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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L inking biodiversity data with the b iological collections ontology

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)


Http code google com p bco

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


What it means to be an obo foundry ontology

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

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)


Initial focus of bco tracking materials and data through sampling chains

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


L inking biodiversity data with the b iological collections ontology

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


Example data processes

Example data: processes


Example data material entities and information artifacts

Example data: material entities and information artifacts


List all processes that took place in 2010 as part of the moorea insect inventory

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


L inking biodiversity data with the b iological collections ontology

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


Future directions technical

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

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


Contributors

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)


Questions

Questions?

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


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