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Biocode Commons / GSC14- bioCollections Ontology Hackathon Sep 19-20, 2012 OERC, Oxford, UK

Biocode Commons / GSC14- bioCollections Ontology Hackathon Sep 19-20, 2012 OERC, Oxford, UK.

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Biocode Commons / GSC14- bioCollections Ontology Hackathon Sep 19-20, 2012 OERC, Oxford, UK

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  1. Biocode Commons / GSC14- bioCollections Ontology HackathonSep 19-20, 2012OERC, Oxford, UK John Deck, Norman Morrison, SujeevanRatnasingham , PhillipeRocca-Serra, Barry Smith, Ramona Walls, Trish Whetzel, John Wieczorek, Jai Rideout, Matthew Bietz , Steve Stones-Havas, Gabi Droege, ÉamonnO’Tuama, Peter Sterk, Robert Robbins, Pier Buttigieg, Reed Beaman, Michelle Koo

  2. Our whiteboard - Diagramming samples and sample processes

  3. What is a Sample • A sample is a material entity that is taken out of its normal environment and is submitted to an institution or a measurement device. • Processes involving sampling or samples: • Collecting process • Data Sampling Process • Identification Process • Material Sampling Process • Observing Process • Physical Extraction Process • Process that yields a material representation of a material entity • Process that yields an information artifact that is a representation of a material entity • Selecting process • Statistical sampling process • Submitting process

  4. Linking Samples and Sampling Processes The sampling process can be characterized by a chain of distinct stages involving samples and processes. For example, assume we are studying the metagenome from a fish gut.   The following steps could be identified as distinct samples and associated processes in this chain: • ProcessX (removing Fish from a reef by method at location) to derive sampleX • ProcessY (remove goop from sampleX stomach bymethodA) to derive sampleY • ProcessZ (remove DNA extract from sampleY) to derive sampleZ • ProcessA runs sequencing on sampleZ to derive sequenceA

  5. What we accomplished • bioCollections/Sample OWL output:http://biocode-commons.googlecode.com/svn/trunk/ontologies/biocollections/biocode.owl • 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)

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