Difference between revisions of "Digitization"

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===Data Standards and Mobilization===
 
===Data Standards and Mobilization===
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To share our respective datasets, the data must be '''mapped''' to a single set of terms and concepts. By doing this, we can aggregate data into one searchable resource. It's rather similar to agreeing on a common language. Our collections community currently uses both [https://dwc.tdwg.org/ Darwin Core] and [https://github.com/tdwg/abcd Access to Biological Collections Data (ABCD)] to share biodiversity data. European collections use ABCD more often that Darwin Core. Current discussions are underway to work on merging these standards. Note that [https://dwc.tdwg.org/ Darwin Core] is a widely adopted standard for biodiversity data sharing. It was developed by the organization Biodiversity Information Standards (TDWG; historically known as the Taxonomic Databases Working Group) in 2009. A number of resources exist for its use:
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To share our respective datasets, the data must be '''mapped''' to a single set of terms and concepts. By doing this, we can aggregate data into one searchable resource. It's rather similar to agreeing on a common language. Our collections community currently uses both [https://dwc.tdwg.org/ Darwin Core] and [https://github.com/tdwg/abcd Access to Biological Collections Data (ABCD)] to share biodiversity data. European collections use ABCD more often that Darwin Core. Current discussions are underway to work on merging these standards. [https://www.tdwg.org/standards/ac/ Audubon Core (AC)] standard provides a common language for sharing information about media (2D, 3D, etc.). Note that [https://dwc.tdwg.org/ Darwin Core] is a widely adopted standard for biodiversity data sharing. It was developed by the organization Biodiversity Information Standards (TDWG; historically known as the Taxonomic Databases Working Group) in 2009. A number of resources exist for its use:
 
* [https://www.gbif.org/darwin-core What is Darwin Core, and why does it matter?]
 
* [https://www.gbif.org/darwin-core What is Darwin Core, and why does it matter?]
 
* [https://dwc.tdwg.org/terms/ Darwin Core quick reference guide]
 
* [https://dwc.tdwg.org/terms/ Darwin Core quick reference guide]

Revision as of 21:59, 9 April 2019

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 and standards community are encouraged to 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:

  • Text 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)
  • Specimen-associated literature
  • Collection-level metadata

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.

The process of digitization has been analyzed by Nelson et al. (2012), and five task clusters that comprise the digitization process leading up to data publication have been identified:

  1. Pre-digitization curation and staging
  2. Specimen image capture
  3. Specimen image processing
  4. Electronic data capture
  5. Georeferencing locality descriptions

We expect these groupings to change over time as standards of practice for digitization processes and procedures evolve. For example, it makes sense to add Data mobilization as a task cluster, as after data capture in a local database, the data need to be shared outside the local database.

Contributors

Current content contributors: SPNHC members Breda Zimkus, Jessica Cundiff, Genevieve Tocci, Nicole Fisher, and Deborah Paul. We hope that others will add their names to this list as information is added and updated.

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), and Gregory Watkins-Colwell (Yale Peabody Museum, Herps and Fishes, Collection Manager).

Digitization Resources

Data Aggregation

Data mobilization (getting the data out of your local collection management database) involves contributing data and media to a designated aggregator/s. These data are then integrated with data from other institutions to provide access to more complete datasets. The aggregation resource scope may be taxonomic-focused (e.g. SCAN), organization or institution-based (e.g. C. V. Starr Virtual Herbarium), regional (e.g. SEINet), national (e.g. the Atlas of Living Australia), global (e.g. GBIF), or otherwise. Aggregating data offers collections unique opportunities to enhance collections data, facilitate discovery, and increase re-use. The following resources introduce the aggregator's point-of-view and what to expect.

Data Aggregators

Natural history collections commonly contribute to these data aggregators:

Data Management

Data Mobilization

Consider what needs to be done to get data out of a local collections database and into one or more other online resources. Some of the other categories on this wiki page that relate to this topic are data standards, data management, data aggregation, and workflows. Sharing data is often a cyclic process. Once shared, aggregators provide feedback and collections staff need to evaluate which items to address and how. After updates, data can be published again, with the enhancements.

Data aggregators often differ somewhat in what they expect collections data to look like to simplify aggregation. Overall, the community is moving toward shared aggregation practices. For example, most aggregators today accept darwin core archives (i.e. zippped text files in a specific format) for ingestion.

In the process of preparing to share data, there are many known issues to consider. Have a look at the iDigBio Data Ingestion Guidance for an idea of the scope of the issues. Some overall topics that will come up include:

  • globally unique identifiers
  • collection-level metadata
  • data quality issues (e.g. date formats, missing higher taxonomy, geo-coordinate issues,...)
  • rights information (e.g. Creative Commons licenses for images)

Data Standards and Mobilization

To share our respective datasets, the data must be mapped to a single set of terms and concepts. By doing this, we can aggregate data into one searchable resource. It's rather similar to agreeing on a common language. Our collections community currently uses both Darwin Core and Access to Biological Collections Data (ABCD) to share biodiversity data. European collections use ABCD more often that Darwin Core. Current discussions are underway to work on merging these standards. Audubon Core (AC) standard provides a common language for sharing information about media (2D, 3D, etc.). Note that Darwin Core is a widely adopted standard for biodiversity data sharing. It was developed by the organization Biodiversity Information Standards (TDWG; historically known as the Taxonomic Databases Working Group) in 2009. A number of resources exist for its use:

Data Transcription

Transcription is an essential part of the digitization process but can pose a number of challenges:

Database Software

Those curating natural history collections are currently using a number of different platforms to track data:

Georeferencing

A number of resources pertaining to the process of georeferencing, defining a location using map coordinates and assigning the coordinate system of the map frame, are available:

iDigBio Digitization Resources Wiki

  • The iDigBio Digitization Resources wiki page provides resources and information regarding digitization, including training workshops being conducted by iDigBio, digitization information and resources, and links to documents, websites, videos, presentations, and other important information related to biological collection digitization.

Imaging and Media

A number of techniques are available for two-dimensional (2D) and three-dimensional (3D) digitization, including X-ray computed tomography (CT):

Key References and Further Reading

  • Nelson, G., D. Paul, G. Riccardi, and A.R. Mast. 2012. Five task clusters that enable efficient and effective digitization of biological collections. Zookeys 209:19-45. [1]
  • Vollmar, A. J.A. Macklin, and L.S. Ford. Natural History Specimen Digitization: Challenges and Concerns. 2010. Biodiversity Informatics 7:93-112. [2]
  • ZooKeys Special Issue (No specimen left behind: mass digitization of natural history collections (2012)
  • Search iDigBio for all available digitization materials

Webinars

Access to various webinars regarding digization is available:

Workflows

Various general and discipline-specific materials regarding digitization are available via iDigBio:

Workshops and Symposia

A number of workshops and conference symposia have focused on the subject of digitization:

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