L inking biodiversity data with the B iological Collections Ontology
description
Transcript of 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/
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:
transect
depth
* **
*
*
*sample collection point
water sample at depth X
aliquot
*
metagenome
Environmental samples:
Collections of organisms and their parts(museum or voucher specimens):
Surveys, ecological observations:plot
sub-plottransect (within plot)
individual (within plot)
individual (within sub-plot)
Initial focus of BCO: tracking materials and data through sampling chains
Moorea Biocode bioinventory event
Museum specimens
Tissue sample at Smithsonian Institution
Gut sample Metagenomic sequencesat CAMERA portal
Genbank sequence
Digital image stored on Morphbank
identification
Insect specimen
KEY:
subclass of
has specified output
has specified input
instance of
derives from
BCO:material sampling process
BCO:identification process
BCO:material sample
OBI:sequencing assay
OBI:sequence data
Genbank sequence B
TaxonID A
TaxonID B
Tissue sampling
DNA extraction
Identification using key
Identification using BLAST
Sequencing
Biocode Sampling
Tissue sample
DNA molecules
BCO:taxonomic name
rdfs:Class
Example data: processes
Investigation Study process ID process type has input has ouput date
Moorea Biocode Project
Moorea Biocode project planned process
Moorea Biocode Project
Moorea insect inventory
Moorea insect inventory planned process
Moorea Biocode Project
Moorea insect inventory insect collection 01
material sampling process insect 01 insect 01 2010
Moorea Biocode Project
Moorea insect inventory tissue sampling 01
material sampling process insect 01 tissue sample 01 2010
Moorea Biocode Project
Moorea insect inventory
insect gut sampling 04
material sampling process insect 01 insect gut sample 04 2010
Moorea Biocode Project
Moorea insect inventory
insect gut sampling 05
material sampling process insect 02 insect gut sample 05 2010
Moorea Biocode Project
Moorea insect inventory dna isolation 01
material sampling process tissue sample 01 DNA sample 01 2010
Moorea Biocode Project
Moorea insect inventory dna isolation 04
material sampling process
insect gut sample 04 DNA sample 04 2010
Moorea Biocode Project
Moorea insect inventory
insect observation 06 observing process insect in situ 06 image 01 2010
Moorea Biocode Project
Moorea insect inventory identification 01.1 tax. iden. by morph. key insect 01 insect taxon 01 2010
Moorea Biocode Project
Moorea insect inventory identification 01.2
tax. iden. using dna barcode dna isolation 01 insect taxon 01 2011
Moorea Biocode Project
Moorea insect inventory identification 04.1 tax. iden. using BLAST dna isolation 04 microbial taxon 01 2010
Moorea Biocode Project
Moorea insect inventory identification 06.1
morph. tax. identification image 01 insect taxon 01 2010
Moorea Biocode Project
Moorea insect inventory identification 07.1
morph. tax. identification image 02 insect taxon 02 2011
Example data: material entities and information artifacts
Individual Type Inferred type
insect 01 organism or virus or viroid material sample
insect 02 organism or virus or viroid material sample
tissue sample 01 organism part material sample
tissue sample 02 organism part material sample
insect gut sample 04 material entity material sample
DNA sample 01 DNA material sample
DNA sample 02 DNA material sample
insect in situ 06 organism or virus or viroid material target of observation
image 01 photographic image information artifact
insect taxon 01 taxonomic name information artifact
insect taxon 02 taxonomic name information artifact
microbial taxon 01 taxonomic name information artifact
microbial taxon 02 taxonomic name information artifact
List all processes that took place in 2010 as part of the Moorea insect inventory
BFO: process and BFO:part of occurent BCO_example:Moorea insect inventory and date=2010
Study process ID process type dateMoorea insect inventory insect collection 01 material sampling process 2010Moorea insect inventory insect collection 02 material sampling process 2010Moorea insect inventory tissue sampling 01 material sampling process 2010Moorea insect inventory tissue sampling 02 material sampling process 2010Moorea insect inventory insect gut sampling 04 material sampling process 2010Moorea insect inventory insect gut sampling 05 material sampling process 2010Moorea insect inventory dna isolation 01 material sampling process 2010Moorea insect inventory dna isolation 02 material sampling process 2010Moorea insect inventory dna isolation 04 material sampling process 2010Moorea insect inventory dna isolation 05 material sampling process 2010Moorea insect inventory insect observation 06 observing process 2010Moorea insect inventory identification 01.1 tax. iden. by morph. key 2010Moorea insect inventory identification 02.1 tax. iden. by morph. key 2010Moorea insect inventory identification 04.1 tax. iden. using BLAST 2010Moorea insect inventory identification 04.2 tax. iden. using BLAST 2010Moorea insect inventory identification 04.3 tax. iden. using BLAST 2010Moorea insect inventory identification 04.4 tax. iden. using BLAST 2010Moorea insect inventory identification 04.5 tax. iden. using BLAST 2010Moorea insect inventory identification 06.1 morph. tax. identification 2010
List the output (“has specified output”) of every “taxonomic identification process” that has as input
(“has specified input”) the "insect 03".
Study process ID process type has specified input
has specified output
Moorea insect inventory
identification 03.1 tax. iden. by morph. key
insect 03 insect taxon 01
Study process ID process type has input has ouputMoorea insect inventory
tissue sampling 03 material sampling process
insect 03 tissue sample 03
Moorea insect inventory
dna isolation 03 material sampling process
tissue sample 03 DNA sample 03
Moorea insect inventory
identification 03.2 tax. iden. using dna barcode
DNA sample 03 insect taxon 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
Contributors:Steve Baskauf, Vijay Barve, Jim Beach, Reed Beaman, Matthiew Bietz, 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, Éamonn O’Tuama, Cynthia Parr, Sujeevan Ratnasingham, Jai Rideout, Robert Robbins, Phillipe Rocca-Serra, Joel Sachs, Inigo San Gil, Herbert Schentz, Mark Schildhauer, Barry Smith, Peter Sterk, Steve Stones-Havas, Brian Stucky, Andrea Thomer, Mellisa Tulig, 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?
https://groups.google.com/forum/?fromgroups#!forum/bco-discuss