Speciforum 2021 Abstracts

Additional information and abstracts for Speciforum talks.

Session 2: Workflow Stories and Solutions


The Collection Record Set at the Bailey-Matthews National Shell Museum, Sanibel, Florida

José H Leal, PhD, Bailey-Matthews National Shell Museum
Interim Director & Curator

The Bailey-Matthews National Shell Museum was officially dedicated in November 1995. Its collection consists of about 130,800 lots of dry-shells and wet-preserved mollusks. He collection is fully digitized; presently, the number of catalogued lots is about 130,800. It has been classified as a “Medium–Large” molluscan collection according to today’s standards. These records were cataloged in Microsoft Access, and in 2018 we migrated the record set to Specify 7 (Cloud Version). In this presentation I’ll discuss some interesting challenges we faced during and after our migratory journey.”


Digitizing Amber collections – Challenges & Solutions

Fedor Steeman, Danish Natural History Museums

The Baltic sea has always been a rich provider of amber. As a former branch of the ancient Tethys sea and Eridanos river, it was a natural repository for deposits of the former Fenno-Sarmatian landmass, where coniferous forests thrived during the Eocene. Later transport during more recent Ice ages has further added to this age-old treasure trove. For thousands of years, amber pieces were a valued commodity of which trade reached far beyond the shores of Northern Europe they wash up on. Many modern day collectors continue to stock up thousands of these primeval relics. In 2018, the museum received a huge collection from private collector Karin Nordmann Ernst, which were special in that many of them appeared to contain the remains of Eocene life forms, mainly insects. After funding was secured, the museum employed Sree Gayathree Selvantharan who has been diligently cataloguing and digitizing these 58.0000 specimens for many years now. As this projects is nearing its close, many challenges have been tackled but several still remain for the post-digitization process. Among these can be mentioned the fact that many pieces contain more than one individual, sometimes spanning widely diverging taxonomic groupings. Another conundrum is the need to document the occurence of non-biotic or even anorganic inclusions such as sediments and air bubbles. These posed many dillemas for the choice of discipline and its taxonomy with repercussions from everything to classification to labels. Under discussion will be preliminary solutions and perspectives for future expurgating of this invaluable source of high scientific significance.

Development of Specify installation for the Biological Collections Portal of Western Siberia (Russia)

Nina Filippova, Yugra State University

Specify was used since 2015 in Yugra State University (YSU) for management of the YSU biological collection data (mainly two collections of fungi and mosses). Currently the installation on YSU server includes Specify 6, Specify 7, Attachment server and Web Portal. Yugra State University has become an associate member of the Consortium since 2020.

Since 2018 we initiated a regional program for biological data digitization and mobilization. The Specify installation has been developed to accommodate other regional collections, including Universities, Nature Protected Areas and private collections. The Specify installation is prepared to serve different collections structure and needs. We started training workshops to teach potential users and prepare Russian localisation, as well as translation of video-instructions and manuals. This activity is shared with the Russian Specify working group, which includes other two research organizations using Specify in Russia.

Our mission is to promote Specify in Russia and the Yugra region to provide contemporary tools for biological collections data management.

Our goals include:

1) development of a regional Specify installation for management of different types of collections data
2) establishing a Russian working group for promotion of Specify at national level
3) development of Specify for ‘sampling event’ data format of Nature Protected areas monitoring data
4) providing educational materials and support for potential users and newcomers
5) communication with Specify Collections Consortium for further product development

Web site of the regional initiative for biodiversity data digitization and mobilization: https://nwsbios.org/

Specify Web Portal installation on YSU server, including 6 collections currently uploaded: https://nwsbios.org/

Quality Control Quality Assurance Workflows in Specify

Sarah Huber, Virginia Institute of Marine Science (VIMS)

The VIMS Nunnally Ichthyology Collection began using Specify 6 to manage collection records in 2015. Prior to this date, records had been digitized into Microsoft Access and then transferred to an in-house database in 2008. Previous digitization was incomplete, with over 80% of records with incomplete or missing collecting event data. Specimen records were imported into Specify 6 through the workbench. In 2017, we transitioned to Specify 7 exclusively for database management. This year, the covid pandemic has necessitated remote work, and I have begun the process of Quality Control Quality Assurance for specimen records that were originally uploaded with incomplete data. In this talk I will discuss workflows for doing QAQC of collection records through Specify 7.


