Abstract

DigIn: About 75% of the 250,000 described marine species are invertebrates, an enormously diverse, paraphyletic assemblage of over 30 animal phyla. Despite their importance, marine invertebrates remain poorly known and are poorly represented in the online databases that underlie modern biodiversity research and education. The NSF-funded Documenting Marine Biodiversity Through Digitization of Invertebrate Collections (DigIn) TCN project aims to change that by creating a robust marine biodiversity resource that will power research and education in systematics, ecology, oceanography, and other disciplines. DigIn will achieve this by digitizing and mobilizing specimen, image, and sequence data on marine invertebrates (other than mollusks) across taxa and geography. The project aims to digitize 835K lots (7.5 million specimens) from 19 collections, more than doubling current online records from non-federal collections. In addition, it will enhance records by updating nomenclature, georeferencing, and linking sequence data, will mobilize 464K images, and will make data broadly accessible through diverse outlets (iDigBio, GBIF, OBIS, etc), including the Symbiota portal InvertEBase. Specimens and associated data will be further augmented through an array of Broader Impacts activities that engage K-16 educators and the public alike. 

ESB: The Eastern Seaboard of the United States spans nearly 6,000 km of coastline and 18 U.S. states. Habitat loss, pollution, overfishing, and climate change threaten commercially and ecologically important marine species along the ESB, creating a great need for baseline data. Mollusks are among the best sampled group of animals, with some species having large numbers of records available in natural history collections making them extremely well-suited for environmental and biogeographical studies that track faunal change over time and space. This NSF-funded project, using the Symbiota platform InvertEbase, covers the ca. 3,000 molluscan species of that area. With the 18 partner institutions holding nearly 90% of known ESB material in the U.S., project aims include the digital mobilization of 4.5 million specimens through de-novo data entry and improvements, collaborative georeferencing (CoGe) with further development of GeoLocate (including layers for bathymetric data, benthic habitat, and marine conservation areas), improvements to WoRMS/MolluscaBase, and providing training and educational opportunities. For the first time, molluscan occurrence data distinguish between live- and dead-collected specimens, with a defined vocabulary for traits added to each record. Due to the long persistence of molluscan shells, the live/dead-collected distinction is crucial for all studies of biotic change using mollusks.

This talk provided an overview of the active grants, their aims, participants, and progress made to date.

Abstract

Until recently, the use cases that have guided the development of technologies to assist georeferencing primarily focused on specimens collected from terrestrial and freshwater environments. As such, marine digitization efforts have traditionally lacked sufficient resources to streamline large-scale georeferencing. The ESB and DigIn Thematic Collections Networks(TCN), both of which are focused on the digitization of marine invertebrates are utilizing the GEOLocate platform for georeferencing and have resulted in the development of numerous advancements in support of marine georeferencing, such as bathymetric mapping, complex spatial representations, and improved integrations with collection management systems.  While specifics of each workflow differ, ESB and DigIn each rely upon the Collaborative Georeferencing (CoGe) data portal within GEOLocate to define geographically-scoped datasets and distribute workloads amongst georeferencing technicians. In the case of ESB, georeferencing technicians are distributed amongst collaborating institutions while the DigIn model consolidates georeferencing activities through a single organization (Quantitative Aquatics, Inc.) with expertise in marine data and informatics. Here we present these two workflows and the recent technological advances within GEOLocate to help overcome the georeferencing challenges faced by DigIn and ESB.

Abstract

While the Santa Barbara Museum of Natural History (SBMNH) Invertebrate Zoology Collection is perhaps best known for its mollusk holdings, it also houses a large collection of non-molluscan marine invertebrates that fall under the purview of the Documenting Marine Biodiversity through Digitization of Invertebrate Collections (DigIn) grant. Notable groups in this portion of the collection include worldwide bryozoan holdings, material from Velero cruises, and deepwater material from Oregon State University collections and the Monterey Bay Aquarium Research Institute. Prior to the start of the DigIn grant in November 2020, nearly 100,000 of these non-molluscan lots had not yet been cataloged, and the majority of this material had not been looked at or updated since original acquisition. From various levels of volunteers to curators, with some individuals in between funded through DigIn, we have a team of people helping to identify, rehouse, and catalog the collection. While some taxonomic groups were cataloged remotely using specimen images and catalog scans throughout the length of COVID-19 lockdowns, the large majority of lots are entered directly with the presence of the physical specimen and original label. Nearly all cataloging is done directly into a Specify 6 database. Before starting work on DigIn, a majority of common collecting localities and stations had been previously georeferenced and in use in our database, in addition to having a relatively robust, continually updated taxonomic tree. New localities, station data, and taxonomy are entered as needed during the cataloging process to keep our process simplified. Databased records are available on our Specify Web Portal, as well as iDigBio. Both of these outlets have provided an increase in collection accessibility and interest from researchers around the world.

