Application of Semantic Technology to Define Names for Fungi Nathan Wilson Tuesday, July 17, 12 Who am I? • Naturalist • Mycologist • Software Professional • Director of Biodiversity Informatics for EOL • Director of the MBL Center for Library and Informatics Tuesday, July 17, 12 Mushroom Observer http://mushroomobserver.org/ Tuesday, July 17, 12 Linnaeus, We Have a Problem! • Cryptic Species • Paraphyletic & Polyphyletic Groups • Convergent Evolution • Changing Circumscriptions Tuesday, July 17, 12 Cryptic Species Tuesday, July 17, 12 Who spiked the pine? Tuesday, July 17, 12 Candidates • Pine Spike • Chroogomphus vinicolor • Chroogomphus rutilus • Chroogomphus ochraceus Tuesday, July 17, 12 Chroogomphus vinicolor Tuesday, July 17, 12 Para/Polyphyly Tuesday, July 17, 12 What’s white or red and spicy!? © Nathan Wilson © Dimitar Bojantchev © Oluna & Adolf Ceska Tuesday, July 17, 12 Convergent Evolution Tuesday, July 17, 12 Who likes truffles? © Noah Siegel © Mary Smiley © Daniel B. Wheeler © Nathan Wilson © Oluna & Adolf Ceska Tuesday, July 17, 12 Gasteromycetes anyone? © Nathan Wilson © Noah Siegel Tuesday, July 17, 12 Changing Circumscriptions Tuesday, July 17, 12 Definition of a Scientific Name Reference Latin name Type Circumscription Cap: 2-10cm wide; usually overlapping or in a row or a rosette; kidney shaped, also described as fan shaped, sometimes fused laterally; can be flat to wavy; multicolored concentric zoning on the upper surface; zones alternate between Tuesday, July 17, 12 Definition of a Scientific Name Reference Latin name Type Circumscription(s) Cap: 2-10cm wide; usually overlapping or in a row or a rosette; kidney shaped, also Cap: 2-10cm wide; described as fan shaped, overlapping or in a row or a sometimes fused laterally; rosette; kidney shaped, also Cap: 2-10cm wide; can be flat to wavy; described as fan shaped; can overlapping, also rosette; can multicolored concentric be flat to wavy; multicolored be flat to wavy; multicolored Cap: 2-10cm wide; zoning on the upper surface; concentric concentric; zones alternate overlapping, wavy; zones alternate between Tuesday, July 17, 12 Why Bad Things Happen to Good Taxonomists Tuesday, July 17, 12 Observations & Scientific Names Circumscription(s) People Observations Scientific Names Barcodes Type Tuesday, July 17, 12 Can Technology Save (or at least help) Our Heros? Tuesday, July 17, 12 The Semantic Web • A particular system for representing and extracting ‘meaning’ from the World Wide Web • Sparse data is easy • Data merging is trivial Tuesday, July 17, 12 A ‘Triple’ • (<subject>, <predicate>, <object>) • “Laetiporus sulphureus” “is a” “Laetiporus” • :Laetiporus_sulphureus rdfs:subClassOf :Laetiporus . Tuesday, July 17, 12 An OWL Description Tuesday, July 17, 12 Semantic Vernacular Description Identifier: SV1234 SVD Name: PineSpike EquivalentTo: Fungus and (hasOverallShape some StipitateAgaric) and (hasHymenophoreShape some Gilled) and ((hasPileusDiscColor some Brown) ... Chroogomphus rutilus Chroogomphus ochraceus Chroogomphus vinicolor Tuesday, July 17, 12 Definition of a Scientific Name Reference Latin name Specimen Circumscription(s) SV9876543 SV8756431 SV7564627 SV6643978 Tuesday, July 17, 12 Observations, Scientific Names & SVDs Circumscription(s) People Observations SVDs Scientific Names Barcodes Type Tuesday, July 17, 12 Features of an SVD • Explicit, fixed collection of observable features • If it ‘looks’ like a PineSpike, it is a PineSpike • Amenable to peer review/codification • Inherently unique • Stable Tuesday, July 17, 12 Complementary to Scientific Names • Real world / Computable • Phylogenetic / Observable • Scientific literature / Field identification • Connections easy to make Tuesday, July 17, 12 How Do We Get Started? Tuesday, July 17, 12 May I Have a Few Volunteers from the Audience? Tuesday, July 17, 12 Need a Fungal Ontology • References for features and values • Online definitions • Open collaborative process • Start with macroscopic features • Move into microscopic, chemical & molecular features Tuesday, July 17, 12 Peer Review Process • Review should be online & reasonably fast • Need review before use • Alternative names & semantic definitions • Support from some number of people • Measurable collaborative process • Is there a role for anonymous review? Tuesday, July 17, 12 Acknowledgements • Deborah McGuinness • Kathryn Dunn • Han Wang • Tom Volk Tuesday, July 17, 12 Questions? Tuesday, July 17, 12.