Arctos Happenings
April 2021
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Update from GBIF North American Node Quarterly Meeting
Teresa Mayfield-Meyer
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Teresa attended the GBIF North American Node Quarterly meeting on March 11, 2021.
Highlights from the meeting included:
Upcoming events
- April 2021: Community webinar on training opportunities for the GBIF community
- 28 June - 2 July: Virtual Global Nodes Meeting paced across time zones
- August-September: Regional engagement webinars designed to engage a broad audience of stakeholders from regional organizations and countries not yet participating in GBIF and will be open to anyone who is interested.
New Digital Documentation
GBIF has updated its system for creating and maintaining documentation using GitHub, AsciiDoc and Crowdin
Community Consultation
The consultation on Converging Digital Specimens and Extended Specimens - Towards a global specification for data integration is complete - no mention of what comes next. Take some time to read through the conversation.
GBIF Hosted Portals
GBIF has created new hosted portals which consist of data hosted directly at GBIF and scoped to display the relevant subset of GBIF-mediated data (use GBIF data to create your own facet). We are part of the new North American Portal, (you can find the Arctos Network GBIF profile here). This hosted portal aims to display data at a regional scale (Canada, US and Mexico) and to facilitate communication among the participants.
Please browse this new portal and pass along comments. You can make suggestions directly on GitHub
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Award and Challenge Opportunities for Arctos Collections
Teresa Mayfield-Meyer
Heads up Arctos Collections!
As members in the GBIF network, Arctos collections may know people who could apply for or participate in the following GBIF Award Programs:
The 2021 program will provide a pair of €5,000 prizes recognizing the work of two early-career researchers—preferably, one master’s and one PhD candidate—nominated by the heads of delegation and node managers from GBIF Participant countries.
A jury organized by GBIF Science Committee will select two award recipients from the pool of nominees whose names are received by the GBIF Secretariat by 21 June 2021. The winners will be announced in early fall 2021.
The 2021 Ebbe Nielsen Challenge has opened with the aim of recognizing innovative entries that leverage biodiversity data and tools from the GBIF network to advance open science. An expert jury will judge entries on their openness and repeatability, relevance and novelty and present a selected pool of winners with a total of up to €20,000 in prizes.
Between 20 January and 2 August 2021, individuals and teams can prepare tools and techniques that improve the access, usefulness and quality of open biodiversity data and submit them to this annual open-ended incentive competition.
Challenge entries can take any number of approaches. Entrants may choose to develop new applications, visualizations, methods, workflows or analyses, often (but not always) making use of the GBIF API to access data. You may also build on or extend the capabilities of existing tools and features available across the GBIF network. We encourage entrants to review previous winners as well as previous winning entries for ideas, problems or approaches you may wish to pursue (see reference).
Entries should benefit multiple stakeholder groups, including data users, data holders and data managers. You may wish to review the GBIF Communications Strategy to see how we describe GBIF's audiences.
Winners will be announced at the 28th GBIF Governing Board meeting in October 2021.
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Arctos Feature Highlights
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New Basis of Record Code Table
Teresa Mayfield-Meyer
It was recently discovered that fossil specimens in Arctos were not being properly translated to aggregators. A search in GBIF for UTEP Fossils (Arctos) with BasisOfRecord = "fossil specimen", resulted in nothing, yet this entire collection is fossils. While we could take the easy way out and just send all ES collection types as "fossil specimen",we have decided to offer the option for collections to be more precise as there are fossils in other collections as well. In order to accomplish this, we will make better use of CATALOGED_ITEM_TYPE and use some of the categories suggested by TDWG for Basis of Record. However, we didn't want to introduce a lot of work for collections so we have two ways to accomplish assigning a cataloged item type to catalog records.
Collection Assignment
Each collection should select a Default Cataloged Item Type in Manage Collection. This "basis of record" will be assigned to all records in the collection unless it is specifically changed in an individual record.
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Single Catalog Record Assignment
Individual records can be assigned a CATALOGED_ITEM_TYPE when they are entered or by editing a previously entered record.
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New Component Loader Format
Arctos has a new format for Bulkloading Components in the Bulkloading toolkit
Things are a bit different than the last time you used the Bulkloader to add information on attributes, identifiers, relationships, etc. But do not worry, things are not as scary and new as they appear.
We'll walk through an example below, and you can also check out the new Arctos How-to Page, and Tutorial. Big kudos to Teresa, Andy and Nicole for putting all this fantastic info together for us!
How to use the New Batch Tools (with the example of Bulkloading Identifiers and Relationships)
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The tool takes you to the Review and Load page. If you have already loaded data, you will see it here. If you need to load data, click on ‘Load csv’ and following the instructions for how load your file.
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Once your file is loaded this is where things get new and exciting. Click on the Review and Load option and you will go to to the new Review and Edit page.
