Databasing References: Difference between revisions

!scope="col"; style="vertical-align:top";  | Description ||  

Bees, as the main pollinators of food crops, represent a critical natural resource which needs to be carefully exploited and managed. In recent years, however, destruction of bee's native habitats, infestations, and displacements of native bees by alien bee species have reduced and disturbed bee populations and this is already having considerable impact on global agriculture. A further concurrent problem is that there are probably fewer than 50 taxonomic experts worldwide able to identify bee species. ABIS (Automatic Bee Identification System) is a suite of software tools created for the identification and monitoring of bees. Bee species are rapidly and reliably determined from images of the bees' wings by means of linear and non-linear statistics in conjunction with image processing. Work is currently in progress to couple the bee identification tools within a geographic information system and to make a bee recognition service available over the Intenet.

|}

{|

== BNHM Digitization Projects – Results of Survey. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col"; style="vertical-align:top";  | Description ||  

Results of a digitization survey by the Berkeley Natural History Museum assessing digitization efforts of various collections.

|}

{|

== Collaborative databasing of North American Bee Collections (NSF-BRC Grant), by Yanega. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||  http://www.ecnweb.org/dev/files/21b_Yanega_2010.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

A mostly pictorial report of bee databasing at ten bee collections.

|}

{|

== Collection Data Registration at the Nationaal Herbarium Nederland: Data Guidelines, by L. P. M. Willemse, J. B. Mols. ==

!scope="col" width="15%" | Pub Date || March 2007

|-

!scope="col" | URL || http://www.nationaalherbarium.nl/virtual/Data-guidelines-NHN.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

The aim of this protocol is to present a detailed description of data entry rules and data entry procedures in order to standardize data entry at the NHN. Doing this will create maximum compatibility between the various databases and facilitate data exchange. A complete list of all fields and their dimensions and characteristics is found in Annex A.For most fields lookup lists (using F9) are available in BRAHMS, these should be used to enter the majority of the data. This protocol is in principle a guideline into what kind of information is stored in each field and how to enter the data if it is not available using the look-up lists.

|}

{|

== Darwin Core Terms. ==

!scope="col" width="15%" | Pub Date || 2011-10-26

|-

!scope="col" | URL || http://rs.tdwg.org/dwc/terms/index.htm#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

This quick guide provides a list of all current terms of the Darwin core. The terms are organized by categories (in bold) in the index. The categories correspond to Darwin Core terms that are classes (terms that have other terms to describe them). The terms that describe a given class (the class properties) appear in the list immediately below the name of the category in the index. The index provides links to the term descriptions in the table below the index.

|}

{|

== Digital Bee Collection Network : DBCNet ( NSF-BRC Grant ), by Yanega. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||  http://www.ecnweb.org/dev/files/21a_Yanega_2010.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

Collaborative specimen databasing of bees at ten collections: AMNH, UC Riverside, UC Davis, UC Berkeley, CSCA, Cornell, Uconn, Rutgers, Vermont, USDA Bee Systematics Lab. Includes a brief but important imaging protocol.

|}

{|

== Digital Imaging of Biological Type Specimens: A Manual of Best Practice, Results from a study of the European Network for Biodiversity Information, by Christoph L. Häuser, Axel Steiner, Joachim Holstein, Malcolm J. Scoble. ==

!scope="col" | URL ||   

http://imsgbif.gbif.org/CMS_ORC/?doc_id=2429&download=1http://imsgbif.gbif.org/CMS_ORC/?doc_id=2429&download=1#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

This book addresses a number of important issues about the digital imaging of biological objects. These topics were explored in two workshops organised by the European Network for Biodiversity Information (ENBI), and the Global Biodiversity Information Facility (GBIF). With the digital imaging of a growing number of biological objects, it has become of great importance to agree on common approaches and standards. Such standardization is particularly important for natural history specimens so as to compare specimens often with only subtle differences in morphology. Emerging technologies are leading to exciting new opportunities in scientific studies and the field of biodiversity is notable among them. This publication includes serveral chapters on important issues, including color management, image file management, metadata standards and practices, and several approaches to varying organismal groups.

|}

{|

== Digital Imaging: Ethics, by D. Cromey, The University of Arizona. ==

|-

!scope="col" | URL ||   

http://swehsc.pharmacy.arizona.edu/exppath/resources/pdf/Digital_Imaging_Ethics.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

Scientists are usually considered to be respected sources of information and there is the understanding within the scientific community that data must not be inappropriately manipulated or falsified. When this essay was first composed in 2001, there were very few written guidelines for scientists. Now some of the major professional societies have issued policy statements regarding digital imaging, and many scientific journals have revamped their instructions to authors to provide clearer guidance of how they require images to be handled. Publications like the Journal of Cell Biology have begun testing images in accepted articles to ensure compliance with their guidelines and the Office of Research Integrity (HHS) has been watching this issue closely. In this author’s experience the inappropriate manipulation of scientific digital images typically does not arise from an intent to deceive or to obscure information. More often the inappropriate manipulations are simply due to ignorance of basic principles. It seemed to this author that often what is needed is an explanation of why manipulations are right or wrong. These twelve guidelines are an attempt to address this issue. It should be noted that the author has extensive experience in the microscopic imaging of biological specimens and these guidelines reflect his personal experience in this field.

