Arctos Happenings
July 2021
|
|
Arctos Receives NSF Sustainability Grant!
Collaborative Research: Sustaining Arctos as a Community of Practice and as a Collection Management Solution for Biodiversity Research and Education
|
|
|
Arctos was just awarded a three-year grant from the National Science Foundation's "Sustained Availability of Biological Infrastructure" (SABI) program. Awards were made to three partner institutions (the Museum of Vertebrate Zoology (Univ. California Berkeley), Museum of Southwestern Biology (Univ. New Mexico Albuquerque) and Texas Advanced Computer Center (Univ. Texas Austin) for critical technical and infrastructure work that will establish a sustainable framework for Arctos.
The Arctos community is a group of museum-based professionals representing natural and cultural history collections at over 40 institutions that share in the governance, design, maintenance, and development of Arctos. A primary objective of the Arctos community is to make high quality data on biodiversity and cultural collections openly accessible and richly networked for multidisciplinary research and public understanding.
Arctos views collections comprehensively and promotes linkages across biological, earth science, art, archival, and ethnographic collections to add value and relevance for education and research. Many museums curate more than one type of collection, and Arctos provides a comprehensive management solution integrating diverse disciplines. For the last 20 years, Arctos has practiced the concept of the 'extended specimen network'. The richly annotated data in Arctos creates a web of knowledge with deep comprehensive relationships between cataloged records and all of their derived and associated data, and by using reliable published resources for globally shared information such as taxonomy, people names, and geography. To sustain this community-driven infrastructure and resource, the Arctos database platform will complete migration to open-source technologies removing the need for costly software. This will provide additional benefits to the Arctos community and database, including stabilizing web services, query responses and delivery, spatial functionality, among other core features.
Simultaneously, the Arctos community will establish a legal non-profit entity to administer its operations. This step will allow Arctos to have more opportunities to participate as a professional organization on national and international stages, thereby bringing collective expertise and 20+ years of experience in informatics to a greater audience. Achieving these aims will allow Arctos to sustain itself as a community, serve a larger network of extended specimens, and support itself financially. Stay tuned for exciting Arctos developments through participation in the Arctos Working Group and other connections to the community (see the end of the Newsletter for suggestions on how to stay connected)!
|
|
|
New Way to Share Information about Arctos
Michelle Koo
Arctos has a beautiful 2-page downloadable and sharable PDF that highlights the wonderful things that Arctos can do for your collections, users, and the public. In a handsome graphic, it explains what Arctos values, what Arctos delivers, and how Arctos handles the data and work you care about. Another wonderful product from the Arctos Working Group with special thanks to Emily Braker for her graphic design talents. Enjoy and share widely!
|
|
|
Opportunities and Events in the Wider Museum Community
|
|
Digital Extended Specimen Consultation
Teresa Mayfield-Meyer
Please participate in Converging Digital Specimens and Extended Specimens - Towards a global specification for data integration Phase 2.
Our community can contribute a lot to the discussions in this phase of the consultation. Please consider taking the time to look through the topics, contribute where you can and monitor the discussion if possible. The topics in this consultation include:
- Robust access points and data infrastructure alignment
- Persistent identifier (PID) scheme(s)
- Meeting legal/regulatory, ethical and sensitive data obligations
- Workforce capacity development and inclusivity
- Transactional mechanisms and provenance
- Partnerships to collaborate more effectively
GBIF, under the umbrella of the Alliance for Biodiversity Knowledge, is leading the consultation as part of the European Commission-funded SYNTHESYS+ project.
|
|
GBIF North American Node Update
Teresa Mayfield-Meyer
On June 30, 2021, I attended the quarterly meeting of the GBIF North American Node. This virtual meeting was held in conjunction with the GBIF Regional Nodes Meeting held the same week. Pre-recorded sessions for the larger meeting can be found here.
Did you know?
All Arctos collections within the appropriate boundaries that publish data are part of the GBIF North American Node.
The GBIF North American Node has a dedicated portal page and the node has three main goals:
- Encourage regional collaborative efforts to define best practices for participation, knowledge-sharing, training and capacity enhancement in the North American data-sharing community.
- Solicit ideas for better coordination across the region, define roles and responsibilities, and clarify the pathway for data mobilization.
- Encourage future projects to participate in the community using the outcomes from the first two goals.
This portal is still in development, and will soon be live. You can learn more about GBIF hosted portals here.
