Difference between revisions of "Digitization"

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== Statement of Purpose ==
 
== Statement of Purpose ==
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These links and documents contain information about digitizing natural history collections and their associated data.
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Realizing the import of collections, SPNHC recognizes the need to collaborate to develop, discover, disseminate and update best (better, current, recommended) practices for creating digital collections resources and publishing them for global access. Materials linked here represent the efforts of many collections data mobilization projects worldwide. All in the collections community are encouraged to contribute.
  
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===Introduction to Digitization===
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Page - ''IN Development''. Please contribute.
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In the context of the SPNHC wiki ‘digitize’ means converting ALL analog data to digital data according to standard vocabularies such as DarwinCore and AudubonCore. That is, we start with the concept of a specimen that has been accessioned in a collection. We envision these digital data eventually to include the entirety of analog data that are associated with a particular specimen. This may include but is not limited to: textual data from labels and ledgers associated with specimens, images of specimens, DNA and other ‘omics, field notes, tomographic imaging data, specimen history (including preservation), and specimen-associated literature. Digitizing might be accomplished by collections managers, technicians, contractors, and other entities, the results of which are included within the institution’s collection management system. In many instances these data may be generated off site by investigators.
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 +
===Defining Digitization===
 +
In the context of the SPNHC wiki 'digitize' means converting ALL analog data to digital data according to standard vocabularies such as DarwinCore and AudubonCore. That is, we start with the concept of a specimen that has been accessioned in a collection. We envision these digital data eventually to include the entirety of analog data that are associated with a particular specimen. This may include but is not limited to: textual data from labels and ledgers associated with specimens, images of specimens, DNA and other 'omics, field notes, images, tomographic imaging data, specimen history (including preservation), and specimen-associated literature. Digitizing might be accomplished by collections managers, technicians, contractors, and other entities, the results of which are included within the institution’s collection management system. In many instances these data may be generated off site by investigators.
  
 
==Contributors==
 
==Contributors==
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Content generated during The American Society of Ichthyologists and Herpetologists (ASIH) Annual Joint Meeting - 2016, during an iDigBio sponsored workshop by the following individuals participating in the "Digitization" working group of the aforementioned workshop:
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Current content contributors: SPNHC members Breda Zimkus, Jessica Cundiff, Genevieve Tocci, Nicole Fisher, Deborah Paul, and you.
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[[Media:Digitization_Workshop_ASIH_2016|Original digitization page content]] now found [[Media:Digitization_Workshop_ASIH_2016|here]] was generated during The American Society of Ichthyologists and Herpetologists (ASIH) Annual Joint Meeting - 2016, during an iDigBio sponsored workshop by the following individuals participating in the "Digitization" working group of the aforementioned workshop:
  
 
*Gil Nelson - Florida State University, Courtesy Faculty
 
*Gil Nelson - Florida State University, Courtesy Faculty
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*Gregory Watkins-Colwell - Yale Peabody Museum - Herps and Fishes, Collection Manager
 
*Gregory Watkins-Colwell - Yale Peabody Museum - Herps and Fishes, Collection Manager
  
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===iDigBio’s workflows for digitization===
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== Digitization ==
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iDigBio, the U.S. National Science Foundation’s national resource for facilitating and enabling collections digitization throughout the United States has developed several sets of digitization workflows (including transcription and imaging) for various disciplines and preparation types, including fluid-preserved specimens. These workflows are the product of several working groups and workshops and are publically available at:
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===Data Aggregation===
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https://www.idigbio.org/content/workflow-modules-and-task-lists#spirits
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:ALA
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:BISON
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'''Drafts of revisions of workflows for making digital photographs of specimens:'''
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:CRIA
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:iDigBio
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https://drive.google.com/drive/folders/0B9zqKK80tdzhUFhmUW9KeUxkRWc
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:GBIF
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:VertNet
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https://docs.google.com/document/d/1mk2Hu6agItvhfNq9dkt2cAYbhIO_qdgyfAXOelVrQ6w/edit
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===Six task clusters of digitization===
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''Foundation for above workflows''
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1. Predigitization Curation
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*locating specimens
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*checking determinations (nomenclature) and other information in database
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*Insert institutionally and/or globally unique identifiers for specimens.
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*transferring specimens to work station
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2. Data Entry 
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*Transcribing label data into an electronic database.
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3. Imaging and other media
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*Recording digital representations
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*2D photographs
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*3D tomographic images such as CT, MRI and PET scanning
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*audio recordings
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*video recordings
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4. Image processing
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5. Georeferencing
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*Specialized Georeferencing Tools: https://www.idigbio.org/wiki/index.php/Georeferencing#Specialized_Georeferencing_Tools
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*iDigBio Georeferencing Working Group-Georeferencing Community Protocols and Workflows: https://www.idigbio.org/wiki/index.php/Georeferencing#Georeferencing_Community_Protocols_and_Workflows
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*Georeferencing Quick Reference Guide: http://manisnet.org/GeoreferencingQuickReferenceGuide.pdf
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*A guide to the best practices for georeferencing biological species written by the BioGeomancer Consortium: http://www.gbif.org/resource/80536
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6. Data mobilization
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By data mobilization we mean contributing your data and media to a designated aggregator (e.g. iDigBio, GBIF, VertNet) via a protocol similar to GBIF’s Integrated Publishing Toolkit. These data are then integrated with data from many institutions to ensure research and other access to more complete datasets. Examples include:  
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===Data Management===
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*https://www.idigbio.org/sites/default/files/DataIngestionGuide.pdf
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:[https://dataoneorg.github.io/Education/ DataONE]
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*https://www.idigbio.org/wiki/images/9/92/SantaBarbaraData.pdf
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===Data Standards and Mobilization===
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:links to be added
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:links
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:Darwin Core Hour
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===Data Transcription===
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:iDigBio
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:DataONE
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links to be added
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===Database Software===
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:ARCTOS
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:Axiell EMu
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:Collection Space
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:Past Perfect
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:Specify
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:Symbiota
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===Georeferencing===
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:georeferencing.org
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:iDigBio georeferencing resources
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:Biogeomancer Guide to Best Practices
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:GEOLocate
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===iDigBio Digitization Resources Wiki===
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===Imaging and Media===
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:2D
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:CT
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:3D
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:Other
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:[https://www.idigbio.org/biblio?f[search]=imaging iDigBio Biblio search = imaging]
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===Literature and Papers===
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:5 Task Clusters
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:links to be added
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::ask Shari Ellis at iDigBio(iDigBio Biblio?, Mendeley?, …)
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:other?
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:[https://www.idigbio.org/biblio?f[search]=digitization iDigBio Biblio – search ="digitization"]
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===Webinars===
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:iDigBio Webinars
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:[https://github.com/tdwg/dwc-qa/wiki/Webinars Darwin Core Hours]
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:Paleo Webinars
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:http://smallcollections.net/tags/webinar-recordings SCNet Webinars}
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…
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Workflows
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[link] Discipline specific materials at iDigBio
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Workshops and Symposium
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idigbio workshops https://www.idigbio.org/wiki/index.php/IDigBio_Workshops
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SPNHC-sponsored ASIH Workshop 2016
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?relevant GBIF workshops
  
