Georeferencing for Research Use

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

Wiki URLs

1. Agenda (this page)
2. Logistics
3. Useful links
4. Photos

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

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:

• link to logistics page or pdf

Meet the Participants:

• Participant list
• Map of Participants and Instructors for TTT1 and TTT2
• Wiki for all TTT1 and TTT2 Participants

Pre-Workshop Assignments

1. Attend pre-workshop online meeting (date / time to be announced). One hour.
2. 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 our hands-on sessions.
3. 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
   2. Geographical Concept: https://vimeo.com/53008556
   3. Point Radius Method and Best Practices: https://vimeo.com/53006303
   4. OPTIONAL video: BITC Global Online Seminar #25: Simple Workflow for Data Cleaning
4. Please install the following software
   1. QGIS
   2. Open Refine

OpenRefine
OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. 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.

• Go to the OpenRefine <a href="http://openrefine.org/download.html">download page</a>
• Click on Linux kit to download the install file
• Download and extract
• Type ./refine in your terminal and Google Refine will then open in your web browser.
• 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.

1. 1. 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/
2. OPTIONAL software install - 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:

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

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.

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

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

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 FSU Georeferencing Protocol (Collaborative using GEOLocate) FSU Georeferencing Protocol (Excel and GEOLocate) Online Videos: Georeferencing and Symbiota, Georeferencing and Specify Documentation Check: Short Questionnaire, Long Questionnaire	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?

Optional Friday night activities: