GloBI @ Berkeley Institute for Data Science Feb 5, 2015

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Jorrit Poelen introduces Global Biotic Interactions (GloBI, http://globalbioticinteractions.org) at Berkeley Institute for Data Science (BIDS, http://bids.berkeley.edu/events/jorrit-poelen-global-biotic-interactions ).

Science

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 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

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&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

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.

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

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?

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GloBI @ Berkeley Institute for Data Science Feb 5, 2015

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?

Editor's Notes

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 =&gt; 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(&quot;...&quot;) (archive) save results to csv open in open office (collaborate) show references.html click on data tab different formats.

GloBI @ Berkeley Institute for Data Science Feb 5, 2015

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Editor's Notes