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:
Collections of organisms and their parts
(museum or voucher specimens):
Environmental samples:
transect
*
*
*
depth
Surveys, ecological observations:
transect
(within plot)
sub-plot
aliquot
individual
(within sub-plot)
*
*
*sample collection point
water
sample at
depth X
plot
individual
(within plot)
*
metagenome
Initial focus of BCO: tracking materials and
data through sampling chains
Museum
specimens
Digital image stored
on Morphbank
identification
Genbank
sequence
Tissue sample at
Smithsonian Institution
Moorea Biocode
bioinventory event
Gut sample
Metagenomic sequences
at CAMERA portal
BCO:material
sampling
process
BCO:material
sample
Biocode
Sampling
Tissue
sampling
Insect
specimen
Tissue
sample
BCO:identifica
tion process
BCO:taxonomic
name
Identificatio
n using key
TaxonID A
Identification
using
BLAST
TaxonID B
Sequencing
Genbank
sequence B
DNA
extraction
DNA
molecules
KEY:
rdfs:Class
subclass of
has specified output
has specified input
instance of
derives from
OBI:sequencin
g assay
OBI:sequenc
e data
Example data: processes
Investigation
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Moorea Biocode
Project
Study
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
process ID
Moorea Biocode
project
Moorea insect
inventory
insect collection 01
tissue sampling 01
insect gut sampling
04
insect gut sampling
05
dna isolation 01
dna isolation 04
insect observation
06
identification 01.1
identification 01.2
identification 04.1
identification 06.1
identification 07.1
process type
has input
has ouput
date
insect 01
insect 01
2010
insect 01
tissue sample 01
2010
insect 01
insect gut sample 04
2010
insect 02
insect gut sample 05
2010
planned process
planned process
material sampling
process
material sampling
process
material sampling
process
material sampling
process
material sampling
process
material sampling
process
tissue sample 01 DNA sample 01
insect gut sample
04
DNA sample 04
2010
insect in situ 06
image 01
2010
tax. iden. by morph. key insect 01
tax. iden. using dna
barcode
dna isolation 01
insect taxon 01
2010
insect taxon 01
2011
tax. iden. using BLAST
morph. tax.
identification
morph. tax.
identification
dna isolation 04
microbial taxon 01
2010
image 01
insect taxon 01
2010
image 02
insect taxon 02
2011
observing process
2010
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
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
Moorea insect inventory
process ID
insect collection 01
insect collection 02
tissue sampling 01
tissue sampling 02
insect gut sampling 04
insect gut sampling 05
dna isolation 01
dna isolation 02
dna isolation 04
dna isolation 05
insect observation 06
identification 01.1
identification 02.1
identification 04.1
identification 04.2
identification 04.3
identification 04.4
identification 04.5
identification 06.1
process type
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
material sampling process
observing process
tax. iden. by morph. key
tax. iden. by morph. key
tax. iden. using BLAST
tax. iden. using BLAST
tax. iden. using BLAST
tax. iden. using BLAST
tax. iden. using BLAST
morph. tax. identification
date
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
2010
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
Moorea insect
inventory
identification 03.1
tax. iden. by morph.
key
Study
Moorea insect
inventory
Moorea insect
inventory
Moorea insect
inventory
process ID
tissue sampling 03
process type
material sampling
process
material sampling
process
tax. iden. using dna
barcode
dna isolation 03
identification 03.2
has specified
input
insect 03
has specified
output
insect taxon 01
has input
insect 03
has ouput
tissue sample 03
tissue sample 03 DNA sample 03
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