Data Sharing Data Standards and Demystifying the IPT

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This wiki supports the Data Sharing, Data Standards and Demystifying the IPT Workshop to be held simultaneously at the University of Florida at iDigBio and at the Canadian Biodiversity Information Facility (CBIF) on 13-14 January 2015. It is the second in a series of four biodiversity informatics workshops planned in the fiscal year (2014-2015). The first one was Data Carpentry.

General Information

Description and Overview of Workshop. Are you a taxonomist collecting biological specimens in your research and vouchering them in collections? How does your specimen data get published? How does it get into collections databases? Are you a collection manager or data manager who would like to use the GBIF Integrated Publishing Toolkit v.2 (IPT) to publish your collection's datasets?

This workshop is for you if you:

  • have a dataset and need/want to get it into a standard format for sharing
  • manage data for a museum collection and would like to learn how to use the GBIF IPT
  • want to understand more about Darwin Core and Data Sharing Standards
  • would like to understand just what is meant by "Darwin Core Archive file (DwC-A)"
  • want to learn how to create or update Darwin Core Archive files using the IPT
  • would like to understand just a bit more about where data goes and how it gets there once it leaves your collection
  • are a taxonomist with an occurrence dataset who would like publish your dataset as a DwC-A with your related taxonomic publication

We'll discuss the concepts, skills, and tools we need to share biodiversity occurrence data and related data such as genomics, and media. Datasets will be taken from organismal and evolutionary biology, biodiversity science, ecology, and environmental science. The workshop format includes lectures and hands-on work, so participants are required to bring their own laptops. We will provide information and instructions on software installations and a pre-workshop online meeting is required for those participants wishing to install the IPT software on their own laptop.

Updates will be posted to this website as they become available.

Software Installation Requirements and additional information is available at this (web site) for the installation of a local IPT (on your laptop).

Planning Team

(Alphabetical order) Reed Beaman (NSF), Cathy Bester (iDigBio),Kyle Braak (GBIF), Matt Collins (ACIS - iDigBio), Shari Ellis (iDigBio), Alberto González-Talaván (GBIF), Chris Lewis (CBIF), Anissa Lybaert (CBIF), Kevin Love (iDigBio), James Macklin (CBIF), Derek Masaki (USGS - BISON), Andrea Matsunaga (ACIS - iDigBio), Joanna McCaffrey (iDigBio), Deborah Paul (FSU - iDigBio), Bénédicte Rivière (Canadensys), Laura Russell (VertNet), David Shorthouse (Canadensys), Dan Stoner (ACIS - iDigBio), Alex Thompson (ACIS - iDigBio)

About

Instructors (iDigBio): Bénédicte Rivière (Canadensys), Laura Russell (VertNet), Derek Masaki (USGS), GBIF Staff

Instructors (CBIF/Canadensys): David Shorthouse (Canadensys), James Macklin (CBIF)

Assistants (iDigBio): Andrea Matsunaga (ACIS - iDigBio), Dan Stoner (ACIS - iDigBio), Deborah Paul (FSU - iDigBio),

Assistants (CBIF):

Who: Regardless of title, if you manage data for biological specimens collections, perhaps as Data Manager or Collection Manager, this workshop is for you if you have a dataset, and want to learn about data sharing and standards, and how to share data using the DwC-A format the IPT tool produces. If you are a taxonomist and would like to publish your specimen data in a DwC-A format with your taxonomic publications, you're also welcome to apply.

Skill Level: While we don't expect experts, we do expect computer skills commensurate with a Data Manager / Collection Manager.

Where: iDigBio in Gainesville, FL and (CBIF in Ottawa, ON, Canada via teleconference using Adobe Connect)

Requirements: Participants must bring a laptop.

Contact (iDigBio Participants): Please email Deb Paul dpaul@fsu.edu for questions and information not covered here.

Contact (CBIF, Ottawa Participants): Please email James Macklin james.macklin@agr.gc.ca

Twitter: https://twitter.com/hashtag/

Tuition for the course is free, but there is an application process and spots are limited. You can apply (link here.)

Workshop Evaluation

  • link here at end of workshop

Software Installation Details

Software needed for Demystifying the IPT Workshop at iDigBio and CBIF

  • If you desire to have IPT on your laptop, you must attend the pre-workshop installation session.
    • link to Wrapper for IPT install
    • (link to register for pre-workshop installation)
    • You must RSVP that the required software is installed, prior to the workshop.

We use Adobe Connect extensively in this workshop. Please perform the systems test using the link below. Also, you will also need to install the Adobe Connect Add-In to participate in the workshop.

  • Adobe Connect Systems Test
  • Note when you follow the link to install and perform the test, some software will install (but it doesn't look like anything happens). To check, simply re-run the test.