GBIF North American Node FAQ
Get Involved
You can participate in the GBIF Community via Slack, Discourse, or GitHub, or you can get email notifications about GBIF happenings by joining their Google Group.
Current GBIF Discourse
Now through July 27, 2021, GBIF is hosting a virtual consultation on Discourse. The topic is Converging Digital Specimens and Extended Specimens - Towards a global specification for data integration and everyone is invited to participate! Discourse from Phase 1 of the consultation can also be viewed, although it has officially been closed. Synthesized results are expected to be available for roadmap development with the aim of finishing up and reporting for the autumn round of meetings including TDWG 2021 and others such as Anthropological, Living collections, Cultural heritage collections community / GLAMS, Archeological, Botanical (e.g., Botany 2021), African and Asian meetings, Digital Data, and CBD.
GBIF Strategic Planning
The Future GBIF Strategy for 2023-2027 is discussed in the plenary sessions of the Global Nodes Meeting and is summarized below.
|
|
As data providers, our participation in the aggregator activities can help make our lives easier in the long run. I suggest that Arctos create a new Working Group position: GBIF Representative. This person would be responsible for attending the quarterly North American Node meetings and reporting back to the community and organizing Arctos membership when necessary to ensure that our voice is heard. Volunteers are appreciated! This is a great way to mingle with others in the North American and global biodiversity informatics community. If you are interested, please email the Arctos Working Group Officers. |
|
Arctos Feature Highlights
|
|
Separation of Parts and Preservation
Teresa Mayfield-Meyer
In the first week of July you may have noticed big changes in the Part Names and Part Preservation Code Tables. After multiple years of discussion, the Arctos Community agreed to take the first step in the separation of part names from preservation by moving all preservation types that had been included in part names with parentheses to a new part attribute - preservation. The values available for this part attribute can be found in the Part Preservation Code Table. This action helped trim our Part Names significantly, making selection from the dropdown in data entry easier and information about parts more discoverable while providing a path to deeper description of preservation as each preservation attribute includes its own determiner and date.
Changes to Data Entry
There are two ways to approach data entry when a given part includes more than one part attribute.
- Enter your parts using the "Extras" section of the data entry form.
|
|
This allows you to enter up to six attributes for a single part.
|
|
- Load your catalog records without parts and use the Part Bulkload Tool to load your parts after the basic catalog record is loaded. The Part Bulkload Tool allows you to load up to six attributes with each part.
In either scenario, your parts and their attributes will end up in the Part Bulkload Tool and will need to be loaded to the catalog records by setting them to autoload. For more on the Part Bulkload Tool, see How To Bulkload Parts.
Our work in this process is not complete as some preservation information remains embedded in part names without the standard parentheses and we are considering how best to handle compound part names. Follow the discussion here
|
|
New Data Quality Report - Publications/Identifications
Teresa Mayfield-Meyer
After working to fix a problem in which a bunch of citations were made that predated the IDs of the objects, it was suggested that the year field of the publication should be compared to the object ID date field and if the publication is younger or of equal age to/than the ID it would save. Otherwise the addition of the publication would fail.
For example:
A publication is 2008 but the object has 1 identification from 2011. There is no way this object can be a voucher for a citation from 2008... (even if the specimen was collected in 2002).
Now you can find such instances of previous failure with a new Data Quality Report. Select Reports/Services > Find Low-Quality Data > Publication/Identification Problems from the main Arctos menu and find these kinds of issues!
|
|
Arctos Group Photo!
Arctos will be taking a remote group photo to document and preserve a record of the amazing group of people who use, work, and collaborate on the Arctos database. At the Arctos Working Group (AWG) meeting on 9 September 2021 (1030 PT) we will be turning on all of our cameras to take a photo of everyone. Please come! We want to see everyone's smiling faces :)
Do not know how to participate in the AWG? The AWG is open to any participating institution, and is the best way to contribute to Arctos governance, development, and sustainability. Check out this information on how to join: Joining the Arctos Working Group
|
|
|
New Github Template for Social Media Content
|
|
The Arctos Newsletter Github Repository has a new template for suggesting social media content!
If you have any suggestions use the Arctos Tweet Suggestion template.
Templates on Github have suggested content sections (in ** ** brackets) and handy descriptions of the info for each section.
For the new Social Media Template here are the content sections you will see:
**Idea/Topic** should be a brief summary of the proposed Tweet. It should be a topic of interest to Arctos members or a discussion of something happening in Arctos.
