ORCIDs and Arctos

by Teresa J. Mayfield-Meyer

ORCID is an alternate address in Arctos. 

What’s an ORCID? ORCID provides a persistent digital identifier that distinguishes you from every other researcher and supports automated linkages between you and your professional activities ensuring that your work is recognized. An ORCID is also one of the ways to get your name into to Bloodhound which will use your ORCID or Wikidata entry to claim the natural history specimens you collected or identified, track their use in new science, and help acknowledge your peers, mentors, and organizations (even outside of Arctos). ORCID’s were used in Ozymandias, a 2018 GBIF Ebbe Nielsen Challenge prize-winning project which lets people explore millions of relationships to investigate a particular species, the range of a researcher’s activities or the research output associated with a particular institution. Find out more about ORCID by visiting https://orcid.org/.

If you already have an ORCID, please edit your Arctos Agent record and add it. Don’t have an ORCID? Get one! ORCID is becoming the accepted place for biodiversity data aggregators to suss out agent names. Including your ORCID in your Arctos Agent profile will make you and your work more discoverable.

You’ve got GenBank Submissions!

by Teresa J. Mayfield-Meyer

Arctos has a tool that can help you find GenBank submissions to which you haven’t linked your specimens. From the main menu select Reports/Services>Find Low-Quality Data>GenBank Discovery Tool.

GenBank Discovery Tool is a script that periodically crawls GenBank looking for sequences that may be related to Arctos specimens and which do not already have an Arctos LinkOut (newly-linked may continue to appear in the table for a few days).

The results are displayed in a table for ALL Arctos collections and show counts of potential specimen records that are in GenBank but not in Arctos. Scroll down to find your collection(s). This example shows UMNH before we checked the report and added GenBank links.

Click the open GenBank link next to the collection of interest, and you will be rewarded with a list of GenBank records which potentially reference your specimens. You can download the list by selecting Send to.

In the pop-up select Complete Record, File, and Summary format, then Create File.

Use Notepad to open the file. You can then copy the text in the file, paste it to an Excel workbook, and with a little manipulation, create a file that can be used with the Identifiers/Relationships Bulkload Tool to get the GenBank IDs added to your specimen records.

Denver Museum of Nature & Science’s Phyllis Sharp on WoRMS

Until recently, Arctos members could select either Arctos Plants or Arctos (everything else) as their Taxonomic Source.  Beginning December 2018, we uploaded the entire database of the WoRMS – the World Register of Marine Species (http://www.marinespecies.org) – as an additional Source named WoRMS (via Arctos).  Currently, it is being used only by DMNS Marine Invertebrate Collections.  Because the collection includes terrestrial mollusks not necessarily in WoRMS, DMNS occasionally adds needed taxa to WoRMS (via Arctos).

Using the WoRMS (via Arctos) source has dramatically reduced the amount of taxonomic work done by the collection administrators.  In the past, we were adding many taxa every day.  Also, because the classifications in WoRMS (via Arctos) have a unique aphiaID and are automatically updated via webservice, we no longer have to use the Hierarchical Classification Editor to move genera to a different family or make similar changes.  And we know that all taxa in a given genus or family have the same higher taxonomy so they can be easily searched.

But there are occasional surprises.  The automatic update of WoRMS (via Arctos) means that a genus may have been moved to a new family without us being aware of the change.  For example, we were rearranging our Mitridae family and couldn’t find an entry for our specimens of Charitodoron agulhasensis that we labeled in 2017.  That genus had been recently moved to a new family Charitodoronidae Fedosovc, Herrmann, Kantos & Bouchet, 2018.  So keeping our specimens in the exact same organization as our Arctos database is an ongoing task.

Arctos can add additional local sources, links to webservices or a unique taxa database developed by a participating institution. We are in the process of adding classifications from the Paleobiology Database to the Arctos taxonomy source and eventually may be able to add the WoRMS-like functionality of updating them via the PBDB taxon ID.

We’d like to Welcome Angelo State Natural History Collections into Arctos!

The Biology Department maintains the Angelo State Natural History Collections, which contains nearly 150,000 specimens of all types of living organisms. The collections are preserved, documented and curated assemblages that are important to a wide array of human activities.
The collections are essential to the management of natural resources because they document the diversity and biology of organisms that impact agriculture, health, and urban and other rural activities. They also characterize the ecosystems that we all depend on.
The collections are a resource for many fields of biological research. The presence and growth of the collections at ASU are important to the university, San Angelo and the Concho Valley because they are a readily available local resource for the region.
Interested in joining Arctos or know a collection that is looking for an amazing collection management solution? Have them contact the Arctos Working Group at arctos-working-group@googlegroups.com.

We’d like to Welcome the Ohio Wesleyan’s Brant Museum of Zoology into Arctos!

Ohio Wesleyan’s Brant Museum of Zoology houses teaching collections of mammals, birds and their eggs and nests, insects, mollusks, and corals, with smaller collections of other taxa.
This natural history museum features more than 400 mounted birds, including a golden eagle. It draws researchers from across the country, but its collections are used primarily for classroom and laboratory teaching, including helping students to better understand both taxonomic and evolutionary relationships.

Search the Data!

Interested in joining Arctos or know a collection that is looking for an amazing collection management solution? Have them contact the Arctos Working Group at arctos-working-group@googlegroups.com.

We’d like to Welcome the Arkansas Center for Biodiversity Collections into Arctos!

The Arkansas State University Museum of Zoology (ASUMZ) is an active group of research and teaching collections that joined with the herbarium in 2016 to unify as the Arkansas Center for Biodiversity Collections (ACBC) within the Department of Biological Sciences at Arkansas State University.

1. Feather mite.
2. From the Dirty Jobs visit with Mike Rowe in 2009 and the pinned dung beetle specimen for the collection. See Glass Maker Episode on Netflix for the episode.

ASUMZ includes collections of aquatic macroinvertebrates (mostly larval insects), bivalves, recent mammals, reptiles and amphibians, fishes, insects, and birds. There is a heavy regional focus within Arkansas, with specific geographic areas of interest being the Ozark Plateaus region, Crowley’s Ridge, and the Mississippi Alluvial Plain. Some of the ASUMZ collections represent the largest collections in Arkansas for the taxonomic group, including aquatic macroinvertebrates, bivalves, fishes, reptiles and amphibians, and mammals.