Collections Digitization Background Documents

Overviews | Databasing | Georeferencing | Imaging | Mobilization | Standards | Tools

An annotated list of resources (with links) relevant to the digitization of biological collections. This is targeted to those initiating a biological collection digitization effort. If you would like to suggest a resource, do so below by leaving a comment.

Overviews

Databasing | Georeferencing | Imaging | Mobilization | Standards | Tools
  1. Title: Canadensys Digitization webpage
    Date: 2015
    Author(s): P. Desmet & Pierre Bélisle
    Organization: Canadensys
    Note: Background information about natural history collections digitization with tools and references to relevant resources.
    Link: website
  2. Title: GBIF Resources
    Date: 2015
    Organization: GBIF
    Note: A link to the GBIF resources website, which includes training manuals and many other items.
    Link: website
  3. Title: GBIF Training Manual 1: Digitisation of Natural History Collections Data
    Date: 2008 Version: 1
    Author(s): multiple
    Organization: GBIF
    Note: A complete package of background information and guidance for the curators and managers of natural history collections and herbaria. Chapters from this document are provided in the relevant sections below.
    Link: document
  4. Title: iDigBio Digitization Resources
    Date: 2015
    Organization: iDigBio
    Note: Provides resources and information for the series of digitization training workshops being conducted by iDigBio as well as a plethora of digitization information and resources.
    Link: website

Databasing (text digitization)

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  1. Title: CNH-Symbiota Crowdsourcing module how-to
    Date: 11 June 2014 Version: 1
    Author(s): P. Sweeney
    Organization: CNH
    Note: A brief how-to on using Symbiota's crowdsourcing module.
    Link: document
  2. Title: Darwin Core standard
    Date: 09 October 2009 Version: rs.tdwg.org/dwc/2009-09-23/
    Author(s): Darwin Core Task Group
    Organization: TDWG
    Note: This links to the cover page, an entry-level document to the Darwin Core standard. It describes the purpose of the standard and orients the reader to the documents that cover specific topics within the standard, such as the quick guide to the list of terms.
    Link: website
  3. Title: Initiating a Collection Digitisation Project
    Date: 2008 Version: 1
    Author(s): C.K. Frazier, J. Wall, S. Grant
    Organization: GBIF
    Note: This document is designed to give the reader the confidence to get started and to make the right decisions when planning a natural history collection digitisation project.
    Link: document
  4. Title: Principles and Methods of Data Cleaning
    Date: 2005 Version: 1
    Author(s): A.D. Chapman
    Organization: GBIF
    Note: Error prevention is far superior to error detection and cleaning, but no matter how efficient the process of data entry, error will still occur. Therefore, data validation and correction cannot be ignored, especially when dealing with legacy biodiversity data and this manual helps to correctly face these issues.
    Link: document
  5. Title: Principles of Data Quality
    Date: 2005 Version: 1
    Author(s): A.D. Chapman
    Organization: GBIF
    Note: The rapid increase in the exchange and availability of taxonomic and species-occurrence data has made data quality principles important, as users of the data begin to require more and more detail on the quality of this information.
    Link: document
  6. Title: Relational database design and implementation for biodiversity informatics.
    Date: 2005
    Author(s): P.J. Morris
    Publication: Phyloinformatics
    Note: This paper discusses the principles of good relational database design, how to apply those principles in the practical implementation of databases, and examines how good database design is essential for long term stewardship of biodiversity information.
    Link: article

Georeferencing

Overviews | Databasing | Imaging | Mobilization | Standards | Tools
  1. Title: Georeferencing of museum collections: A review of problems and automated tools, and the methodology developed by the Mountain and Plains Spatio-Temporal Database-Informatics Initiative (Mapstedi)
    Date: 07 September 2004
    Author(s): P.C. Murphey, R.P. Guralnick, R. Glaubitz, D. Neufeld & J.A. Ryan
    Publication: Phyloinformatics
    Note: A review of some of the most common problems inherent to the retrospective georeferencing of biological collections. An attempt is made to classify the most common types of locality descriptions according to a rule-application for georeferencing, which was developed as part of a larger funded effort to create an online mapping and biodiversity analysis portal for the North-central Rocky Mountains and adjacent plains. As a means of comparison with a manual computer-assisted georeferencing method, four currently available automated georeferencing tools are evaluated.
    Link: article
  2. Title: Georeferencing Quick Reference Guide
    Date: 08 October 2012
    Author(s): John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto
    Organization: MaNIS/HerpNET/ORNIS
    Note: A simple table that summarizes the MaNIS/HerpNET/ORNIS georeferencing guidelines. For a given locality type, it suggests what is the most common georeferencing procedure and how to determine the extent and error.
    Link: document
  3. Title: georeferencing.org
    Date: 2015
    Organization: VertNet
    Note: A comprehensive source of gazetteers, data sources, and traning materials related to georeferencing.
    Link: website
  4. Title: Guide to Best Practices for Georeferencing
    Date: August 2006
    Author(s): A.D. Chapman and J. Wieczorek (eds).
    Organization: GBIF
    Note: The document provides guidelines to the world’s best practice for georeferencing biological species (specimen and observational) data.
    Link: document
  5. Title: MaNIS/HerpNET/ORNIS Georeferencing Guidelines
    Date: 8 April 2007 Version: Rev. 8
    Author(s): J. Wieczorek
    Organization: MaNIS, HerpNET, ORNIS
    Note: This document contains information about assigning geographic coordinates, and maximum error distances for those coordinates, to locality descriptions. This document does not attempt to describe the tools and methods for finding named places on maps or in gazetteers.
    Link: website
  6. Title: The point-radius method for georeferencing locality descriptions and calculating associated uncertainty
    Date: 2004
    Author(s): J. Wieczorek, Q. Guo, R. Hijmans
    Publication: International Journal of Geographical Information Science
    Note: This paper describes a method for georeferencing locality descriptions that accounts for the idiosyncrasies, sources of uncertainty, and practical maintenance requirements encountered when working with natural history collections.
    Link: article