Workflows for a TCN in Specify7

Paul Larson, Florida Fish and Wildlife

This talk will be about the workflow we will be using to get data into Specify through the workbench for the DigIn TCN and the Mobilizing Millions of Marine Mollusks TCN – especially addressing the data cleaning and formatting issues that can result in unexpected cleanups after the data is uploaded into the database.


TCN participation and Specify: Drawing Closer?

Richard K. Rabeler, Garth Holman, Brad Ruhfel, Erika M. Tucker

The University of Michigan Museums has been a participant in 12 Thematic Collection Networks (TCNs) since 2012; four are currently active and two new projects will be starting soon. This talk will focus on workflows that we have created for three of these projects using Specify 6/7 for both creating new records and enhancing existing records within Specify. We also will be touching on current efforts to incorporate crowdsourcing and for reconciling Specify records that have been enhanced within a Symbiota portal during an earlier TCN project.


Exporting data for GGBN using Specify 7

Andy Bentley, University of Kansas

Exporting data to aggregators is key yo increasing exposure of your collection and its data to the many end-user communities that intend to use that data. Darwin Core provides a structure for exporting that data in a standardized format to most of the common aggregators. Extensions to the Darwin Core provide the utility for exporting different types of data and to specialized aggregators. One such example is the Global Genome Biodiversity Network (GGBN) for tissues and genomic data. In this demonstration I will highlight the Specify 7 publishing process as it pertains to this example including some of the benefits and pitfalls to publishing GGBN compliant data.

Session 3: Specify Out of the Box

CryoArks: challenges and successes of setting up the UK’s first national zoological biobank

Mafalda Costa1, Gill Murray-Dickson2,3, Kirsty Lloyd4, Michael W Bruford1 and the CryoArks consortium
1School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
2National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
3The Royal Zoological Society of Scotland, Edinburgh Zoo, 134 Corstorphine Road, Edinburgh EH12 6TS, UK
4Molecular Collections Facility, Natural History Museum, Cromwell Road, London SW7 5BD, UK

CryoArks is a UK-wide consortium of academic institutions, museums, zoos, and biobanks led by Cardiff University that is establishing the UK’s first comprehensive zoological biobank. This BBSRC-funded project is creating the physical and bioinformatics infrastructure needed to connect the diverse and disconnected collections of animal frozen material held in zoos, aquariums, museums, research institutes, and universities across the country. The main aim of the initiative is to make this material publicly visible and accessible to researchers and conservation practitioners. The project is also creating common quality standards among partners and collaborators, developing protocols for collection, transport, and storage of samples, producing outreach materials, and preparing operational guidelines to help the community improve the status and sustainably manage their collections. This talk will give a general overview of CryoArks and summarise the achievements and challenges faced by the project in the first two years of its existence.

Website: www.cryoarks.org


Registering specimens in the field using Specify

Diana Macpherson1, Sadie Mills1, Jill Scott1, Kate Neill1, Jane Robbins2
1National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand; 2NIWA Auckland, New Zealand

The National Institute of Water and Atmospheric Research (NIWA) Invertebrate Collection is a Nationally Significant Collection consisting of around 385,000 marine invertebrate specimen jars collected from New Zealand, Antarctic and Pacific waters from the 1950’s until now. We estimate approximately 40% of our collections are registered and digitally accessible (about 154,000 records since digital registering began in 2004), with most of our unregistered material being historical collections.

In recent years we focused on streamlining the registration of specimens in the field onboard NIWA’s research vessel Tangaroa. Our field registration and curation techniques allow us to capture data directly into a shipboard copy of Specify immediately after collection and sorting, then printing labels with a portable thermal printer onboard. At the end of the voyage, the specimen and station data are exported into an Excel file and reimported back to our home version using Specify‘s Workbench feature. This process reduces the time spent double-handling specimens and cuts the need to use paper record sheets.


