Sharing SpeciesInteraction

Data

GoMexSI / GLoBIWorkshop

Texas A&M Corpus Christi3-5 Dec 2014

food web visualization by Slyusarev et al. (2014)see http://blog.globalbioticinteractions.org/2014/06/06/a-food-web-map-of-the-world/

who's who?

Gulf of Mexico Species Interactions (GoMexSI)To synthesize and synergize ecological research in the Gulf ecosystem to address questions on taxonomic and spatial scales larger than now possible. Led by Jim Simons.

Global Biotic Interactions (GloBI)Provides a method to share, link, discover and use existing biotic interaction data for scientific and educational purposes. Led by Jorrit Poelen.

workshop goal

Make it easier for GoMexSI team to share species integration data using readily available tools like R, GitHub, and Neo4j Cypher.

history

2011-03 Jim and Jorrit start collaboration2013-01 GoMexSI paper published2013-01 http://eol.org funds GloBI2013-09 http://gomexsi.tamucc.edu online 2014-01 GloBI available through eol.org2014-10 GloBI paper published2014-12 GoMexSI/GloBI workshop

GloBI GoMexSI

25 data sources> 40k taxa ~ 1k taxa> 10k references 61 references~ 800k interactions ~ 38k interactionspredator-prey predator-preyparasite-hostpollinator-plantpathogen-host

(Dec 2014)

GloBI log10

(total interactions)

GloBI log10

(distinct interactions)

GloBI log10

(interactions w/ time)

GloBI log10

(distinct sources)

GloBI log10

(distinct locations)

how to contribute data?

iNaturalist.org take a picture, describe the interaction.

GitHub.com fork/create a github 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)

using rglobi, an R package

>prey <- rglobi::get_prey_of('Ariopsis')>head(prey) source_taxon_name interaction_type target_taxon_name1 Ariopsis felis preysOn Deuterostomia2 Ariopsis felis preysOn Actinopterygii3 Ariopsis felis preysOn Brevoortia4 Ariopsis felis preysOn Teuthida5 Ariopsis felis preysOn Dendrobranchiata6 Ariopsis felis preysOn Brachyura

acknowledgments

Jen Hammock; Chris Mungall; Brian Hayden; Goran Bodenschatz; Michael Casavecchia; Peter Roopnarine; Jeff Holmes; Cyndy Parr; Stephan Gosnell; Sergey Slyusarev; Robert Reiz; 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?

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

GoMexSIJim Simons james.simons@tamucc.eduhttp://gomexsi.tamucc.edu

discussion topics

How would you use GoMexSI/GloBI interaction data?

What prevents your colleagues from sharing their interaction data?