Unleashing SpeciesInteraction

Data

Jorrit PoelenGlobal Biotic Interactions

5 Feb 2015 @ Berkeley Institute for Data Science (BIDS) Tea

food web visualization by Slyusarev et al. (2015) http://dx.doi.org/10.6084/m9.figshare.1297762

Sea otter

Sea otter lunch

(c) edward_rooks, some rights reserved (CC BY-NC)accessed at http://www.inaturalist.org/observations/563486 on Feb 4, 2015

What do sea otters eat?

... is a surprisingly hard question to answer.

Why? Data is hard to access due to cultural reasons. Ecologists (and their institutions) are still catching up to embrace open-data science as a way to accelerate ecological research.

Soranno et al., 2014 @ http://dx.doi.org/10.1093/biosci/biu169

Global Biotic Interactions

... is many thingsdata normalization tool (in java/neo4j)

online graph database (neo4j)online rdf/triple store (apache jena)

various data archives (DwC, ttl/rdf)apis /libs (web api, R, javascript)

open data + open source = a community of folks that share and use interaction data

demo

how to contribute data?

iNaturalist.org take a picture, describe the interaction.

GitHub.com fork/create a github template repo, add your data.Share an open-access dataset using figshare.com, zenodo.org (or similar) and send the DOI to us.

Publish an open-access (data) paper and share the DOI with us.

Or, contact us and we'll figure something out.

how to access data?

download data archives (darwin core, neo4j db, ttl/rdf)

use library (javascript, R)

use web apis (fuseki/sparql, neo4j/cypher, globi/api)

recent past, near future

Sept 2014 GloBI paper published Dec 2014 GoMexSI / GloBI Workshop at Texas A&MJan 2015GloBI funding renewedJan 2015ropensci/rglobi published in CRAN Feb 2015 Jorrit presents at BIDS tea (now)Feb 2015 Stephen Gosnell presents on rglobi /

ratlantis and ecosystem modeling? Brian Hayden et al. (in prep) Global dietary

niche width vs. biodiversity.

more interaction data . . . incl pathogen/host/disease

acknowledgments

Jim Simons; Jen Hammock; Chris Mungall; Brian Hayden; Goran Bodenschatz; Peter Roopnarine; Jeff Holmes; Cyndy Parr; Stephan Gosnell; Sergey Slyusarev; Scott Chamberlain; Malcolm Storey; Joel Sachs; Ken-ichi Ueda; Allen Hurlbert; Ben Raymond; Carolyn Barnes; Jarrett Byrnes; Colt Cook; José Ferrer-Paris; Anne Thessen; Institute for Marine Resources and Ecosystem Studies (IMARES); International Council for Exploration of the Sea (ICES); UK Species Inventory at the Angela Marmont Centre for UK Biodiversity, the Natural History Museum, London; and many others.

GloBI is supported by the Encyclopedia of Life.

learn more?

Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. http://dx.doi.org/10.1016/j.ecoinf.2014.08.005

Jorrit Poelen jhpoelen@xs4all.nlhttp://globalbioticinteractions.org

discussion topics

How would you use GloBI interaction data?

What prevents your colleagues from sharing their (species interaction) data?

Why provides GloBI, a young project, one of the largest, openly accessible species integration datasets? Why didn't this happen earlier?