**Details** Please provide a draft of the Tweet or details that would be useful in drafting it.
**Link(s)**Please provide any links that would lead to where further information can be found. (For example Github issue, Arctos newsletter, Arctos handbook, Arctos database, etc.)
**At(s)** Please provide the Twitter handle for any accounts you would like to "at" in the Tweet. (For example @UTEPBC)
**Image** Attach a jpg to this issue if you would like to suggest an image for the Tweet.
|
|
Arctos Working Group (AWG) Slack Channel is for everyone to use: https://arctos-workspace.slack.com
Please use your preferred email to send a request for an invitation to arctos-working-group-officers@googlegroups.com.
The Arctos Slack Channel is not needed for Arctos issues work or to get help on problems, but it is a good way to reach people quickly if you have a project or non-issue question. And puns...there are definitely puns. |
|
Arctos People
Introducing the Summer 2021 Arctos Interns!
|
|
|
In summer 2021 our Arctos interns both come from Colorado, and in true Arctos fashion are working with mentors in diverse locations. Genevieve (Genna) comes from the Masters of Science in the Museum and Field Studies program at the University of Colorado Museum of Natural History (CUMNH) working with Michelle Koo at the Museum of Vertebrate Zoology (MVZ). Cynthia (Cindy) is working on her M.A. in Museum Studies plus the Digital Curation Certificate Program at Johns Hopkins University mentoring under Mariel Campbell at the Museum of Southwest Biology (MSB). Both Cindy and Genna are working on data clean-up and helping to make Arctos more accessible and connected. A lot of their time is going towards improving the Arctos Projects (https://handbook.arctosdb.org/documentation/projects.html). This work will help Arctos Projects "serve as a useful source of information on museum and employee research history, provide metrics for overall museum productivity, and connect to other relevant Arctos records (agents, publications, and specimen records)" (Genna Anderegg).
Before Genna and Cindy started working on their masters in Colorado they had finished degrees at the University of Wisconsin Madison in Evolutionary Biology (Genna) and at Princeton and MIT in Molecular Biology and Biology (Cindy). During the day, when not in the digital sphere with Arctos, Cindy volunteers at the Denver Museum of Nature and Science Entomology collection in Denver, CO and was a former intern with the University of Colorado for Invertebrate Paleontology, and Genna is learning about collection techniques and specimen preparation at the CUMNH in Boulder, CO. In their current program, both Arctos interns have been learning about different museum curation areas and procedures, from hands on specimen organization to georeferencing.
In the future, both Cindy and Genna would like to work in museums with collections management and digital curation. They're enjoying their dive into the Arctos ecosystem, learning about the tools and connections that Arctos helps create between museum objects and data. Both interns are active participants in Arctos Working Group (AWG) and Issues meetings, and attending an AWG meeting this summer is a great way to meet them!
Welcome Genna and Cindy!
|
|
Arctos People
Introducing Mary Beth Prondzinski!
|
|
|
|
Mary Beth Prondzinski (on right) and Edward O. Wilson (on left)
|
|
|
Arctos would like to introduce Mary Beth Prondzinski (mbprondzinski@gmail.com). Mary Beth was the Collections Manager of Natural History at the Alabama Museum of Natural History (ALMNH) until her retirement in May 2021. At the ALMNH Mary Beth managed the Archival, History and Ethnology, Geology, Paleontology, Invertebrate, Insect, Bird, Herp, Mammal, and Teaching collections. She was the main person in the museum who worked with the Arctos database platforms, helping the diverse ALMNH collections join Arctos in 2018. "I wear many hats, so I do a bit of everything...data migration, data entry, creation of projects, photo documentation, associating citations, creating new classifications..." (Including video creation! Check out this informative video Mary Beth helped put together on spiders for the ALMNH before her retirement.)
With her focus on curatorial work at the ALMNH, Mary Beth has gained a lot of experience with the ins and outs of the curation tools on Arctos. One area that helped her a lot were the loan tools. By entering all of the ALMNH's outstanding loans, Arctos was able to help Mary Beth through notifications on due dates of loans to both her and the loanee. Through all of her hard work in the set-up of the ALMNH Mary Beth has allowed its collections, such as Paleontology, to become more easily accessible for statistical uses. She's also been a huge help to Arctos by being an "unwitting troubleshooter" by finding problems and glitches. If Mary Beth could do anything with Arctos she'd love to see documentation for each feature and tool added directly to the Arctos interface page. She'd also love a notebook feature added to the "My Stuff" page to allow the recording of notes, ideas, and questions while working in the database.