Imaging

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  1. Title: Audubon Core standard (draft)
    Date: 06 December 2012 Version: draft
    Author(s): Multimedia Resources Task Group
    Organization: GBIF
    Note: This links to the cover page, an entry-level document to the Audubon Core Multimedia Metadata. It describes the purpose of the standard and orients the reader to the documents that cover specific topics within the standard, such as the quick guide to the list of terms.
    Link: website
  2. Title: Digital Imaging of Biological Type Specimens: A Manual of Best Practice
    Date: 2005
    Author(s): C.L. Hauser, A. Steiner, J. Holstein, M.J. Scoble (eds)
    Organization: European Network for Biodiversity Information (ENBI)
    Link: report
  3. Title: Digital preservation for libraries, archives, and museums.
    Date: 2014
    Author(s): Edward M. Corrado and Heather Lea Moulaison
    Organization:
    Note: An accessible introduction to the topic of preserving digital assets.
    Link: book
  4. Title: Proceedures and recommendations for photographing and archiving type specimens of the New York Botanical Garden Herbarium
    Date: 2001
    Author(s): G. Mariano, S. Becker, A. Forsythe, G. Lemon
    Organization: New York Botanical Garden
    Note: This manual is a guide for photographing and archiving herbarium specimens at the New York Botanical Garden. The manual does not describe how each piece of equipment functions, but rather takes the user through the steps necessary to complete the process.
    Link: document
  5. Title: Specimen Imaging Documentation
    Date: 2010
    Author(s): Ben Legler
    Organization: Consortium of Pacific Northwest Herbaria
    Note: These documents describe the technology and workflows used by the PNW for imaging specimens at regional herbaria. The instructions should be sufficient to replicate their setup elsewhere, although modifications may be required.
    Link: website

Mobilization

Overviews | Databasing | Imaging | Georeferencing | Standards | Tools
  1. Title: VertNet: A New Model for Biodiversity Data Sharing
    Date: 16 February 2010
    Author(s): H. Contable, R. Guralnick, J. Wieczorek, C. Spencer, A.T. Peterson, et al.
    Publication: PLoS Biology
    Note: Provides perspectives on the sociological and technical developments that brought vertebrate biodiversity networks to their current point and discusses solutions to the immediate and anticipated challenges.
    Link: article

Standards

Overviews | Databasing | Imaging | Georeferencing | Mobilization | Tools
  1. Title: Basic Standards Recommendations
    Date: 2015
    Organization: TDWG
    Note: Biodiversity Information Standards (TDWG) is a not for profit scientific and educational association that is affiliated with the International Union of Biological Sciences. TDWG was formed to establish international collaboration among biological database projects. TDWG promoted the wider and more effective dissemination of information about the World's heritage of biological organisms for the benefit of the world at large. Biodiversity Information Standards (TDWG) now focuses on the development of standards for the exchange of biological/biodiversity data.
    Link: website

Tools

Overviews | Databasing | Imaging | Georeferencing | Mobilization | Standards
  1. Title: Integrated Publishing Toolkit
    Date: 2014
    Organization: GBIF
    Note: The GBIF IPT is an open source, Java (TM) based web application that is used to publish and share biodiveristy assets. The data registered in a GBIF IPT instance is connected to the GBIF distributed network and made available for public consultation and use. The IPT can be used to publish Darwin Core Archives that can be used as a means to share specimen occurrence data.
    Link: website
  2. Title: NEVP resources page
    Date: 2015
    Author(s): Patrick Sweeney
    Organization: NEVP
    Note: Provides links to workflows, software, and proceedures used by the New England Vascular Plants project, a NSF ADBC TCN.
    Link: website
  3. Title: reBar
    Date: 2015
    Author(s): Patrick Sweeney
    Organization: NEVP
    Note: reBar is a perl wrapper script that uses ZBar to rename images based on one dimensional barcodes that are visible in the image.
    Link: website
  4. Title: Specify Software Project
    Date: 2015
    Organization:
    Note: The Specify Software Project offers Specify 6 & 7 and allied applications for museum and herbarium research data processing. Specify 6 handles specimen information for computerizing collection holdings, for tracking specimen and tissue management transactions, and for mobilizing species occurrence data to the Internet. Specify runs on Windows, Mac OS X, and Linux computers; it is free and open source licensed.
    Link: website