|}

{|

== Digitizing the Yale Collections – it takes a Village, by L. Munstermann and L. Gall. ==

!scope="col" width="15%" | Pub Date || 2010

|-

!scope="col" | URL ||  http://www.ecnweb.org/dev/files/gall-ecn-posted.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

Report presented at Entomology 2010 using KE Emu software; includes dilineation of the protocols for curation, imaging, and databasing.

|}

{|

== Exchangeable image file format for digital still cameras : Exif Version 2.2 (2002). ==

!scope="col" width="15%" | Pub Date || 2002

|-

!scope="col" | URL ||  http://www.exif.org/Exif2-2.PDF#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

This standard specifies the formats to be used for images, sound, and tags in digital still cameras and in other systems handling the image and sound files recorded by digital still cameras.

|}

== From Ink to Electrons: Issues to be Considered, by Larry Speers, Agriculture and Agri-Food Canada. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||  http://www.canadensys.net/wp-content/uploads/montreal-2009-digitization.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

A presentation outlining the challenges, needs, and uses of scientific collections data, including import decisions to be made about establishing and conducting a collection digitization program, and the potential problems with such projects and their data.

|}

== GBIF Training Manual 1: Digitization of Natural History Collections Data. ==

|-

!scope="col" | URL ||   

http://www.infoandina.org/system/files/recursos/GBIF_TM1.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

The Global Biodiversity Information Facility (GBIF) is a worldwide network that makes primary, scientific, biodiversity data (documented species occurrence data) from many sources openly available via the Internet. It does this by building an information infrastructure that interconnects hundreds of databases, and by promoting the digitisation and sharing of data that are not currently available via the Internet, such as those associated with specimens in natural history museums. This promotion of digitisation is approached in a number of ways: seed money awards to stimulate digitisation projects; the development (with partners) of community-accepted standards for data and metadata, as well as software tools that enable interconnectivity and interoperability; workshops for training in digitisation and data-sharing; and guides such as this training manual and its components. GBIF’s hope is to help collections and database personnel around the world share best practices in the tasks and operations required in building a web-based, global “natural history collection and herbarium” that can be accessed any time any where by any one via the Internet.

|}

== How to Digitize Large Insect Collections? Preliminary Results of the Dig Project, by D. Lampe, K-H. Striebing. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||  http://phthiraptera.info/Publications/9073.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

In practice the overall efficiency of data-basing the inventory of traditional entomological collections depends on two factors: suitable software and management measures to ensure the highest possible data quality already in the input process. Lessons learned from the development of the specimen-based database BIODAT and preliminary results of the DIG-(Digitization of key Insect groups at ZFMK) project, which is especially designed to develop a 'good practice', recommend: (1) a lockstep programme for data-basing, (2) data entry of collection units & split record function, (3) visualisation of georeferenced location/sites during data entry, (4) semi-automatic/automatic data transformation from original format into additional alternative ones, (5) semiautomatic data transfer of taxa- and geo-referenced information units. Current activities deal with the introduction of semantic feedback mechanisms into the practice of data-basing entomological collections.

|}

== Image Capture and Processing: An Overview, Consortium of Pacific Northwest Herbaria, by Ben Legler. ==

!scope="col" width="15%" | Pub Date || July 26, 2010

|-

!scope="col" | URL ||  http://www.pnwherbaria.org/documentation/imaging-overview.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

This document describes the general processes used for image capture, image processing, data capture, and data/image dissemination used by the Consortium of Pacific Northwest Herbaria, as carried out under the Consortium’s 2010-2013 collaborative NSF Grant (DBI0956414). Details are omitted in an attempt to provide an overall understanding of the process.

|}

== Imaging of Specimens: Issues to be Considered, by Larry Speers, Agriculture and Agri-Food Canada. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||  http://www.canadensys.net/wp-content/uploads/montreal-2009-imaging.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

A short presentation on specimen vs. label imaging, with consideration of image type, format, storage, and work flow.

|}

== Initiating a Collection Digitisation Project, by C. K. Frazier, J. Wall, S. Grant. ==

!scope="col" width="15%" | Pub Date || 2008, GBIF

|-

!scope="col" | URL ||  http://www.gbif.org/orc/?doc_id=2176#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

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. The authors have years of experience working with collections and they have instilled this expertise into this paper so one can more efficiently ask the right questions and make the appropriate plans prior to committing any resources to the task.

|}

{|

== Innovative workflows for efficient data capture in an entomological collection: The MCZ Lepidoptera Rapid Data Capture Project, by P. Morris, R. Eastwood, L. Ford, et. al. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||   

http://www.ecnweb.org/dev/files/12_Eastwood_2010.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

Presentation made at Entomology 2010. Significant detail on the rapid data capture project at Museum of Comparative Zoology, including an efficient workflow.

|}

{|

== Moving Theory into Practice: Digital Imaging Tutorial. ==

!scope="col" width="15%" | Pub Date ||  

|-

!scope="col" | URL ||   

http://www.library.cornell.edu/preservation/tutorial/tutorial_English.pdf#

|-

!scope="col"; style="vertical-align:top";  | Description ||  

An excellent online tutorial about digital imaging, including basic terminology, selection, conversion, quality, and metadata.

|}