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EEnnccyyccllooppeeddiiaa ooff LLiiffee''ss 
GGlloobbaall BBiioottiicc IInntteerraaccttiioonnss –– 
UUnnlleeaasshhiinngg EEOOLL''ss IInntteerraaccttiioonn 
DDaattaasseettss 
JJoorrrriitt PPooeelleenn 
2233 MMaayy 22001133 
UUAAMM,, MMeexxiiccoo CCiittyy 
““BBiigg FFiisshh EEaatt LLiittttllee FFiisshh,,”” 11555577 
PPiieetteerr vvaann ddeerr HHeeyyddeenn aafftteerr PPiieetteerr BBrruueeggeell tthhee EEllddeerr 
RReettrriieevveedd ffrroomm hhttttpp::////wwwwww..mmeettmmuusseeuumm..oorrgg//ttooaahh//wwoorrkkss--ooff--aarrtt//1177..33..8559 oonn 2200 MMaayy 22001133
““BBiigg FFiisshh EEaatt LLiittttllee FFiisshh,,”” 11555577 
PPiieetteerr vvaann ddeerr HHeeyyddeenn aafftteerr PPiieetteerr BBrruueeggeell tthhee EEllddeerr 
RReettrriieevveedd ffrroomm hhttttpp::////wwwwww..mmeettmmuusseeuumm..oorrgg//ttooaahh//wwoorrkkss--ooff--aarrtt//1177..33..8559 oonn 2200 MMaayy 22001133
EOL GloBI – Why? 
Challenge: Species interaction datasets exist, 
but are not easy to access and typically not 
machine readable. 
Idea: To aggregate interaction datasets and 
make them legible to humans and machines.
Retrieved from http://eol.org on 20 May 2013
Retrieved from http://eol.org/pages/223038/overview on 20 May 2013
Retrieved from http://eol.org/pages/223038/details#trophic_strategy on 20 May 2013
EOL GloBI – Use Case 1 
Jane, Jim, James and Joanna make their 
individual interaction datasets available. 
GloBI retrieves, normalizes and indexes the 
four interaction datasets. 
John uses GloBI to find species interactions, 
retrieve reference information and download 
raw data for offline analysis. 
John attributes Jane, Jim, James and Joanna in 
a published paper for the use of their data.
EOL GloBI – Use Case 2 
Jane shares an interaction dataset. 
GloBI retrieves, normalizes and indexes the 
Jane's interaction dataset. 
Jane uses GloBI to check that her dataset is 
correctly normalized and finds that a scientific 
name didn't match against any external 
taxonomy. 
Jane corrects the name Ariopsis felix to Ariopsis 
felis in her original dataset. 
GloBI detects the changes within 24 hours and 
updates automatically.
EOL GloBI – Some Concepts
EOL GloBI – Connecting the Pieces 
I nInteterraacctitoionn D Daatatasseetsts 
EExxteterrnnaal lT Taaxxoonnoommieiess 
.csv 
.txt 
Postgres .xls 
WebService MySQL 
.tsv PLoS 
EEOOLL's's G GloloBBII 
ITIS 
GulfBase 
WoRMS 
AAnnaalylyssisis T Toooolsls / /A Apppplilcicaatitoionnss EExxisistitningg O Onntotolologgieiess 
EOL 
NCBI 
Envo: 
Environments 
Biomes 
Uberon: 
Life Stage, 
Body Parts 
OBO Taxrank: 
Relations 
NCBI: 
Taxonomy 
GO: 
Interaction 
Processes 
Excel R 
SAS 
SPSS 
Cytoscape 
Gephi 
Web 
Applications 
Custom 
Programs 
Index 
Match 
Model 
Consume
EOL GloBI – Human Readable 
You ask: 
Could you provide some examples of what a 
hardhead catfish eats? 
GloBI answers: 
A hardhead catfish (Ariopsis felis) was collected 
with a stomach containing a brown shrimp 
(Farfantepenaeus aztecus) at latitude 28.645 
and longitude -96.100 at a depth of 0.7 m on 
9 April 1999 (Akin et al. 2006). 
...
