keydocs.en.adoc

Key documentation

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

API

• GBIF API beginners guide

• (Almost) everything you want to know about the GBIF Species API

Cloud Computing

• GBIF and Apache-Spark on Microsoft Azure tutorial

• GBIF and Apache-Spark on AWS tutorial

Darwin Core

• Darwin Core Terms: A quick reference guide

• Simple DarwinCore

• Darwin Core Questions & Answers

• Darwin Core extensions registered with GBIF

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
  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

• The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet
  Robertson et al. (2014)

• To install IPT or not to install IPT

• IPT data hosting centres

• IPT Install / Set up webinar

• Installing the IPT video

• IPT in Practice demonstration video

Digitization

• iDigBio Digitization Resources

• iDigBio Collections Digitization Workflows

• iDigBio Digitization Workflows and Protocols

• iDigBio specimen image capture guide

• Canadensys 10-step guide to managing images with your biodiversity data

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

• GRISS - Global Register of Introduced and Invasive Species

• TrIAS - Tracking Invasive Alien Species

Living Atlases

• Living Atlases

• ALA key technical documentation

Miscellaneous

• VertNet Guide to opening text files in Excel

• VertNet data licensing guide

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

• Agile

• What is SCRUM

• SCRUM Framework

• Kanban methodology

• Scrum Guide

• GitHub

Red List Assessments

• IUCN Red List Categories and Criteria

  • IUCN Red List Categories and Criteria v3.1 - ENGLISH

  • Categorías y Criterios de la Lista Roja de la UICN v3.1 - ESPAÑOL

  • Catégories et Critères de la Liste Rouge de l’UICN v3.1 - FRANÇAIS

• Red List Guidelines

  • Guidelines for Using the Red List Categories and Criteria version 15 - ENGLISH

  • Directrices de uso de las Categorías y Criterios de la Lista Roja de la UICN Versión 14 - ESPAÑOL

  • Lignes directrices pour l’utilisation des Catégories et Critères de la Liste rouge de l’UICN Version 14 - Français

• Criteria Summary Sheet

  • Criteria summary sheet - ENGLISH

  • Resumen de los Criterios - ESPAÑOL

  • Résumé des Critères - FRANÇAIS

• Mapping Standards

  • Mapping Standards - ENGLISH

  • Standard Attributes for Spatial Data - ENGLISH

  • Attribute codes for Presence

• Regional and National Levels Guidelines

  • Guidelines for application of IUCN Red List Criteria at Regional and National Levels Version 4 - ENGLISH

  • Directrices para el uso de los Criterios de la Lista Roja de la UICN a nivel regional y nacional Versión 4 - ESPAÑOL

  • Lignes directrices pour l’application des Critères de la Liste rouge de l’UICN aux niveaux régional et national Version 4. - FRANÇAIS

• Spatial Tools and Data for Red List Assessments
  Includes brief overviews of some tools developed to aid mapping of spatial data and estimation of Red List metrics such as EOO and AOO, plus developer information, links to help files, support networks and associated research publications.

• Supporting information guidelines
  The Documentation Standards and Consistency Checks for IUCN Red List Assessments and Species Accounts (also known as the Supporting Information Guidelines) provides guidance on the required and recommended supporting information for Red List assessments. It also provides guidance on the writing style and format that should be used for all IUCN Red List assessments.

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

R

• Data Carpentry-Data Analysis and Visualization in R for Ecologists

• Datacamp- Range of courses in R, Python and SQL

• Introduction to R Manual

• rgbif Manual

• CoordinateCleaner Manual

• Downloading occurrences from a long list of species in R and Python

• Common things to look out for when post-processing GBIF downloads

• Finding gridded datasets & Gridded Datasets Update

• Country centroids

• Using shapefiles on GBIF data with R

• Not a bird download

Sensitive species

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

Taxonomy

• GBIF checklist datasets and data gaps

• GBIF Labs - Names Parser

• GBIF Labs - Species Matching

• Global Names Resolver

• Marine Name Matching Strategy for taxonomic quality control

• Nomenmatch