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If you think everything looks good with your data click the ‘Check All and Change Status to autoload’ button. This will set all of your entries to autoload by entering the text "autoload" to the Status column:
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Once you have the status to autoload for your entries you just need to wait for the bulkloader to process your entries. Check the Review and Load page for the status, and refresh it periodically, to see the Count number decrease (it can be slow, maybe 10 entries/minute).
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Go get a cup of coffee, come back and check to make sure everything is loaded. When they have all loaded your Review and Loaded page will be empty:
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Arctos People
Introducing Phyllis Sharp
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Arctos would like to introduce Phyllis Sharp (sharpphyl@gmail.com). Phyllis has been a volunteer with DMNS since 2005 and as a Departmental Associate helps to train and support the other fourteen volunteers in the Marine Invertebrate Collection so they can master each feature in Arctos. "The daily tasks in this collection are performed by volunteers....None of us are museum or database professionals, so the handbook and tutorials are very helpful."
The Marine Invertebrate Collection at the DMNS joined Arctos in November of 2013, with Phyllis playing a significant role in the transition and development. She sends a lot of thanks to Andrew (Andy) Doll, the DMNS Zoology Assistant Collections Manager, for being the museum's "Arctos guru who is always available to help and keep us out of trouble."
With the addition of the Marine Invertebrate Collection a number of new interests and challenges were brought to Arctos. As expected, a new taxonomic collection might require a new taxonomic source. Through the work of Phyllis and the Arctos Taxonomy Committee (as well as some Dusty magic and Teresa Mayfield-Meyer guidance), Arctos now has available the World Register of Marine Species (WoRMS) as a local source for taxonomic classifications. If you are thinking of bringing marine species to your Arctos collections, this is a must-have resource.
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Other fun projects Phyllis is working on include creating digital images of the Marine Invertebrate Collections specimens, specifically micromollusks (e.g.: DMNS:Inv:15509). There are now over 1,100 images available from the collection online.
Phyllis has also been using the geolocation tools in Arctos to georeference the marine invertebrate specimens at the DMNS. The collection now has mappable coordinates for nearly 70% of the entire collection. This is one area that Phyllis is still working and helping to improve Arctos. "The geography for marine specimens is challenging within the current Arctos system. It works great for our terrestrial specimens, but ideally, it would work just as smoothly for our offshore marine specimens." Using the GitHub Arctos community, Phyllis has several issues and suggestions currently under progress focused on this issue. She encourages everyone to participate on GitHub or on an Arctos Committee if they can. "[I]t is the best way to have your needs heard and addressed."
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Arctos New Collection Spotlight
Arctos Welcomes the University of Wisconsin Zoological Museum!
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The University of Wisconsin Zoological Museum (UWZM) is a research focused natural history museum based in the University of Wisconsin in Madison, Wisconsin. In addition to their focus on research, the museum contributes to a variety of University of Wisconsin class labs and a summer intern program for undergraduate students.
The UWZM is composed of approximately 100,000 cataloged specimens, which make up over 500,000 individual objects. There are a wide variety of collections including, ornithology, mammalogy, herpetology, ichthyology, aquatic invertebrates, osteology, paleontology, and scientific instruments. The museum's current research is focused on preserving examples of the native species of Wisconsin.
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Seeking Volunteers for Treasurer and Membership Manager Arctos Officer Positions
Are you interested in becoming more involved in Arctos and the Arctos Working Group? A great way to help is to volunteer as an Officer for the Arctos Working Group!
We are currently searching for Co-Treasurer and Co-Membership Manager Officers. A Co-Officer position works alongside the current Officer for a year, and then takes over as the the Officer for the next two years.
Responsibilities of the Treasurer Officer focus on:
- Working with the Steering Committee, Arctos Working Group Officers, and programers to determine costs and fees for existing and incoming collections.
- Helping Incoming Collections understand and estimate potential fees and costs.
- Providing a yearly financial report to the Steering Committee.
Responsibilities of the Membership Manager Officer include:
- Managing the Arctos Working Group Membership and Agent lists.
- Assisting new collections staff in joining Arctos, including the Arctos GitHub repositories.
- Working with other Arctos Officers to invite and welcome new collections to Arctos.
If you are interested in either position or have any questions, please email the Arctos Working Group Officers (arctos-working-group-officers@googlegroups.com ).
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Become Part of the Arctos Community
Arctos is a growing community, with many new developments, and everyone is invited to participate. Please see below for ways you can contribute to the Arctos community and participate in ongoing discussions about improving Arctos for collections management, research, education, and outreach:
1) Subscribe to Arctos Github and Participate in the monthly Critical Issues Meetings! to be able to post and watch issues, comments, suggestions; provide and receive community input.
2) Joining the Arctos Working Group is open to any participating institution; contribute to Arctos governance, development, and sustainability. We meet monthly. We need one person from each institution on the Arctos Working Group and GitHub.
3) Participate in outreach and webinars - help develop the Learn tab on our website, arctosdb.org!
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