EOL GloBI – Machine Readable 
Your computer asks: 
http://api.globalbioticinteractions.org/taxon/Ariopsis 
%20felis/preysOn?includeObservations=true 
GloBI answers:
EOL GloBI – Where Are We? 
18 datasets containing 25K taxa, 422K 
interactions, spanning about 3K locations 
Alpha version of automated ingestion, 
normalization, aggregation and export 
methods* 
Alpha version of web API* used by 
gomexsi.tamucc.edu project 
Alpha version of data exports* used to 
visualize food web in Gulf of Mexico 
* see github.com/jhpoelen/eol-globi-data/wiki
See http://globalbioticinteractions.org/browse for up-to-date info.
See http://globalbioticinteractions.org/references.html for up-to-date info.
Retrieved from http://globalbioticinteractions.wordpress.com/2013/04/10/ on 20 May 2013
EOL GloBI – Citizen Science
EOL GloBI – Where Are We Going? 
Help liberate more interaction datasets 
Use GloBI to enhance EOL pages 
Continue to work with scientists and software 
engineers to make machine-readable global 
species interaction data available for scientific 
and educational purposes
EOL GloBI – Who's Who? 
Contributors: Jorrit Poelen (lead/software), Chris 
Mungall (ontologies), James Simons (biologist) 
and Robert Reiz (software) 
Datasets shared by: Peter D. Roopnarine, 
Rachel Hertog, Carlos García-Robledo, James 
Simons (GoMexSI), Jenny L. Wrast, C. Barnes, 
International Council for the Exploration of the 
Sea (ICES), Jose R. Ferrer Paris, Senol Akin, 
Malcolm Storey (BioInfo.org.uk), Ivy E. Baremore, 
Joel Sachs (SPIRE), Colt W. Cook, David A. 
Blewett, Ken-ichi Kueda (iNaturalist.org) and 
others.
EOL GloBI 
Funded by EOL's Rubenstein Fellows Program. 
Big thanks to Jen Hammock, Jeff Holmes and 
Cyndy Parr at EOL for supporting and providing 
input for the EOL-GloBI project. 
Want to share a dataset? Contact Jorrit Poelen 
at jhpoelen+eol@gmail.com. 
http://globalbioticinteractions.wordpress.com 
http://github.com/jhpoelen/eol-globi-data/wiki

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GloBI Status Update 23 May 2013

  • 1. EEnnccyyccllooppeeddiiaa ooff LLiiffee''ss GGlloobbaall BBiioottiicc IInntteerraaccttiioonnss –– UUnnlleeaasshhiinngg EEOOLL''ss IInntteerraaccttiioonn DDaattaasseettss JJoorrrriitt PPooeelleenn 2233 MMaayy 22001133 UUAAMM,, MMeexxiiccoo CCiittyy ““BBiigg FFiisshh EEaatt LLiittttllee FFiisshh,,”” 11555577 PPiieetteerr vvaann ddeerr HHeeyyddeenn aafftteerr PPiieetteerr BBrruueeggeell tthhee EEllddeerr RReettrriieevveedd ffrroomm hhttttpp::////wwwwww..mmeettmmuusseeuumm..oorrgg//ttooaahh//wwoorrkkss--ooff--aarrtt//1177..33..8559 oonn 2200 MMaayy 22001133
  • 2. ““BBiigg FFiisshh EEaatt LLiittttllee FFiisshh,,”” 11555577 PPiieetteerr vvaann ddeerr HHeeyyddeenn aafftteerr PPiieetteerr BBrruueeggeell tthhee EEllddeerr RReettrriieevveedd ffrroomm hhttttpp::////wwwwww..mmeettmmuusseeuumm..oorrgg//ttooaahh//wwoorrkkss--ooff--aarrtt//1177..33..8559 oonn 2200 MMaayy 22001133
  • 3. EOL GloBI – Why? Challenge: Species interaction datasets exist, but are not easy to access and typically not machine readable. Idea: To aggregate interaction datasets and make them legible to humans and machines.