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===Adam Summers workflow for CT scanning===
 
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Bullet list of how I get many specimens scanned at the same time:
 
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https://docs.google.com/document/d/1mMvCIee4uIVqaDEgc6vSsljRdx60wTwNECAIvwWdHFs/edit
 
  
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Adam’s example of a lot of data associated with specimens:
 
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https://osf.io/ecmz4/wiki/Fishes/
 
  
 
==Links==
 
==Links==

Revision as of 22:36, 20 August 2018

Statement of Purpose

Realizing the import of collections, SPNHC recognizes the need to collaborate to develop, discover, disseminate and update best (better, current, recommended) practices for creating digital collections resources and publishing them for global access. Materials linked here represent the efforts of many collections data mobilization projects worldwide. All in the collections community are encouraged to contribute.

Page - IN Development. Please contribute.

Defining Digitization

In the context of the SPNHC wiki 'digitize' means converting ALL analog data to digital data according to standard vocabularies such as DarwinCore and AudubonCore. That is, we start with the concept of a specimen that has been accessioned in a collection. We envision these digital data eventually to include the entirety of analog data that are associated with a particular specimen. This may include but is not limited to: textual data from labels and ledgers associated with specimens, images of specimens, DNA and other 'omics, field notes, images, tomographic imaging data, specimen history (including preservation), and specimen-associated literature. Digitizing might be accomplished by collections managers, technicians, contractors, and other entities, the results of which are included within the institution’s collection management system. In many instances these data may be generated off site by investigators.

Contributors

Current content contributors: SPNHC members Breda Zimkus, Jessica Cundiff, Genevieve Tocci, Nicole Fisher, Deborah Paul, and you.

Original digitization page content now found here was generated during The American Society of Ichthyologists and Herpetologists (ASIH) Annual Joint Meeting - 2016, during an iDigBio sponsored workshop by the following individuals participating in the "Digitization" working group of the aforementioned workshop:

  • Gil Nelson - Florida State University, Courtesy Faculty
  • Larry Page - The Florida Museum of Natural History, Ichthyology Curator
  • Cristina Cox-Fernandes - UMass Amherst Biology, Adjunct Research Associate Professor
  • Mark Sabaj - ANSP, Ichthyology Collection Manager
  • Adam Summers - University of Washington, Professor - Friday Harbor Labs
  • Kevin Love - iDigBio, IT Expert
  • Ken Thompson - Lock Haven University, Professor (Retired)
  • Randy Singer - Florida Museum of Natural History
  • Gregory Watkins-Colwell - Yale Peabody Museum - Herps and Fishes, Collection Manager

Digitization

Data Aggregation

ALA
BISON
CRIA
iDigBio
GBIF
VertNet

Data Management

DataONE

Data Standards and Mobilization

links to be added
links
Darwin Core Hour

Data Transcription

iDigBio
DataONE

links to be added

Database Software

ARCTOS
Axiell EMu
Collection Space
Past Perfect
Specify
Symbiota

Georeferencing

georeferencing.org
iDigBio georeferencing resources
Biogeomancer Guide to Best Practices
GEOLocate

iDigBio Digitization Resources Wiki

Imaging and Media

2D
CT
3D
Other
[search=imaging iDigBio Biblio search = imaging]

Literature and Papers

5 Task Clusters
links to be added
ask Shari Ellis at iDigBio(iDigBio Biblio?, Mendeley?, …)
other?
[search=digitization iDigBio Biblio – search ="digitization"]

Webinars

iDigBio Webinars
Darwin Core Hours
Paleo Webinars
http://smallcollections.net/tags/webinar-recordings SCNet Webinars}

… Workflows [link] Discipline specific materials at iDigBio Workshops and Symposium idigbio workshops https://www.idigbio.org/wiki/index.php/IDigBio_Workshops SPNHC-sponsored ASIH Workshop 2016 ?relevant GBIF workshops


Links

Consensus Documents

Community Standards

Review Documents

References

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