Abstract

The digitization of specimen data is an increasingly important priority for many nature and science museums and is a major component of both the Mobilizing Millions of Marine Mollusks of the Eastern Seaboard (ESB) and the Documenting Marine Biodiversity Through Digitization of Invertebrate Collections (DigIn) TCN grants. However, digitizing thousands of historical specimens is no small feat and requires the development of workflows that promote both accuracy and efficiency, while being flexible enough to meet the challenges presented by a large and diverse collection of historical specimens.  Thinking about MCZ’s digitization workflows for both the ESB and DigIn grants requires novel and flexible approaches. At each step of this workflow, I will examine the pros and cons of different methods and the value of adaptability in maximizing the efficiency of digitization procedures. The first step in all of these workflows involves locating uncatalogued specimens. This is a challenge especially for the ESB grant, as mollusk specimens from the Eastern Seaboard are often interspersed throughout the collection with shells collected from other localities. For the next step, data entry, I will describe how the options of record cloning, single record entry, and bulkloading allow the MCZ to adjust its digitization workflows to best utilize the time and experience of a variety of employee types and specimen groups. The value of linking entered records to searchable collectors, localities, accessions, and collecting events will also be addressed. Finally, the application of digital attributes and named groups in vetting records and tracking grant progress will be discussed. Taken together, these methods contribute to an adaptable workflow that promotes efficiency and accuracy in digitizing a variety of historical specimens, creates meaningful, searchable connections between specimen records, and produces trackable results.

Abstract

All natural history collections benefit from digitization projects, and many thematic collections network (TCN) projects include imaging as a deliverable. The imaging of DigIn-related historic type specimens at the Museum of Comparative Zoology at Harvard University provides examples and approaches to consider in any organismal imaging project.

There are a variety of organisms, conditions, and ages of specimens on the shelves but no one single solution for creating the best images in the allotted time. Starting with wet or dry preservation with marine invertebrates and adding organismal considerations help determine where to spend time and energy. The purpose of an image dictates some choices: whether to target research or collections care.

By creating high-resolution digital images, specimens can be studied remotely and there is an opportunity to reduce the need for physical handling. Additionally potential researchers get information about a given specimen or lot and whether accompanying data may be novel or erroneous.

Digital images can also be used to detect and document any specimen damage, which can inform conservation and preservation efforts. This is particularly important for specimens that may be fragile or rare as a means to document risk of deterioration. By regularly imaging and monitoring the condition of the collection, museums can ensure that the specimens are being properly cared for, and they can take steps to address any issues that may arise. This will help to ensure that these specimens are available for future research and education.

Imaging a marine invertebrate collection involves a combination of strategies. To determine which imaging techniques are most appropriate for a wide variety of marine invertebrates a collection team needs to prioritize the imaging of those specimens that are of greatest value, consult with experts and collaborators, and consider the cost and time required.

Abstract

The marine invertebrate specimen collections at the American Museum of Natural History (AMNH) are extensive, but until recently have remained largely undigitized, meaning that the specimens and their data have not been easily accessible to researchers or the public. The NSF-funded Documenting Marine Biodiversity through Digitization of Invertebrate Collections (DigIn) Thematic Collections Network (TCN) grant has provided an opportunity to digitize (database and image) the non-mollusk fluid-preserved collections at AMNH. This talk will discuss the digitization workflow of wet specimens for the project, with a focus on the bryozoan collection. Bryozoans are sessile, colonial aquatic invertebrates. Although they are distributed world-wide, they are an often overlooked phylum. The bryozoan collection at AMNH is currently made up of more than 2,500 specimen records representing all continents. The collection dates range from 1899 to 2003. Digitizing this collection will help to generate a more complete understanding of the oceans in the past, help us to understand current distributions, and make these specimens and their associated data more readily available to researchers world-wide.

Digitizing wet specimens presents different issues than dry specimens. It can take time to retrieve the labels and specimens from inside the jar, position them to be photographed and then return them to the jar. At AMNH, we use the collections management software, EMu for specimen digitization. Excel is used to upload batches of specimen images and catalog records to EMu. The images are then attached to their corresponding catalog record, which allows our volunteers to transcribe verbatim collection labels from the images directly into EMu. Digitizers then fill in the collection details in their respective fields. Some labels can be challenging to transcribe and interpret, so having images of the collection label online is important because it permits people to view the original content and format of the label. This workflow allows for the efficient transfer of information from the specimen jar to our online database.