Documenting Data from Remote Underwater Video in Specify

Willem Coetzer, South African Institute for Aquatic Biodiversity

Data related to physical specimens or samples are not the only kinds of records that can be accommodated by the Specify schema. Biodiversity observations (which our physical specimens are bound to become once they have deteriorated and disappeared) are fair game too, and naturally have the same properties – an event, a location and a determination. I will describe how I used the Specify workbench, database schema and data exporter application to archive and publish data from underwater photographic surveys, including still photographs of marine macrobenthos and Stereo Baited Remote Underwater Video Systems.

Session 3: Specify Extensions and Integrations

Benefits of connecting the Specify MySQL Database to Microsoft Access

Kesler Randall, San Diego Natural History Museum

Paleontologists often use faunal analyses to compare the relative abundance of species across multiple fossil localities in order to reconstruct paleoecological settings, as the common presence of certain species can be indicative of a particular environment. At the San Diego Natural History Museum, the Department of Paleontology’s collections manager worked with the Department of Botany’s database manager and the museum-wide database administrator to use the Open Database Connectivity (ODBC) standard to connect the Specify MySQL paleontology database to Microsoft Access in order to run complex queries on the data in Access. Our Botany database manager wrote code in Visual Basic for Applications (VBA) to run queries on the live paleontology database and to design user-friendly search forms in Access. This interface enables Access to perform data counts (something that cannot currently be done directly in Specify). As a result, we are now able to produce summary tables of species relative abundance across a set of localities with one click. This connection also allows data managers to directly view a read-only version of the raw back-end Specify data. Data managers have now been able to utilize “hidden” data fields like unique ID numbers to provide update query criteria to our database administrator, in order to make large batch edits to fields that are not accessible through Specify’s Batch Editor tool. Linking MySQL and Access has proven to be a powerful time-saver for Department of Paleontology staff, and may have additional uses that have yet to be uncovered.


Herbarium interactions in Specify

Catherine Gallagher, Alison Vaughan, Niels Klazenga
Royal Botanic Gardens Victoria

One of the great features of Specify is its robust handling of transactions – interactions in Specify – between collections, such as loans and exchange. Transactions is also an area where standards do not really apply and where institutions already have their own procedures in place when they migrate into a new Collections Management System. Different types of collections will have different procedures and there will even be differences between collections of the same type. At MEL, we were prepared to adapt our procedures to the database, but soon found out that the way certain aspects of the transactions were implemented in the Specify client would not work for us. Herbarium loans tend to be much larger than loans from natural history museums, so especially the way partial loan returns are done would be very tedious for our curation officers. On the other hand, herbarium loans are less varied in terms of preparation types, so we could take some shortcuts that natural history museums cannot and the Specify client will not let us. In this talk we will show some of the tools we have built around the Specify Interactions that make our processes more efficient while still adhering to the Specify data model. We will also discuss an online loan and exchange system that we will build in the near future.

Session 3: SCC Outreach, Engagements, and Meetings

People and people identifiers in Specify

Alison Vaughan, Elspeth Haston, Niels Klazenga
Royal Botanic Gardens Victoria; Royal Botanic Gardens Edinburgh

Driven by the TDWG Attribution Interest Group, projects like the Biodiversity Heritage Library (BHL) and citizen scientists, a strong interest in people and the contributions they make to biodiversity data has emerged in the TDWG community. For the Collections community, linking specimens to clearly identified people has advantages for specimen data curation and linking between different collections. In this presentation we will talk about various ways to efficiently link collectors and determiners of specimens to shareable people identifiers, how we can best store this information in Specify and how we try to store collector information in a way that reduces the disambiguation that will have to be done later on.


Taxon concepts in Specify

Niels Klazenga, Jeff Gerbracht
Royal Botanic Gardens Victoria; Cornell Lab of Ornithology

Handling of taxa is a recurring problem in biodiversity data because there is no straightforward relationship between taxa and their names. A taxon name that was put on a specimen many years ago might refer to a different group of organisms today and at any given time usages of taxon names by different people might reference different taxa. It is important therefore to provide sufficient taxonomic context with our determinations. Taxon concepts, by combining a taxonomic name with a publication where it was used – which can for example be an identification work or a national census – provide this context and provide long term resolvability. In this talk we will outline some options on how taxon concepts can be captured in Specify and exchanged in Darwin Core. We will also discuss how robust handling of taxon concepts in Specify will aid management of taxonomies in Specify and curation.