Agenda

  • (Adobe Connect Room Registered Room Link)
  • Pre-workshop IPT Install and Set-up Webinar: January 7th, 2015 12-2 PM EST
  • Pre-workshop informal dinner at (TBD).

Schedule - subject to change.

Course Overview - Day 1 - Tuesday January 13th
8:30-8:45 Check-in, name tags, log in, connect to wireless and Adobe Connect, populate iDigBio google doc for self-introduction All, (both locations)
8:45-9:00 Local logistics, etiquette for questions Deb Paul, iDigBio (Gainesville); James Macklin, CBIF (Ottawa)
9:00-9:20 1A: Introductions, overview of day 1 day 2, Adobe Connect, Goals of the Workshop Deb Paul, David Shorthouse, James Macklin
09:20-10:15 1B: Theory: publishing basic primary biodiversity data: IPT and other methods.

Benefits: data papers, Nature data descriptors Standards: Darwin Core, Darwin Core Archive, TDWG and ratification process Workflow: GBIF registry, harvesting, presentation

Alberto Gonzalez-Talavan (Gainesville); James Macklin (Ottawa); Laura Russell (Gainesville)
10:15-10:45 Break
10:45-11:40 1C: Theory: What are the metadata?
  • Ecological Markup Language (EML)
  • Licensing, norms
  • Identifiers, former identifiers

Demo: instructor creates a resource in IPT and fills out metadata while everyone follows along Exercise: Participants create resource and metadata

David Shorthouse
11:40-12:00 1D: Theory: publishing with the IPT
  • data sources
  • data quality, character encoding
  • mapping (discuss the different cores)
 Laura Russell
12:00-1:00 Lunch
1:00-1:30 1D cont'd:

Demo: adding a data source and mapping data Exercise: data sources and mapping

  • Adding data sources
  • Mapping terms to DwC in IPT
 Laura Russell
1:30-2:30 1E: Theory: Complex primary biodiversity data
  • What are extensions to DwC?
  • Audubon Core & multimedia
  • Determination histories
  • Genomics extension (GGBN)

Demo: multimedia (Audubon Core) ext

TBD , Laura Russell
2:30-3:00 Break
3:00-4:30 1E continued:

Demo: determination histories ext Exercise: complex primary biodiversity data

  • adding data sources
  • determination histories

Audubon Core & multimedia

TBD
4:30-5:00 1F: wrap-up and review for tomorrow
  • need to have pairs set up for tomorrow
Course Overview - Day 2 - Wednesday January 14th
8:30-9:00 Check-in, log in, pairing, connect to wireless...
9:00-10:15 2A: Open Practical session (work in pairs: admin + data manager)
  • participant data
  • break-outs as required
10:15-10:45 Break
10:45-12:00 2B: Open Practical session
  • publishing a dataset & producing a DwC-A file
  • participant data
  • break-outs as required
12:00-1:00 Lunch
1:00-2:30 2C: Administration functions and user management in the IPT (roles, permissions), registering data sets with GBIF (production mode instance)
  • live publication (talk to Oliver Meyn @ GBIF)
  • feedback with regard to data quality
  • expectations from aggregator
  • expectations from providers / collectors
  • point-of-view: Canadensys, VertNet, iDigBio, GBIF
  • lightning talk from participants*
 Laura Russell
2:30-3:00 Break
3:00-4:00 2D: Collaboration and the way forward:
  • Where to find IPT help: mailing lists, interest group, (web) resources, personalized support through Participant nodes.
  • What are the current limitations of the IPT and DwC-A + Future of the IPT
  • Upgrading the IPT when new versions are released
 Alberto González-Talaván
4:00-4:30 2E: Summary of the webinar and workshop, evaluation and feedback, next steps (participants present at their own institutions - and report back/share presentation), wrap-up.

Link to Workshop Report

Logistics

Adobe Connect Access

Adobe Connect will be used to provide access for participants at The Canadian Biodiversity Information Facility (CBIF) in Ottawa, ON, Canada to instruction from iDigBio in Gainesville. Some instruction may come from CBIF to Gainesville. Workshop participants in both locations will be required to log in to the Adobe Connect room to facilitate communicating with each other. Already registered and accepted?

  • Link to Adobe Room for Registered Participants
  • Group Notes Document

Presentation Documents and Links

  • links to any presentations (like power points) here.

Workshop Recordings

Day 1

  • 8:30am-10:00am
  • 10:30am-12:00pm
  • 12-12:30
  • 1:00pm-5:00pm

Day2

  • 8:30am-10:00am
  • 10:30am-12:00pm
  • 1:30pm-5:00pm

Resources and Links

  • Got a favorite resource - a book?, a website? to share with your classmates?

Digitization Training Workshops Wiki Home

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