Abstract

To exemplify the wide diversity of collections, workflows, and data involved in digitizing marine invertebrate collections by the DigIn and ESB TCNs, this joint presentation describes three specific challenges across collaborating institutions. First we explore how the Museum of Comparative Zoology (MCZ)’s Malacology Collection is approaching ESB across staff, then we consider practices for accurately digitizing collector-specific specimens. Finally we examine a diversity of DigIn approaches that the California Academy of Sciences Invertebrate Zoology (CASIZ) Collection is using to capture label data from historical collections.

The Malacology Department at the MCZ includes a team of staff digitizing the Mollusks of the Eastern Seaboard (ESB). Spanning 2020–2024, this project seeks to locate, digitize, and georeference 7,500 lots, as well as produce photographs of the primary types relevant to ESB. To hit our targets, with a pandemic intruding in the middle of our efforts, we have adapted our efforts to mobilize data and collaborate, both internally at the museum and externally, with our grant partners. Working to achieve numerous goals of finding, databasing, georeferencing and photographing specimen lots, our team promotes best practice standards and troubleshoots problems along the way. The people and processes behind museum specimens are the cornerstone to a successful project.

As an example ESB workflow, in the summer of 1944, the MCZ partially funded the Burry-Foster Expedition led by Leo A. Burry. Burry and his colleagues collected thousands of mollusks off Key Largo and other lower Florida Keys. As of September 2022, over 2,000 uncatalogued lots of the total 3,000+ lots collected during this expedition were scattered throughout MCZ’s malacology collection. Databasing Burry’s collection serves as a use case of the process and difficulties of digitizing specimens from a single collector. In particular, this workflow highlights practices to minimize erroneous data entry in order to best support future curatorial and research work.

As DigIn TCN collaborators, the CASIZ Collection targeted nearly 60,000 non-molluscan lots to digitize across dozens of phyla, many with aging handwritten labels bearing cryptic field numbers and outdated taxonomy. To maximize workflow efficiency we capture existing taxonomic determinations, eliminating the need for specimen labeling and reorganization. Building a complete taxon tree based on our taxonomic authority (WoRMS) ahead of the project permits valid digital name capture for each record. Rich skeletal specimen data are transcribed to spreadsheets, which are checked and augmented by staff, then run through a script to populate valid higher taxonomy before import to Specify. Other labels are scanned with document scanners, tagged with GUIDs and QR codes, then transcribed by volunteers. While working exclusively remotely (2020-2021), we also crowdsourced transcription of label catalog cards via a Zooniverse - Notes from Nature project, Invertebrate Time Machine.

Abstract

The study of marine biodiversity is a critical aspect of understanding the diversity and distribution of life in the oceans. However, documenting and understanding this biodiversity is a challenging task, particularly when it comes to invertebrates, which constitute the majority of marine life. The DigIn TCN project is an ambitious NSF-funded initiative aimed at digitizing and standardizing marine invertebrate collections from 19 collaborating institutes in the U.S. The project aims to provide a comprehensive and standardized representation of global marine invertebrate specimens, covering a diversity of taxa from 30 phyla and more than 150,000 species.

One of the main challenges of the project is the combination of data from heterogeneous collection practices, standards, volumes, collection management systems, and information technology expertise. The project is also facing challenges in standardizing nomenclature across different institutions and in integrating data from different sources. The project is following the Darwin Core standard to ensure that the data can be easily integrated, shared, and reused by the scientific community.

The DigIn is a significant step forward in understanding and documenting marine biodiversity, and it will provide a valuable resource for researchers, conservationists, and policy-makers. The project will publish the final dataset on iDigBio and GBIF, making the data available to a global audience, ultimately contributing to a better understanding and conservation of marine biodiversity, which is essential for the sustainability of our oceans.

Abstract

Mollusks are ecologically diverse and have a robust fossil record making them well-suited for research examining faunal change over time and space. There are over 100 million individual mollusk specimens in US natural history collections, with an average of 1,100 specimens per species.  Collections are currently standardizing taxonomy, expanding and improving georeferencing, and taking photographs of holdings to expand and improve the amount and quality of data available for research.  

Historically, mollusk photography has focused on high-quality images of characters required for identification. Providing standardized views with carefully aligned specimens minimizes measurement error but increases handling time.  Consequently, far fewer specimens are photographed than are available in collections.  Finding ways to increase the number of individuals photographed while minimizing the potential for measurement error will expand the reach of digital natural history collections and encourage their use in course-based undergraduate research experiences (CUREs).  

Here, we discuss ways that digitized data records are currently being used in CUREs developed through the Biological Collections in Ecology and Evolution Network (BCEENET).   We present a photography setup and workflow that maximizes the number of specimens photographed while providing sufficient quality for taxonomic identification.  Finally, we compare measurements of shell length and width taken on images with those taken from physical specimens.  

