GBIF Community Practices
https://repository.oceanbestpractices.org/handle/11329/1485
2024-03-28T14:37:33ZPublishing DNA-derived data through biodiversity data platforms. version 1.0.
https://repository.oceanbestpractices.org/handle/11329/1726
Publishing DNA-derived data through biodiversity data platforms. version 1.0.
Andersson, A.F.; Bissett, A.; Finstad, A.G.; Fossøy, F.; Grosjean, M.; Hope, M.; Jeppesen, T.S.; Kõljalg, U.; Lundin, D.; Nilsson, R.N.; Prager, M.; Svenningsen, C.; Schigel, D.
When genetic information is used to describe or classify a taxon, most users will foresee its use in
the context of molecular ecology or phylogenetic research. It is important to realize that a sequence
with coordinates and a timestamp is a valuable biodiversity occurrence which is useful in a much
broader context than its original purpose. To realize this potential, DNA-derived data needs to be
discoverable through biodiversity data platforms. This guide will teach you the principles and
approaches of exposing “sequences with dates and coordinates” in the context of broader
biodiversity data. The guide covers choices of particular schemas and terms, common pitfalls and
good practice, without going into platform-specific details. It will benefit anyone interested in better
exposure of DNA-derived data through general biodiversity data platforms, including national
biodiversity portals.
2020-01-01T00:00:00ZBest Practices for Publishing Biodiversity Data from Environmental Impact Assessments. Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/1501
Best Practices for Publishing Biodiversity Data from Environmental Impact Assessments. Version 1.0.
Rodrigues, Andrew; Endresen, Dag; Figueira, Rui; Villaverde, Cristina; Vega, Miguel; King, Nick; Rajvanshi, Asha; Treweek, Jo
This guide aims to help practitioners, consultants and other Interested & Affected Parties (I&APs)
working with environmental impact assessments to improve the curation, archiving and
management of primary biodiversity data captured during EIA processes and to share data freely
and openly in standardized, accessible and interoperable formats through the Global Biodiversity
Information Facility (GBIF). I&APs are encouraged to share the most detailed data possible, to
support knowledge about species distributions and provide baseline data for future assessment.
2020-01-01T00:00:00ZGeoreferencing Calculator Manual. Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/1487
Georeferencing Calculator Manual. Version 1.0.
Bloom, David A.; Wieczorek, John R.; Zermoglio, Paula F.
The Georeferencing Calculator (Wieczorek & Wieczorek 2020) described in this document is a tool
created to aid in the georeferencing of descriptive localities such as those found in museum-based
natural history collections. It was originally designed for the Mammal Networked Information
System (MaNIS) and has been widely adopted in other large-scale collaborative georeferencing
projects to supplement semi-automated georeferencing tools. The application makes calculations
using the theory given in Georeferencing Best Practices (Chapman & Wieczorek 2020), derived from
the earlier MaNIS/HerpNET/ORNIS Georeferencing Guidelines (Wieczorek 2001), and The pointradius
method for georeferencing locality descriptions and calculating associated uncertainty
(Wieczorek et al. 2004). Specific methods for calculating a wide variety of examples of the distinct
locality types are given in Georeferencing Quick Reference Guide ([Bloom] Zermoglio et al. 2020).
Underlined terms throughout this document (e.g. accuracy) link to definitions in the Glossary (the
same glossary of terms used in Georeferencing Best Practices, while terms in italics (e.g. Input
Latitude) refer to fields and/or labels in the Calculator. Darwin Core terms are displayed in
monospace (e.g. georeferenceRemarks) in all GBIF digital documentation and link to the definitions
maintained by Biodiversity Information Standards (TDWG) in the approved List of Darwin Core
terms.
2020-01-01T00:00:00ZGeoreferencing best practices. Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/1486
Georeferencing best practices. Version 1.0.
Chapman, Arthur D.; Wieczorek, John R.
Georeferencing Best Practices provides guidelines to the best practices for georeferencing. Though
targeted specifically at biological occurrence data, the concepts and methods presented here may be
just as useful in other disciplines. This publication provides guidelines to the best practice for georeferencing. Though it is targeted
specifically at biological occurrence data, the concepts and methods presented here can be applied
in other disciplines where spatial interpretation of location is of interest. This document builds on the
original Guide to Best Practices for Georeferencing (Chapman & Wieczorek 2006), which was one of
the outputs from the BioGeomancer project (Guralnick et al. 2006). Several earlier projects and
organizations (e.g. MaNIS, MaPSTeDI, INRAM, GEOLocate, NatureServe, CRIA, ERIN, CONABIO) had
previously developed guidelines and tools for georeferencing, and these provided a good starting
point for such a document. A detailed history of the organizations involved in the development of
BioGeomancer and of the original Guide was given in that source. Throughout this document we
reference tools and methodologies developed by those organizations and we acknowledge the
valuable work by those organizations in their development. This document attempts to bring best
practices up to date with terms, technologies, and georeferencing recommendations that have been
developed and refined since the original document was published.
2020-01-01T00:00:00ZCurrent Best Practices for Generalizing Sensitive Species Occurrence Data. Version 1.
https://repository.oceanbestpractices.org/handle/11329/1460
Current Best Practices for Generalizing Sensitive Species Occurrence Data. Version 1.
Chapman, Arthur D.
The unprotected distribution of Sensitive Primary Species Occurrence Data (for example the exact
localities of rare, endangered or commercially valuable taxa) was a concern of GBIF
[https://www.gbif.org] – the Global Biodiversity Information Facility – from its beginning. The GBIF
Secretariat has a vested interest in making data available via its portals, but at the same time
respecting the wishes of data providers to restrict information on sensitive taxa. In early 2006, GBIF
initiated a process to address this issue, especially in relation to data to be shared through the GBIF
network and made visible through GBIF.org [https://www.gbif.org] and other data aggregating
initiatives.
