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: 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-plot transect (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 sequences at 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:identifica tion process BCO:material sample OBI:sequencin g assay OBI:sequenc e data Genbank sequence B TaxonID A TaxonID B Tissue sampling DNA extraction Identificatio n using key Identification using BLAST Sequencing Biocode Sampling Tissue sample DNA molecules BCO:taxonomic name rdfs:Class

Example data: processes InvestigationStudyprocess IDprocess typehas inputhas ouputdate Moorea Biocode Project Moorea Biocode projectplanned process Moorea Biocode Project Moorea insect inventory planned process Moorea Biocode Project Moorea insect inventoryinsect collection 01 material sampling processinsect Moorea Biocode Project Moorea insect inventorytissue sampling 01 material sampling processinsect 01tissue sample Moorea Biocode Project Moorea insect inventory insect gut sampling 04 material sampling processinsect 01insect gut sample Moorea Biocode Project Moorea insect inventory insect gut sampling 05 material sampling processinsect 02insect gut sample Moorea Biocode Project Moorea insect inventorydna isolation 01 material sampling processtissue sample 01DNA sample Moorea Biocode Project Moorea insect inventorydna isolation 04 material sampling process insect gut sample 04DNA sample Moorea Biocode Project Moorea insect inventory insect observation 06observing processinsect in situ 06image Moorea Biocode Project Moorea insect inventoryidentification 01.1tax. iden. by morph. keyinsect 01insect taxon Moorea Biocode Project Moorea insect inventoryidentification 01.2 tax. iden. using dna barcodedna isolation 01insect taxon Moorea Biocode Project Moorea insect inventoryidentification 04.1tax. iden. using BLASTdna isolation 04microbial taxon Moorea Biocode Project Moorea insect inventoryidentification 06.1 morph. tax. identificationimage 01insect taxon Moorea Biocode Project Moorea insect inventoryidentification 07.1 morph. tax. identificationimage 02insect taxon

Example data: material entities and information artifacts IndividualTypeInferred type insect 01organism or virus or viroidmaterial sample insect 02organism or virus or viroidmaterial sample tissue sample 01organism partmaterial sample tissue sample 02organism partmaterial sample insect gut sample 04material entitymaterial sample DNA sample 01DNAmaterial sample DNA sample 02DNAmaterial sample insect in situ 06organism or virus or viroidmaterial target of observation image 01photographic imageinformation artifact insect taxon 01taxonomic nameinformation artifact insect taxon 02taxonomic nameinformation artifact microbial taxon 01taxonomic nameinformation artifact microbial taxon 02taxonomic nameinformation 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 Studyprocess IDprocess typedate Moorea insect inventoryinsect collection 01material sampling process2010 Moorea insect inventoryinsect collection 02material sampling process2010 Moorea insect inventorytissue sampling 01material sampling process2010 Moorea insect inventorytissue sampling 02material sampling process2010 Moorea insect inventoryinsect gut sampling 04material sampling process2010 Moorea insect inventoryinsect gut sampling 05material sampling process2010 Moorea insect inventorydna isolation 01material sampling process2010 Moorea insect inventorydna isolation 02material sampling process2010 Moorea insect inventorydna isolation 04material sampling process2010 Moorea insect inventorydna isolation 05material sampling process2010 Moorea insect inventoryinsect observation 06observing process2010 Moorea insect inventoryidentification 01.1tax. iden. by morph. key2010 Moorea insect inventoryidentification 02.1tax. iden. by morph. key2010 Moorea insect inventoryidentification 04.1tax. iden. using BLAST2010 Moorea insect inventoryidentification 04.2tax. iden. using BLAST2010 Moorea insect inventoryidentification 04.3tax. iden. using BLAST2010 Moorea insect inventoryidentification 04.4tax. iden. using BLAST2010 Moorea insect inventoryidentification 04.5tax. iden. using BLAST2010 Moorea insect inventoryidentification 06.1morph. tax. identification2010

List the output (“has specified output”) of every “taxonomic identification process” that has as input (“has specified input”) the "insect 03". Studyprocess IDprocess typehas specified input has specified output Moorea insect inventory identification 03.1tax. iden. by morph. key insect 03insect taxon 01 Studyprocess IDprocess typehas inputhas ouput Moorea insect inventory tissue sampling 03material sampling process insect 03tissue sample 03 Moorea insect inventory dna isolation 03material sampling process tissue sample 03DNA sample 03 Moorea insect inventory identification 03.2tax. iden. using dna barcode DNA sample 03insect taxon 03

Future directions - technical SPARQL endpoint with example queries – Check the BCO wiki ( Implement community curation tools such as Quick Term Templates or BioPortal – Requests can go to the Issue tracker now:

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

Questions? #!forum/bco-discuss