OBIS, DarwinCore, and IPTs Workshop -

This workshop has been adapted from the standard 4.5 day OBIS training workshop and is aimed at researchers and data professionals who may be creating or aggregating biological presence data with a desire to report that data to OBIS via their national OBIS Node.

Facilitators

Name - (home OBIS node) - email

Jon Pye - (Ocean Tracking Network) - [email protected]

Brian Jones - (Ocean Tracking Network) - [email protected]

Naomi Tress - (Ocean Tracking Network) - [email protected]

Many thanks to Ward Appeltans, Leen Vandepitte, Pieter Provoost, Daphnis De Pooter, Abby Benson and all those throughout the OBIS community who helped build and refine the source material used in assembling this workshop. We hope that our adaptation is useful, fit for purpose, and results in productive outcomes for all prospective OBIS contributors.

Goals of the Workshop:

Give attendees an idea of what OBIS is and how it functions, why and how to become compliant with OBIS data and metadata formatting and data policy, how OBIS reporting pipelines work. Allow time to investigate solutions to meeting OBIS-compliance from user-held datasets and work in groups with support from trained bioinformaticians to produce DarwinCore archives fit for ingestion into OBIS nodes, especially OBIS-Canada

Highlight the utility of providing data to OBIS Canada (and onward to OBIS), learn how to create Darwin Core Archives.

Provide our own institutionally held project data and metadata in EML/DwC-A format to OBIS Canada for publication/aggregation.

Deliver curriculum via OceanTeacher Global Academy and/or GitHub to provide a permanent resource for users to refer back to.

Schedule:

Day 1

Welcome, Introductions, goals for the workshop

Intro to OBIS (PPT 01)

Intro to WoRMS

Workshop Schedule/Outline

-15m Break-

Intro to Darwin Core (PPT 02)

• History of DarwinCore

• Terms, definitions, Resources for End Users

• Occurrence, Location, Time, and Quantity in Darwin Core

• Occurrence Core and Event Core

• Quiz - DwC Terms (DwC Quiz.ipynb)

-1hr Lunch Break-

Darwin Core II (PPT 03)

• Darwin Core Archives (DwC-A)

  • Using the R package obistools for creating archives

• Minimum required information for a DwC-A

  • How to represent DwC schemas and types

  • Occurrence Core + MeasurementOrFact

  • Examining a MoF table in R

-15m Break-

Darwin Core III (PPT 03)

• Representing Event Core in DwC Archives

• OBIS-ENV-DATA

  • Working with OBIS-ENV archives in R

  • (Quiz - Data Formats Quiz.ipynb)

Day 1 Q+A and Feedback

Day 2

Ecological Metadata Language and OBIS (PPT 04)

Hands-on session 1

• Data processing, taxon matching, QC using the robis and obistools R packages

-15m Break-

Hands-on session 1 cont.

-1hr Lunch Break-

WoRMS

• Accessing WoRMS webservices (REST API)

OBIS

• Using the OBIS Data mapper to discover OBIS held datasets

-15m Break-

• OBIS API v3 – using the REST API

• Using the robis and obistools packages to discovery OBIS-held datasets

Day 3

Publishing your data via OBIS (PPT 05)

• Process of submitting/updating DwC archives to OBIS Canada

  • OBIS IPT Walkthrough

  • Verification of logins

  • OBIS, OBIS Canada and institutions that contribute to it

  • Contributing data to an OBIS Node

-15m Break-

OBIS Guidelines on Data Sharing and Use

• Motivations for sharing data

• Licensing your dataset, CC licenses, OBIS default data licens, implications

• (Quiz)

-1hr Lunch Break-

Hands-on Session 2

Mapping (user-provided) dataset into parseable DwC-A / EML package and submitting to OBIS Canada

-15m Break-

Hands-on Session 2 cont.

Data mapping Check-in/report, Day 3 Q+A and Feedback

Day 4

Hands-on Session 3 (3_visualizations.rmd)

Finding, collecting, visualizing and analyzing data from DwC archives provided from OBIS's data portal or via robis (Binder/JuPyTeR notebook session)

-15m Break-

*Hands-on Session 3 Cont.

-1hr Lunch Break-

Contributing to OBIS and OBIS Canada

• As a data contributor

• As a collections manager

• As a software developer

Discussion / Hands-on session 2 or 3 cont.

-15m Break-

Recap Quiz

Hands-on session 2 or 3 cont.

Continuing Engagement w/ OBIS and OBIS Canada, Day 4 Q+A, and Feedback

Question and Answer, Wrap-up and Next Steps

Answer questions, evaluate workshop content, plan necessary follow-ups

Useful Links

• https://classroom.oceanteacher.org/enrol/index.php?id=430 Ocean Teacher related course
• https://youtu.be/4rVEkWOhkoM Introduction to IOC, IODE, OBIS, OTGA by Ward Appeltans.
• http://ipt.iobis.org/obiscanada/ OBIS Canada