Biocode Commons Hackathon -- bioCollections Ontology Workshop September 19-20, 2012

Hosted at the Oxford e-Research Center, Oxford, UK

Sponsored by GSC, BiSciCol (NSF), Biocode Commons, in collaboration with the Oxford e-Research Center.

The bio-collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples".  Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. We will be modeling these concepts in the context of BFO.  While the TDWG and GSC community has not yet endorsed BFO, we feel this is a useful exercise to: 1) test the utility of BFO for such modeling, and 2) provide a framework for understanding the relationship of terms between biodiversity genomics and other domains, 3) assist in the task of writing better definitions for both Darwin Core and MIxS, and 4) educating those in the community about how to implement and understand semantics for use in biodiversity.

Summary Report of this Workshop

What we accomplished

•Creatred a bioCollections Ontology. Prototype available at:
•Proposed Darwin Core minor clarifications:
Expand Basis of Record to include DNAExtract, Subsampled Tissue

Action Items

•GOs Registry (John D/ Eamonn utilize GBIF registry? will bring up w/ Gos)
•Explore Integration with OBI  (Rocca-Serra/ Deck/Morrison)
•Invite feedback from community via bioPortal (Whetzel/ bioPortal)
•Propose DwC Minor Clarifications at TDWG12 (Wieczorek)
•Whitepaper: SOB, Biocode Commons Hackathon, Darwin Core DNA Extension (Deck/Bob R  leading, Gabi, Ramona)
•Darwin Core DNA Extension follow-up with GGBN (Deck, Gabi, Eamonn)
•Darwin Core Major clarifications: Build concept of Sample, and clarify other concepts (Deck bring up with TDWG-RDF group at TDWG12)

John Deck, Norman Morrison, Sujeevan Ratnasingham , Phillipe Rocca-Serra, Barry Smith, Ramona Walls, Trish Whetzel, John Wieczorek, Jai Rideout, Matthew Bietz , Steve Stones-Havas, Gabi Droege, Éamonn O ’Tuama, Peter Sterk, Robert Robbins, Pier Buttigieg, Reed Beaman, Michelle Koo