L inking biodiversity data with the b iological collections ontology
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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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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)


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

Scope of the BCO:


Collections of organisms and their parts

(museum or voucher specimens):





Environmental samples:




water sample at depth X

*sample collection point

Surveys, ecological observations:



(within plot)




individual (within plot)


(within sub-plot)

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




Metagenomic sequences

at CAMERA portal

Gut sample

BCO:material sampling process

BCO:identification process

BCO:material sample

BCO:taxonomic name


Insect specimen

subclass of

has specified output

has specified input

instance of

derives from

TaxonID A

Biocode Sampling

Identification using key



Identification using BLAST

TaxonID B

DNA molecules

DNA extraction


Genbank sequence B


Tissue sample

OBI:sequencing assay

OBI:sequence data

Example data: processes

Example data: material entities and information artifacts

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

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

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

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


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


  • RCN4GSC: Research Coordination Network for Genomic Standards Consortium (DBI-0840989)

  • IB3 EAGER: An Interoperable Information Infrastructure for Biodiversity Research (IIS-1255035)



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