Community Call – Research Applications of rOpenSci Taxonomy and Biodiversity Tools

Our next Community Call, on March 27th, aims to help people learn about using rOpenSci’s R packages to access and analyze taxonomy and biodiversity data, and to recognize the breadth and depth of their applications. We also aim to learn from the discussion how we might improve these tools. Presentations will start with an introduction to the topic and details on some specific packages and we’ll hear from several people about their “use cases in the wild”.

Agenda

1. Stefanie Butland – welcome (5 min)
2. Scott Chamberlain – introduction and taxize, taxizedb, rgbif, spocc (10 min)
3. Zachary Foster – taxa and metacoder (10 min)
4. Margaret Siple – using taxize to get IUCN statuses for species found via DNA barcoding of seafood samples and compare them among genera (4 min)
5. Kathryn Turner – a use case for taxize and rgbif to get all available occurrence records from GBIF for a handful of species, and scaling up to several thousand (4 min)
6. Kari Norman – learning lessons in building taxadb, a local database approach for working with taxonomic names (4 min)
7. Ciera Martinez – exploring biodiversity data with undergraduate data scientists using taxize and database specific tools like neotomoa, paleoDB, and rglobi (4 min)
8. Q & A (20 min)

???? See speaker bios below.

Join the Call

???? Wednesday, March 27th, 2-3PM PDT; 9-10PM GMT; March 28th in Australia, 8-9AM AEDT (find your timezone)

☎️ Find details for joining on our Community Calls page. Everyone is welcome. No RSVP needed.

???? After the Call, we’ll post the video and notes from the Q & A.

Resources

The Taxonomy Task View lists some relevant packages (not exclusive to rOpenSci).

Blog posts about the tools:

• rOpenSci taxonomy suite
• taxize: seven years of taxonomy in R
• rgbif: seven years of GBIF in R
• posts tagged with taxonomy
• posts tagged with biodiversity

Posts about applications of the tools:

• What are these birds? Complement occurrence data with taxonomy and traits information
• What’s this bird? Classify old natural history drawings with R
• Extracting and Enriching Ocean Biogeographic Information System (OBIS) Data with R
• Checklist Recipe – How we created a template to standardize species data

Manuscripts:

• Foster, Z. S., Chamberlain, S., & Grünwald, N. J. (2018). Taxa: An R package implementing data standards and methods for taxonomic data. F1000Research, 7, 272. https://doi.org/10.12688/f1000research.14013.2
• Foster, Z. S., Sharpton, T. J., & Grünwald, N. J. (2017). Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS computational biology, 13(2), e1005404. https://doi.org/10.1371/journal.pcbi.1005404
• Chamberlain, S. A., & Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. https://doi.org/10.7287/peerj.preprints.3304v1
• Chamberlain, S. A., & Szöcs, E. (2013). taxize: taxonomic search and retrieval in R. F1000Research, 2, 191. https://doi.org/10.12688/f1000research.2-191.v2

Tell us about your use cases

We’ve tried to make it easy for you to tell us about how you have used our packages. Go to the UseCases category in our public forum. Starting a “New Topic” opens a template that suggests what to provide, like the name of the rOpenSci tool or resource you used, a link to a post or code snippet, and a few other optional things. We might share your use case during the Call or tweet about it, so be sure to give your twitter handle.

Have a question for the speakers?

Add yours to the comments below. See a question you’d like to have answered? Give it a ❤️. The moderator may select some of these questions to ask during Q & A.

Speakers

Scott Chamberlain is co-founder and technical lead of rOpenSci, and developer of many packages for working with taxonomy and biodiversity data.
Scott on GitHub, Twitter, Website

Zachary Foster is a graduate student with Niklaus Grunwald in the Department of Botany and Plant Pathology at Oregon State University and a 2018 rOpenSci Fellow.
Zachary on GitHub, Twitter

Margaret Siple is a Postdoctoral Research Associate with the Ocean Modeling Forum at the School of Aquatic and Fishery Sciences at the University of Washington.
Margaret on GitHub, Twitter, Website
photo by Theo Macabeo

Kathryn Turner is an Eberly Research Fellow in the Department of Biology at Pennsylvania State University.
Kathryn on GitHub, Twitter, Website

Kari Norman is a graduate student with Carl Boettiger in the Department of Environmental Science, Policy, & Management at the University of California at Berkeley.
Kari on GitHub, Twitter

Ciera Martinez is a Mozilla Open Science Fellow in Michael Eisen’s group at the University of California at Berkeley.
Ciera on GitHub, Twitter, Website