Documentation

GUID Guide for Data Providers

A Globally Unique Identifier (GUID) is a unique reference number used as an identifier. Complexities associated with specimens and associated, dynamic data in natural history collections have led to differences in opinions about how to create GUIDs and where they are required vs. recommended. This guide is intended to give data providers the information necessary to assign GUIDs that will allow iDigBio to ingest and share data.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/iDigBioGuidGuide-2013-06-26_0.pdf

iDigBio Intellectual Property Policy

iDigBio promotes open-access to sharing data through the iDigBio portal. iDigBio’s goal is to make data for scientific specimens widely available in electronic format. iDigBio strongly urges those who submit content to do so without limitation on use or without limitation on use other than attribution.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/iDigBio_Intellectual_Property_Policy_20141001.pdf

iDigBio Data Ingestion Requirements and Guidelines

This guide describes the formats and requirements for ingesting data into iDigBio.

Supported File Formats: iDigBio strives to make data ingestion into our infrastructure as easy as possible. To achieve this, we have identified two lowest common denominator export file formats that we will initially support for dataset ingestion.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/DataIngestionGuide.pdf

iDigBio Service Level Agreement SLA

INTRODUCTION

The resources of Integrated Digitized Biocollections (“iDigBio”) are free, publicly-available, open-source computing resources and services. The purpose of this Service Level Agreement (SLA) is to define the terms of service for the website, wiki, portal, appliances, Application Programming Interface (API), Data, information, and other products and services offered by iDigBio (“iDigBio Services”). iDigBio is a program of the Florida Museum of Natural History, a unit of the University of Florida, a public body corporate of the State of Florida.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/iDigBio_Service_Level_Agreement_20160303.pdf

Collaborating with iDigBio on Grant Proposals

As part of its role as national resource, iDigBio is often asked to comment on grant proposals to various funding agencies. This document provides guidance on topics related to collaboration with iDigBio, interaction with the iDigBio Portal, and commitment of services by iDigBio for grant proposals.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/Collaborating-with-iDigBio-on-Grant-Proposals_0.pdf

iDigBio Editorial Policy for Original Content and Previously-Published Content

The purpose of the of iDigBio website and e-newsletter is to facilitate the dissemination of information and updates regarding the implementation of NSF grant #EF 1115210, and to inform the broader community about progress, opportunities and obstacles relevant to resource digitization related to natural history museums.

The iDigBio website and e-newsletter serves a broad readership including natural history museum curators, collections managers, technical specialists, volunteers, citizen scientists and the general public.

Standards Documentation: 
https://www.idigbio.org/sites/default/files/iDigBio%20Editorial%20Policy%20v0.pdf

iDigBio Image File Format Requirements and Recommendations

iDigBio’s mission requires that it be able to aggregate and distribute digital images of biological specimens, records, and other objects associated with specimens (e.g., labels and notes) generated by TCNs and other bio- and paleo-collections hosting institutions. Linked below is a document providing current iDigBio policy as well as recommendations for acquiring, processing, archiving, and distributing still, two-dimensional digital images. We recognize the importance of other image types, including three-dimensional images, and will expand this current policy through time as demand dictates.

Current version: https://www.idigbio.org/content/idigbio-image-file-format-requirements-and-recommendations-1

Version history: https://www.idigbio.org/biblio?f%5bkeyword%5d=443

Workflow Modules and Task Lists

One outgrowth of the DROID (Developing Robust Object-to-Image-to-Data) workflow workshop held in May 2012 was the establishment of a series of working groups, each focused on workflow modules and tasks for various preparation types. The first of these groups, informally called the Flat Sheets and Packets Working Group, was charged with fleshing out task lists for digitizing vascular and non-vascular plant collections. The second group, Pinned Specimens in Trays and Drawers, is investing its time developing modules to support effective entomological digitization workflows. Other preservation types will follow, concluding with the development of an overall project management module designed to provide guidance for developing and managing digitization projects across disciplines and preservation types.

iDigBio Specimen Portal Technology Preview 2012

iDigBio's technology preview is the first release of a semi-annual release cycle for a specimen portal that will eventually contain over 1 billion vouchered specimen records. This technology preview contains sample datasets provided by Morphbank and the Florida Museum of Natural History, some of which is research quality specimen data. These datasets allow iDigBio to share its development efforts with the community for feedback and guidance. You can access the technology preview here: portal.iDigBio.org

 

Digitization Workflows

 

Efficient and effective workflows are at the heart of successful biological and paleontological collections digitization. Much work has been done with developing workflows and protocols at the museum and collections level, but few of these workflows have been documented or made available to the larger collections community. iDigBio, through its Documentation pages, is establishing an online repository for sharing existing customized workflows from as many collection types and institutions as possible, an idea that stems largely from the Developing Robust Object-to-Image-to-Data (DROID) workshop held May 30-31, 2012. We have assembled an initial set of workflows, including selected examples from the DROID workshop, as well as those developed by iDigBio staff. Here we offer the beginnings of the repository and encourage those in the community to both discuss the workflows via the forum links, and to contribute to this resource by adding new workflows and updating existing workflows.

Biological Collections Databases, Tools, and Data Publication Portals

 

Launching a biological collections digitization program requires careful selection of a database management system, portal option, aggregator, and associated data enrichment tools. Numerous database systems, data publication portals, and other productivity tools are in use across the collections community, all of which vary in cost, installation requirements, storage methods, approaches to data processing, and other important features. iDigBio has begun the process of reviewing the various systems, tools, and data portals in current use, with the goal of building an annotated list of available products. Our reviews include brief descriptions of features, installation and maintenance requirements, cost, ease of use, and other components that collections managers might find useful when evaluating them for fitness. We include a wide range of products in the list, each of which fits one or more categories as denoted in the parenthetical entries immediately below the product name.

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