GloBI Status Update 23 May 2013

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GloBI Status Update 23 May 2013

  1. 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. 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. 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.
  4. 4. Retrieved from http://eol.org on 20 May 2013
  5. 5. Retrieved from http://eol.org/pages/223038/overview on 20 May 2013
  6. 6. Retrieved from http://eol.org/pages/223038/details#trophic_strategy on 20 May 2013
  7. 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. 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. 9. EOL GloBI – Some Concepts
  10. 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. 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. 12. EOL GloBI – Machine Readable Your computer asks: http://api.globalbioticinteractions.org/taxon/Ariopsis %20felis/preysOn?includeObservations=true GloBI answers:
  13. 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
  14. 14. See http://globalbioticinteractions.org/browse for up-to-date info.
  15. 15. See http://globalbioticinteractions.org/references.html for up-to-date info.
  16. 16. Retrieved from http://globalbioticinteractions.wordpress.com/2013/04/10/ on 20 May 2013
  17. 17. EOL GloBI – Citizen Science
  18. 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. 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. 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

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