Category: Arctos Tips

How to avoid 100 emails a day but still stay in touch via GitHub?

Leave a comment

by Teresa J. Mayfield-Meyer

With GitHub, you can set notifications to be either e-mail or web. As most of us know, you will get an e-mail every time comments on a GitHub issue you are watching. Wait, I’m watching issues?

 

To see what you are watching, in GitHub, click on the small bell with a blue dot next to your avatar. It will first bring up a list of notifications (where you’ll find the list of issues if you subscribe via web) and the next tab is watching. This lists all the threads you are watching and also getting notifications for. Unwatch any you do not want notifications for.

If you want to stop receiving GitHub emails but want to continue to watch, you can switch to the “web” notification method. This method will mean you do not get any of the emails! In your GitHub profile  (drop down from your avatar in the top right), select settings > Notifications and change “watching” and “Participating” to “Web”.

Make sure to then set a reminder on your calendar to go to GitHub to check the notifications!  You can peruse the list, read the issues that interest you and mark those that don’t as “read”.

ORCIDs and Arctos

2 Comments

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!

Leave a comment

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.

Arctos Happenings April 2018

Leave a comment

The April  2018 Arctos newsletter covers new updates such as exploring ways to make Arctos a non-profit entity, new collection spotlight, and project updates from the Arctos Working Sub-Groups. To view the newsletter,  click here.

 

To get onto the mailing list for the Arctos newsletter and other Arctos news, join the Arctos User Group: arctos@googlegroups.com – View instructions

Arctos Newsletter for January 2018

Leave a comment

The Arctos Working Group in collaboration with the Arctos Steering Committee will be putting out a quarterly Arctos newsletter. To view the January 2018 newsletter, click here.

Make sure to join the Arctos google group (arctos@googlegroups.com) to receive quarterly Arctos newsletters, Arctos outage and update notices, webinar announcements, and more delivered directly to your inbox!

 

Arctos Webinar Series: Data Entry and Bulkloading

Leave a comment

Title: Data Entry and Bulkloading

Date: January 9, 2018

Time: 3:00pm ET

Abstract: Arctos is both a community and a collection management information system. It provides fundamental research infrastructure for biodiversity data, and is intended for curators, collection managers, investigators, educators, and anyone interested in natural and cultural history. Over 3 million records are publicly available from 20+ collaborating institutions.

This webinar will cover the two primary methods for getting data into Arctos: data entry and bulkloading. While data entry provides a simple interface to enter data for specimens individually, bulkloading allows the user to upload a .csv file of multiple records. Both methods incorporate tools for data standardization and basic cleaning prior.

Presenter/s:  Emily Braker (Collection Manager of Vertebrate Zoology, CU Museum of Natural History) & Teresa Mayfield (Collection Manager, UTEP Biodiversity Collections)

Moderator: Erica Krimmel (Assistant Collection Manager, Chicago Academy of Sciences)

Links to any relevant pre-reading materials for best experience:

Start Date:
Tuesday, January 09, 2018 – 3:00pm to 4:00pm EST
AdobeConnect URL:
https://idigbio.adobeconnect.com/room

Arctos Webinar Series: Projects, Publications, and Citations

Leave a comment

Location: http://idigbio.adobeconnect.com/room

Title: Projects, Publications, and Citations in Arctos

Abstract: Arctos is both a community and a collection management information system. It provides fundamental research infrastructure for biodiversity data, and is intended for curators, collection managers, investigators, educators, and anyone interested in natural and cultural history. Over 3 million records are publicly available from 20+ collaborating institutions.

This webinar will provide an overview of how Arctos captures and connects information with Projects, Publications, and Citations. These features help track specimens and collection objects for the entirety of their lives, from acquiring project funding to being used for cutting-edge research 50 years in the future.

Presenters: Michelle Koo (Staff Curator, Museum of Vertebrate Zoology, University of California, Berkeley), Jon Dunnum, & Mariel Campbell (Collection Managers, Museum of Southwestern Biology at the University of New Mexico).

Moderator: Erica Krimmel (Assistant Collection Manager, Chicago Academy of Sciences)

Links to any relevant pre-reading materials for best experience:

Start Date:
Tuesday, December 12, 2017 – 3:00pm to 4:00pm EST
AdobeConnect URL:
http://idigbio.adobeconnect.com/room

Arctos Webinar Series: Transactions in Arctos (accessions, loans, permits)

Leave a comment

Location: http://idigbio.adobeconnect.com/room

Title: Transactions in Arctos (accessions, loans, permits)

Abstract: Arctos is a community of museums that collaborate to manage and host their data online. Over 3 million records are publicly available at https://arctos.database.museum, a searchable biodiversity database for scientific research, resource management, and education. The Arctos database is used both for querying museum records (see webinars 1 and 2) and for managing information about the collections.

This webinar will provide a short introduction to how transactions (accessions, loans, and permits) are managed in Arctos. Topics will include collection-level permissions and the basic tools for creating and updating different kinds of transactions, managing agents, and linking transactions to projects and media.

Presenter/s:  Carla Cicero and Michelle Koo (Staff Curators, Museum of Vertebrate Zoology, University of California, Berkeley).

Moderator: Erica Krimmel (Assistant Collection Manager, Chicago Academy of Sciences)

Links to any relevant pre-reading materials for best experience:

Start Date:
Tuesday, November 14, 2017 – 3:00pm to 4:00pm EST
AdobeConnect URL:
http://idigbio.adobeconnect.com/room