Accelerating biodiversity research through DNA barcodes, collection and observation data

Key documentation

The following references provide further detail on the topics covered in this course. All links open in a new window/tab.

Darwin Core

Data publishing

Quick guide to publishing data through GBIF
How to publish biodiversity data through GBIF.org
Become a data publisher with GBIF
Best Practices for Publishing Biodiversity Data from Environmental Impact Assessments
GBIF Secretariat & IAIA: International Association for Impact Assessment (2020).
Guidance for private companies to become data publishers through GBIF: Template document to support the internal authorization process to become a GBIF publisher
Rui Figueira, Pedro Beja, Cristina Villaverde, Miguel Vega, Katia Cezón, Tainan Messina, Anne-Sophie Archambeau, Rukaya Johaadien, Dag Endresen & Dairo Escobar (2020).
Publishing DNA-derived data through biodiversity data platforms
COMMUNITY REVIEW DRAFT
Anders F. Andersson, Andrew Bissett, Anders G. Finstad, Frode Fossøy, Marie Grosjean, Michael Hope, Thomas S. Jeppesen, Urmas Kõljalg, Daniel Lundin, R. Henrik Nilsson, Maria Prager, Cecilie Svenningsen & Dmitry Schigel (2020).
Classes of datasets supported by GBIF
GBIF data quality requirements for publishing
GBIF data licenses
Checklist core templates
Occurrence core templates
Sampling event core templates
Sampling event data best practices
Sharing images, sounds and videos on GBIF
Data papers
Published data papers

Data publishing: IPT

Digitization

GBIF

What is GBIF
Strategic Plan
Become a member
Science Review
Establishing an Effective GBIF Participant Node: Concepts and general considerations
GBIF Secretariat (2019).

Georeferencing

Georeferencing Best Practices
Arthur D. Chapman & John R. Wieczorek (2020).
Georeferencing Quick Reference Guide
Paula F. Zermoglio, Arthur D. Chapman, John R. Wieczorek, Maria Celeste Luna & David A. Bloom (2020).
Georeferencing Calculator Manual
David A. Bloom, John R. Wieczorek & Paula F. Zermoglio (2020).
Georeferencing resources

Invasive Species

Living Atlases

Miscellaneous

OpenRefine

OpenRefine documentation
OpenRefine regular expressions
Guía para la limpieza de datos sobre biodiversidad con OpenRefine
Paula F. Zermoglio, Camila A. Plata Corredor, John R. Wieczorek, Ricardo Ortiz Gallego & Leonardo Buitrago (2021).
Using Google Refine and taxonomic databases (EOL, NCBI, uBio, WORMS) to clean messy data
iPhylo blog post. Rod Page 2012.
Reconciling author names using Open Refine and VIAF
iPhylo blog post. Rod Page 2013.
Validating scientific names with the GBIF Portal web service API
Guest post was written by Gaurav Vaidya, Victoria Tersigni and Robert Guralnick 2013.
iDigBio Cleaning data with OpenRefine
iDigBio 2013.
Have We Got the Names “Right”?
Canadensys 2014.
Cleaning data with OpenRefine
Desmet and Brosens 2016 TDWG.
EasyOpen Redlist
Querying the IUCN Red List, using a species list, OpenRefine, and some pre-written code. Olly Griffin July 2019.

Planning/Collaboration

Quality

Principles of Data Quality
Arthur Chapman 2005.
Principles and Methods of Data Cleaning: Primary Species and Species-Occurrence Data
Arthur Chapman 2005.
Be careful with dates in Excel
DataOne 2014.
Character encoding for beginners
MVZ Guide for Recording Localities in Field Notes

Sensitive species

Current Best Practices for Generalizing Sensitive Species Occurrence Data
Arthur D. Chapman 2020.

Taxonomy