  • 7. EOL GloBI – Use Case 1 Jane, Jim, James and Joanna make their individual interaction datasets available. GloBI retrieves, normalizes and indexes the four interaction datasets. John uses GloBI to find species interactions, retrieve reference information and download raw data for offline analysis. John attributes Jane, Jim, James and Joanna in a published paper for the use of their data.
  • 8. EOL GloBI – Use Case 2 Jane shares an interaction dataset. GloBI retrieves, normalizes and indexes the Jane's interaction dataset. Jane uses GloBI to check that her dataset is correctly normalized and finds that a scientific name didn't match against any external taxonomy. Jane corrects the name Ariopsis felix to Ariopsis felis in her original dataset. GloBI detects the changes within 24 hours and updates automatically.
  • 9. EOL GloBI – Some Concepts
  • 10. EOL GloBI – Connecting the Pieces I nInteterraacctitoionn D Daatatasseetsts EExxteterrnnaal lT Taaxxoonnoommieiess .csv .txt Postgres .xls WebService MySQL .tsv PLoS EEOOLL's's G GloloBBII ITIS GulfBase WoRMS AAnnaalylyssisis T Toooolsls / /A Apppplilcicaatitoionnss EExxisistitningg O Onntotolologgieiess EOL NCBI Envo: Environments Biomes Uberon: Life Stage, Body Parts OBO Taxrank: Relations NCBI: Taxonomy GO: Interaction Processes Excel R SAS SPSS Cytoscape Gephi Web Applications Custom Programs Index Match Model Consume
  • 11. EOL GloBI – Human Readable You ask: Could you provide some examples of what a hardhead catfish eats? GloBI answers: A hardhead catfish (Ariopsis felis) was collected with a stomach containing a brown shrimp (Farfantepenaeus aztecus) at latitude 28.645 and longitude -96.100 at a depth of 0.7 m on 9 April 1999 (Akin et al. 2006). ...
  • 12. EOL GloBI – Machine Readable Your computer asks: http://api.globalbioticinteractions.org/taxon/Ariopsis %20felis/preysOn?includeObservations=true GloBI answers:
  • 13. EOL GloBI – Where Are We? 18 datasets containing 25K taxa, 422K interactions, spanning about 3K locations Alpha version of automated ingestion, normalization, aggregation and export methods* Alpha version of web API* used by gomexsi.tamucc.edu project Alpha version of data exports* used to visualize food web in Gulf of Mexico * see github.com/jhpoelen/eol-globi-data/wiki
  • 17. EOL GloBI – Citizen Science
  • 18. EOL GloBI – Where Are We Going? Help liberate more interaction datasets Use GloBI to enhance EOL pages Continue to work with scientists and software engineers to make machine-readable global species interaction data available for scientific and educational purposes
  • 19. EOL GloBI – Who's Who? Contributors: Jorrit Poelen (lead/software), Chris Mungall (ontologies), James Simons (biologist) and Robert Reiz (software) Datasets shared by: Peter D. Roopnarine, Rachel Hertog, Carlos García-Robledo, James Simons (GoMexSI), Jenny L. Wrast, C. Barnes, International Council for the Exploration of the Sea (ICES), Jose R. Ferrer Paris, Senol Akin, Malcolm Storey (BioInfo.org.uk), Ivy E. Baremore, Joel Sachs (SPIRE), Colt W. Cook, David A. Blewett, Ken-ichi Kueda (iNaturalist.org) and others.
  • 20. EOL GloBI Funded by EOL's Rubenstein Fellows Program. Big thanks to Jen Hammock, Jeff Holmes and Cyndy Parr at EOL for supporting and providing input for the EOL-GloBI project. Want to share a dataset? Contact Jorrit Poelen at jhpoelen+eol@gmail.com. http://globalbioticinteractions.wordpress.com http://github.com/jhpoelen/eol-globi-data/wiki