15:30
 Online Exercises
Review of known answers
16:15
 Georeferencing Using Paper Maps, Paper Maps Handout
16:45
 Day in Review and Considerations for Trainers-to-be

Your Input Needed - Mapping Functions in the iDigBio Portal
Trivia Question of the Day
Hotelwork: create/document your project workflow(s) for discussion on Wednesday
17:30
 END

Dinner on our own - See list of local restaurants. You'll be reimbursed at the standard per diem rates. Optional Evening Activities are: TBA

Day 3, Thursday October 6th

Download zipped dataset The parameters for this dataset are specimens in the family Carabidae, that have geocoordinates, and are in California. It results in about 25,000 records in total.

Time
Activity
 Presenter
9:00
 Review and Questions
 All
9:15
 GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet
9:35
 Exercises: Using Paper Maps
 All
10:30
 Break
11:00
 Exercises: Using Paper Maps (continued)
 All
12:30
 Lunch on our own. See local restaurant map
13:30
 Exercises: Using Paper Maps (continued)
 All
14:30
 Online Exercises - Participant Georeferences Review

Group Results and Answers available upon request

All
14:45
 Examples and Discussion: Process, Workflows, Priorities, and Collaborations

EMu, KUMIP and Specify
FishNet2
ORNIS Workflow and Repatriation
Workflows and Expert or Novice: an Experiment in Progress

 Jessica Utrup, Una Farrell, Nelson Rios, Deb Paul, Dave Bloom
15:30
 Break
16:00
 Process, Workflows, Priorities, and Collaborations (continued)
Discuss Hotelwork: Participant Project workflow(s)
  • Danielle Pace, AMNH, Arthropod Easy Capture
  • Katrina Menard, Sam Noble Museum
  • Mark Uhen, Paleodb.org
 Jessica Utrup, Una Farrell, Nelson Rios, Deb Paul, Dave Bloom
17:00
 Day in Review and Considerations,

Volunteers for Sharing Research Experienes and Issues




Trivia Question of the Day
17:30
 End

Evening Activity is: TBD. Today in Santa Barbara:

Day 4, Thursday August 15th

Time
 		Activity
 		Presenter
9:00
 Questions and Review
9:10
 Paper Maps Review
9:40
 Results: Paper Maps

Group Results and Answers available upon request


10:30
 Break
11:00
 Good and Bad Localities, Field Locality Handout, Review of GPS Locality Descriptions
11:30
 Introduction to GEOLocate
What To Do

12:15
 Lunch on our own. See local restaurant map
13:15
 Using GEOLocate: Basics (Web Application)
 Nelson Rios
13:45
 Using GEOLocate: Batch Processing (Web App and Excel)
 Nelson Rios
14:25
 Using GEOLocate: Collaborative Georeferencing Administrative Portal
 Nelson Rios
15:30
 Break
16:00
 Using GEOLocate: Collaborative Georeferencing Web Client
 Nelson Rios
16:20
 Advanced GEOLocate: Taxon validation, Web services & integration, Building end-to-end georeferencing workflows
Note this topic was covered in a remote recorded session after TTT2. 		Nelson Rios
17:00
 Day in Review and Considerations for Trainers-to-be

Trivia Question of the Day

17:30
 End

Dinner on our own - See list of local restaurants. You'll be reimbursed at the standard per diem rates.

Day 5, Friday August 16th

Time
 		Activity
 		Presenter
9:00
 Review and Questions
 David Bloom
9:10
 Data Cleaning, Processing, and Analysis

Cleaning, Validating, and Enhancing Data with Open Refine
sample CSV and sample script to use with this presentation
(GPS Vizualizer, Google Refine which is now Open Refine, Example of a Refine Call to GEOLocate, r-project, RStudio, QuantumGIS, QGIS Basic Operations)

 Debbie Paul, Nelson Rios, Dave Bloom
10:30
 Break
11:00
 Open Work Session - Participant/TCN Georeferencing Projects (use those data sets)
 All
12:00
 Open Work Session (continued)
 All
12:30
 Lunch on our own. See local restaurant map
13:30
 Open Work Session (continued)
 All
14:15
 Batch Georeferencing in Symbiota
14:30
 Researcher Demos -
  • Edward Davis
  • Shelley James
  • Katja Seltmann
15:30
 Break
16:00
 Post-Workshop Survey
 All
16:30
 Day in Review and Considerations

Your Input Needed - Mapping Functions in the iDigBio Portal - Part 2
Trivia Question of the Day
17:00
 Workshop Summary and Certificates
 All Instructors
17:30
 End

Dinner on our own - See list of local restaurants. Leaving tomorrow? Want to get together for dinner or hang out at the hotel pool?
Some software install instructions from Data and Software Carpentry

Trained Georeferencers

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