This resulted in the Guide to Best Practices for Generalising Sensitive Primary Species Occurrence Data
[https://doi.org/10.15468/doc-b02j-gt10]. That document relied heavily on the results of an online survey
conducted through Survey Monkey [https://www.surveymonkey.com] and subsequent workshops whose
reports were originally made available on the GBIF website (Chapman 2006 [https://doi.org/10.35035/
vs84-0p13]).
A final report on Dealing with Sensitive Primary Species Occurrence Data was developed following
these processes and discussions, and was presented to GBIF in April 2007 (Chapman 2007
[https://doi.org/10.35035/rajc-t668]). This report made a number of recommendations, and many of these
have been included in this document.
The final step in that process was to develop a Guide to Best Practices for Primary Species Occurrence
Data. That document was proposed as an overriding guideline for institutions, data providers and
GBIF Nodes to use to develop their own in-house guidelines. Organizations and institutions were
encouraged to produce their own internal documents that incorporated the practices outlined in the
Guide and related documents such as the Guide to Best Practices for Georeferencing [https://doi.org/
10.15468/doc-2zpf-zf42] (Chapman and Wieczorek 2006) and incorporate them into their own working
environment. Unfortunately, not as many institutions have taken up the challenge and produced
their own internal documents as we had hoped. Two key agencies that have done so, however, are
SANBI in South Africa (SANBI 2010 [http://biodiversityadvisor.sanbi.org/wp-content/uploads/2012/09/SANBIBiodiversity-
Information-Policy-Series-Digital-Access-to-Sensitive-Taxon.pdf]) and the Atlas of Living Australia
(Tann and Flemons 2009 [https://www.ala.org.au/wp-content/uploads/2010/07/ALA-sensitive-data-report-andproposed-
policy-v1.1.pdf], ALA 2018a [https://support.ala.org.au/support/solutions/articles/6000195500-what-issensitive-
data-]) (see Implementations).
It is also important to understand the possible impact that approaches for restricting sensitive data
may have on biodiversity science and, while restricting the availability or resolution of certain data,
not overly restricting the uses to which the data may be put. For that reason, a set of principles are
elucidated below. Key among these is the need to make biodiversity information freely available
wherever possible, in the interests of science, the environment and biodiversity itself.
2020-01-01T00:00:00ZGuide to best practices for generalising sensitive/primary species occurrence-data. Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/605
Guide to best practices for generalising sensitive/primary species occurrence-data. Version 1.0.
Chapman, Arthur D.; Grafton, Oliver
The unprotected distribution of Sensitive Primary Species Occurrence Data (for example the
exact localities of rare, endangered or commercially valuable taxa) has been a concern of the
GBIF Secretariat since its beginning. In early 2006, GBIF initiated a process to address this
issue, especially in relation to data to be shared through the GBIF network and made visible
through the GBIF Data Portal.
A review of current approaches for obscuring or generalising such data was initiated in
February 2006 and an on-line survey conducted through Survey Monkey1
. A separate report
on the results was made available via the GBIF Web site2
in early June 2006 (Chapman
2006). An experts’ workshop was then held in early March 2007 that focussed on the various
technical issues involved (Chapman 2007a).
A final report on Dealing with Sensitive Primary Species Occurrence Data was developed
following these processes and discussions, and was presented to GBIF in April 2007
(Chapman 2007b). It is available via the GBIF Web site. This report made a number of
recommendations, and many of these are included in this document.
The final step in this process has been to develop a Guide to Best Practices. This document
should be seen as an overriding guideline for institutions, data providers and GBIF Nodes to
use to develop their own in-house guidelines. Organisations and institutions should produce
their own internal document that incorporates the practices outlined in this document and
related documents such as the Guide to Best Practices in Georeferencing (Chapman and
Wieczorek 2006) and incorporate them into their own working environment.
It is also important to understand the possible impact that approaches for restricting sensitive
data may have on biodiversity science and, while restricting the availability or resolution of
certain data, not overly restricting the uses to which the data may be put. For that reason, a set
of principles are elucidated below. Key among these is the need to make biodiversity
information freely available wherever possible, in the interests of science, the environment
and the biodiversity itself.
Two issues that this document has not covered, because they will need further discussion and
agreement before robust recommendations can be made, are the issues of the privacy of
living individuals and the development of Data Sharing and Data License Agreements. Both
of these issues have legal implications and vary considerably from jurisdiction to jurisdiction.
Recommendations were made in the Report on Dealing with Sensitive Species Occurrence
Data (Chapman 2007) for GBIF to further explore these issues
2008-01-01T00:00:00ZBest Practice Guidelines in the Development and Maintenance of Regional Marine Species Checklists, Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/446
Best Practice Guidelines in the Development and Maintenance of Regional Marine Species Checklists, Version 1.0.
Nozères, C.; Vandepitte, L.; Appeltans, W.; Kennedy, M.
Technical guides and work plans for best practices in creating species checklists (e.g.,
GBIF 2011) are available from the GBIF online resource center (http://www.gbif.org/orc/). These reports explain how to make best use of the dataset
standard using Darwin Core term
s, presenting and publishing checklists under the
framework of Darwin Core Archive (DwC-A), and by using the Integrated Publishing Tool
(IPT).
The present document covers the more general aspects regarding checklists for marine
regions. It outlines the steps required to compile distribution notes, to set up a register,
and to produce a checklist, but also describes some of stumbling blocks that one might
encounter along the way and offers suggestions on how to handle these issues
2012-01-01T00:00:00Z