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L inking biodiversity data with the B iological Collections Ontology

L inking biodiversity data with the B iological Collections Ontology. Ramona Walls ( iPlant Collaborative, University of Arizona) John Deck (University of California at Berkeley) Robert Guralnick (University of Colorado at Boulder) John Wieczorek ( University of California at Berkeley ).

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L inking biodiversity data with the B iological Collections Ontology

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  1. Linking biodiversity data with the Biological Collections Ontology Ramona Walls (iPlant Collaborative, University of Arizona) John Deck (University of California at Berkeley) Robert Guralnick (University of Colorado at Boulder) John Wieczorek(University of California at Berkeley)

  2. http://code.google.com/p/bco/

  3. What it means to be an OBO Foundry Ontology • Shared commitment to creating a suite of interoperable ontologies that span the biological and biomedical domains • non-redundancy • re-use of existing terms • Adherence to OBO Foundry principles, including: • open access, willingness to collaborate • shared formats, relations, URIs, naming conventions • good documentation, single locus of authority • Access to OBO Foundry community resources • tools • expertise

  4. Scope of the BCO: transect Collections of organisms and their parts (museum or voucher specimens): * * * * Environmental samples: * * depth water sample at depth X *sample collection point Surveys, ecological observations: plot transect (within plot) sub-plot aliquot metagenome individual (within plot) individual (within sub-plot)

  5. Museum specimens Initial focus of BCO: tracking materials and data through sampling chains Genbank sequence Tissue sample at Smithsonian Institution Digital image stored on Morphbank MooreaBiocode bioinventoryevent identification Metagenomic sequences at CAMERA portal Gut sample

  6. BCO:material sampling process BCO:identification process BCO:material sample BCO:taxonomic name KEY: Insect specimen subclass of has specified output has specified input instance of derives from TaxonID A Biocode Sampling Identification using key Tissue sampling Identification using BLAST TaxonID B DNA molecules DNA extraction Sequencing Genbank sequence B rdfs:Class Tissue sample OBI:sequencing assay OBI:sequence data

  7. Example data: processes

  8. Example data: material entities and information artifacts

  9. List all processes that took place in 2010 as part of the Mooreainsect inventory BFO: process andBFO:partof occurentBCO_example:Mooreainsect inventory and date=2010

  10. List the output (“has specified output”) of every “taxonomic identification process” that has as input (“has specified input”) the "insect 03".

  11. Future directions - technical • SPARQL endpoint with example queries • Check the BCO wiki (http://code.google.com/p/bco/) • Implement community curation tools such as Quick Term Templates or BioPortal • Requests can go to the Issue tracker now: http://code.google.com/p/bco/issues/list

  12. Future directions - ontological • Better integration with OBI and other ontologies • More sophisticated treatment of naming/taxonomy/identification • Ontological modeling of surveys/inventories • Mappings to DwC, MIxS, other vocabularies • Testing with real data sets

  13. Contributors: Steve Baskauf, Vijay Barve, Jim Beach, Reed Beaman, MatthiewBietz, Stan Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Gabi Droege, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Michelle Koo, Kris Krishtalka, John Kunze, Andréa Matsunaga, Peter Midford, Chuck Miller, Norman Morrison, Gil Nelson, OBI Developers, ÉamonnO’Tuama, Cynthia Parr, SujeevanRatnasingham, Jai Rideout, Robert Robbins, PhillipeRocca-Serra, Joel Sachs, Inigo San Gil, Herbert Schentz, Mark Schildhauer, Barry Smith, Peter Sterk, Steve Stones-Havas, Brian Stucky, Andrea Thomer, MellisaTulig, Dave Vieglais, Brian Wee, Trish Whetzel, Jamie Whitacre, Greg Whitbread, John Wooley Funding • RCN4GSC: Research Coordination Network for Genomic Standards Consortium (DBI-0840989) • IB3 EAGER: An Interoperable Information Infrastructure for Biodiversity Research (IIS-1255035)

  14. Questions? https://groups.google.com/forum/?fromgroups#!forum/bco-discuss

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