Mary Beth's favorite thing about Arctos is the diverse knowledge and skills she picked up while working with the platform. "It keeps my brain facile! I highly recommend it as the antidote for age-related cognitive decline." Participating with the Arctos Working Group Meetings helped her more easily absorb information on how Arctos and its tools work. She would like to see more participation and input from the rest of the Arctos Community in meetings, and had a final suggestion to help. "I sometimes feel there is no place for me to seriously ask questions that I have... A monthly "users" zoom forum might be helpful where anyone can ask questions and solicit help from other Arctos users." (We started an issue with Mary Beth's suggestion - take a look on the Arctos Github Repository.)
Thanks for all of the hard work and suggestions Mary Beth! We'll miss you finding glitches and helping us improve, but we also really hope you have the very best (well deserved) retirement.
|
|
Arctos New Collection Spotlight
Arctos Welcomes the University of North Carolina Greensboro Biological Diversity Collections!
|
|
The University of North Carolina Greensboro Biological Diversity Collections (UNCG Biological Diversity Collections) is a natural history collection that focuses on mammal specimens and their accompanying biodiversity, based in Greensboro, North Carolina. The UNCG Mammal Collection is actively built and used by graduate student research projects focused on spatial distributions, parasite loads, and landscape genetics of small mammals in the complex landscapes of the Southern Appalachian Mountains. Check out the McLean Lab for current and future research projects.
|
|
|
The collections focus broadly in the region of the southeastern United States, and encompass >500 specimens of alcohols and tissues, with plans to expand to skins and skeletons. Most of the objects in the collection are modern, with multiple parts (tissues, ectoparasites, internal soft tissue preparations), and accompanying data (genetic barcodes, parasite identifications and abundances, microbiome sequences, GI tract measurements, etc.) beginning to be linked together in Arctos. The museum has especially strong collections in small mammals (rodents and shrews) from the Southern Appalachian Mountains, and fluid-preserved specimens.
|
|
|
The UNCG Biological Diversity Collections also trains a diverse undergraduate and graduate student body in both field and specimen-based mammalogy. As a Minority Serving Institution, the University of North Carolina Greensboro had a Fall 2020 class of approximately 35% African American and 13.1% Hispanic or Latinx students. Future plans are to integrate the Arctos hosted collections resources into evolution and ecology-themed undergraduate courses that focus on increasing biodiversity data literacy in this diverse student population.
|
|
Arctos New Collection Spotlight
Arctos Welcomes the David H. Snyder Museum of Zoology!
|
|
|
|
Left-right: Kathy Le (APSU undergraduate CA), Dr. A. Floyd Scott (Curator-Emeritus, deceased), Courtney Weyand (APSU graduate CA)
|
|
|
The David H. Snyder Museum of Zoology (APSU) is a natural history museum focused on the Mid-South region of the United States, with special emphasis on the fishes and herps of Tennessee. Based at the Austin Peay State University in Clarksville, Tennessee, the museum contains ~60,000 specimens and photographic vouchers of herps, fishes, mammals, and birds. The most numerous collections are the fish and herps, with the APSU representing the largest collections of amphibians and reptiles in Tennessee. Objects in the collections consist of skins (including snake skins), skulls, fluids, tissues, and turtle shells.
The museum encompasses both teaching collections and vouchered specimens. Graduate and undergraduate students are very active in the collections, supported by work-study scholarships from the Austin Peay State University Department of Biology. Students working in the museum learn about museum science, and are active researchers and collectors in the collections through specimen-based research on species in the region.
The herp and fish collections are highly active at the APSU, and focus on documenting the biodiversity of Tennessee and Kentucky. The herp collections functioned in support of the Atlases of Amphibians and Reptiles in Tennessee, as well as the recent publication Amphibians and Reptiles of Land Between the Lakes by the late Drs. David H. Snyder and Dr. A. Floyd Scott (long-time curators of the collections) and their co-authors (Zimmerer and Frymire).
|
|
|
|
L-R Dr. Dwayne Estes (PI and Curator of Botanical Collections), Dr. Rebecca E. Blanton Johansen (PI and Curator of Fishes), Dr. C.M. Gienger (PI and Curator of Herps)
|
|
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 ).
|
|
|
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!
|
|
|
|
