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Unleashing Species Interaction Data
- 1. Unleashing Species Interaction Data Jorrit Poelen Global 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
- 2. 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
- 3. 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
- 4. Global Biotic Interactions ... is many things data 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
- 6. demo
- 7. 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.
- 8. 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)
- 9. recent past, near future Sept 2014 GloBI paper published Dec 2014 GoMexSI / GloBI Workshop at Texas A&M Jan 2015GloBI funding renewed Jan 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
- 10. acknowledgments Jim Simons; Jen Hammock; Chris Mungall; Brian Hayden; Göran 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.
- 11. 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.nl http://globalbioticinteractions.org
- 12. 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?
Notas do Editor
- Introduction We found that species interaction data was hard to discover and access, so we built a platform and community to help achieve that.
- What are species interactions? What do sea otters eat? ... an easy question, but hard to answer because observation records are mostly offline, unlinked and siloed.
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- Introducting Global Biotic Interactions . . . rebuilt daily from federated datasets links taxonomies, ontologies, references provides data apis, libraries and archives open collaboration model (GitHub) preliminary results => detected numerous data errors; stimulate ontology development; stimulates research collaboration; used in at least two ongoing academic research projects (Brian Hayden, Stephen Gosnell)
- Learning about Sea otters demo (5 minutes) (discovery) lookup Enhydra in http://globalbioticinteractions.org click on crab (Cancer) to go to http://eol.org in data tab, click on Enhydra and to go to iNaturalist (research) in R look for all Enhydra prey in Cypher go to what do humans eat? change the name into Enhydra after poking around, copy / paste the query in R, do rglobi::query("...") (archive) save results to csv open in open office (collaborate) show references.html click on data tab different formats.