How To Guides

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This guide is intended to help data providers develop digitization workflows for fossil specimens using Symbiota.

Introduction

Digitization workflows for fossil collections

In the context of this guide and other Knowledge Hub documentation, “digitization” is act of translating and capturing metadata describing a physical specimen into a digital form (Nelson & Ellis, 2018). It can encompass tasks related to cataloging, georeferencing, and imaging.

Many paleontological collections are highly heterogeneous in nature–taxonomically, geographically, geologically, and physically. That is, one collection might contain both long-extinct and geologically recent organisms and their traces, including vertebrates, invertebrates, and plants of varying sizes and shapes and in various states of physical preparation.

Careful planning is necessary to efficiently digitize fossil specimen data in paleontological collections, and workflow development a critical part of this process. By designing and streamlining a thoughtful digitization workflow, you can maximize your collection’s visibility and application for research and educational use, in turn generating further justification for its ongoing maintenance to administrators, prospective funders, and other potential stakeholders.

Where to start

Start by defining the goal of your digitization workflow. For instance, do you need to capture specimen records for a specific research project, or is your aim to document core specimen data to make your collection more discoverable? Defining the end goal will allow you to prioritize various workflow elements and digitization tasks given the nature of your collection and its available resources. The content in this guide is designed to facilitate the creation of workflows that output discoverable, interoperable data in the context of the Paleo Data Ecosystem.

Symbiota software is particularly well-suited to is enabling flexible digitization workflows to quickly increase the digital presence of your collection, for example, by facilitating the creation of skeletal specimen records that can be iteratively improved upon as time and resources allow. The content in this guide is tailored to data providers who wish to create Symbiota-based digitization workflows and is intended to be read in parallel with the Knowledge Hub’s various Symbiota how-to guides and related content.

Workflow components

Cataloging

Sometimes “cataloging” is used interchangably with “trasncription” and “databasing”.

Because data transcription inherently involves judgement calls, and not all label data can be accurately represented using existing data standards, imaging specimen label images is recommended whenever possible.

Georeferencing

Georeferencing can be defined as “the process (verb) or product (noun) of interpreting a locality description into a spatially mappable representation using a georeferencing method” (Zermoglio et al., 2020). Georeferencing can be a signficiant component of a digitization workflow; for example, it is often required to assign geographic coordinates to historically collected specimens. Symbiota portals contain a number of built-in tools to facilitate georeferencing on a record-by-record basis, in batch, or collaboratively. Many resources exist that explain georeferencing and how related tools work in Symbiota portals.

Symbiota-specific resources

General georeferencing resources

Imaging

When resources allow, basic 2D digital photography can be highly beneficial to digitization workflows. Some reasons to integrate specimen and label photography into your digitization workflow include:

  • To document your specimens at time of digitization and provide reconaissance images to data users (e.g., researchers), who may then request additional or more detailed specimen images.
  • To facilitate data transciption from specimen label text, which can be completed without additional specimen handling and, when appropriate, remotely via the portal’s interface.
  • To capture verbatim specimen label text, some of which may be difficult to accurately represent using the fields currently available using Symbiota and the Darwin Core data standard.

2D images (e.g., photographs) can be displayed directly in a Symbiota portal, whereas 3D imagery (e.g., surface scans) should be maintained in an external repository/database, such as MorphoSource. In the latter case, links can then be created between your specimen records in Symbiota and the external respository using Symbiota’s resource linking tools.

Reminder: All media files (including images) associated with specimen records where Location Security has been applied will be redacted from public viewing. Users with Administrator permissions can give select individuals read-only “Rare Species Reader” permissions to view media (and all other locality data) associated with a given collection through the Administration Control Panel > Manage Permissions.

Image hosting

If your organization opts to associate media (images or audio) alongside its specimen records in a Symbiota portal, images files can be hosted externally by your institution or with help from the Symbiota Support Hub (SSH). If you would like the SSH to host your images, please contact the SSH Help Desk. The SSH can facilitate batch image ingestion (e.g., to create skeletal catalog records). Fees may apply for SSH-faciliated image hosting, which is currently limited to web-ready files (JPEG format, <10 MB/file). New Symbiota users are strongly encouraged to review related documentation in Symbiota Docs.

Example workflows

📬 Questions? Data providers are encouraged to contact paleoinformatics@gmail.com for assistance with questions related to developing a digitization workflow for fossil collections using Symbiota. Include “Symbiota” in the subject of your email, e.g. “Help with developing a workflow for my fossil collection using Symbiota”.

External resources

Introduction to Biodiversity Specimen Digitization: Elements of Digitization Workflows

Lesson developed as part of a course, Introduction to Biodiversity Specimen Digitization, offered by the iDigBio Digitization Academy with the goal of introducing the creation of digital data about biodiversity specimens to those who are just beginning this activity.