Abstract

Utilizing museum collections can help students evaluate evidence in primary sources, develop skills in visual and contextual analysis, as well as collect and examine raw data. Students are often, however, only exposed to specimens and artifacts on display. Inviting educators into museums enhances understanding of local biodiversity, the role of natural history museums, and collections-based research questions…all while providing an opportunity for collaboration in integrating resources from museums into course plans across disciplines and grade levels. 

In June 2022, the Natural History Museum of Los Angeles County (NHMLA) co-hosted a K-12 Educator Workshop with California State University at Dominguez Hills (CSUDH). DigIn researchers and affiliates from NHMLA, along with two lead teachers, designed a four-day workshop focused on introducing teachers to local scientists and resources for scientific exploration. Workshop participants were tasked with producing lesson plans or units that made use of the resources to which they were introduced over the course of the week. These lessons focused on blending content with practice in alignment with the Next Generation Science Standards (NGSS) in order to encourage students to develop the habits and skills that scientists and engineers use in day-to-day life. Elements of the workshop were designed to be local and/or easily accessible, e.g., through online video conferencing while also being modifiable to DigIn partners and their own local educators around the country. We plan to use this model at educator workshops in 2023 and 2024. During these years, DigIn researchers around the country and educators local to them will attend the workshop together to create and expand partnerships between collections-based institutions and schools.

Abstract

Wet-preserved marine invertebrate collections are some of the most difficult collections to digitize. Most marine invertebrate specimens are small, fluid-preserved, and stored in glass vials with abbreviated or handwritten specimen labels, and often are combined in larger containers. We would make the argument that this is an even greater challenge than the proverbial “snakes in a jar” saying that collections staff know all too well. The number of marine invertebrate specimens in U.S. collections is estimated to be over 4,268,781 lots, and their complicated preservation methods have until now hindered data accessibility. The scale and difficulty of this task necessitates the investment in developing novel high-throughput data capture workflows that will work on these heterogeneous and large collections. At this scale, every additional moment spent digitizing each specimen translates to other specimens that will not be digitized at all. Our guiding principle for workflow development is that removing steps is almost always the best way to make data capture faster and more efficient. We will illustrate this with examples of workflows comparing the strengths and weaknesses of different methods for capturing data. These approaches include photography of labels for later transcription vs. directly entering data from the label into spreadsheets vs. custom-design database layouts with lookup, auto-predict, and data validation.  

Abstract

In the era of digitization, data dissemination, and the extended specimen network, the people behind these efforts are the cornerstone of museum success. This talk examines overall TCN management, institutional team approaches, and social media outreach.

A core team has gathered; common goals are refined; and great effort is put into gathering institutions large and small. Nineteen collections from across the US write a NSF-TCN proposal to database and make available 835k specimen lots (representing 7.5 million specimens), mobilize 464 images of marine invertebrate specimens, and make extended specimen data broadly accessible online through diverse aggregators. You promise to establish best practices for field-to-digitization workflows. You will unify a marine invertebrate collections community. You will develop tools and resources for training and outreach. The team is ambitious.

OMG your proposal gets funded!! Now what? Reality sets in. You are in the thick of COVID. How do you organize yourselves locked away from your specimens, labs, students, with no helpers of any kind? We’ll take you on a journey of solutions for organizing communications, developing working groups and workflows, reporting, outreach, having fun, and more.

Institutional teams problem solve to make the magic happen. The PRI collection houses already-processed bulk samples of mollusks with reliable live-dead trait data from the Atlantic and Gulf Coasts of the United States, including those collected from the Historical Oyster Body Size Program, Research Experience for Undergraduates, and graduate student research. As of January 2023, PRI has digitized over 2,700 previously uncatalogued lots, comprising 75,000 specimens. The live-dead samples we are digitizing can be used to define baselines to compare conditions before and after disturbance, detect recent natural and anthropogenic environmental changes, elucidate historical ranges of variability, and set targets for restoration. These baseline data are a useful tool for guiding management, planning, and restoration efforts.

Now take what we do public. Social media, particularly Twitter, has become a popular and efficient tool to disseminate information within and beyond scientific communities. When used intentionally, social media can strengthen collections communities through the collaborative process of creating, employing, and maintaining a central message to an online audience.

But a coherent and consistent social media campaign doesn’t naturally flow out of a consortium of 19 institutions. The DigIn team constructed a workflow that requires minimal time from contributors (busy curators, collection managers, and digitizers) to produce engaging and informative content efficiently and regularly. This allows the DigIn community to take a public role as an informative and relatable source for specimen and marine invertebrate collections information.