scientific names and descriptions for organisms on the semantic web nathan wilson 1, han wang 2, and...
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Scientific Names and Descriptions for Organisms on
the Semantic Web
Nathan Wilson1, Han Wang2, and Deborah McGuinness3
1 Marine Biological Laborary, 7 MBL St., Woods Hole, MA 02556, USA
[email protected] Tetherless World Constellation, Rensselaer Polytechnic Institute, 110 8th Street Troy, NY 12180, USA
[email protected] Tetherless World Constellation, Rensselaer Polytechnic Institute, 110 8th Street Troy, NY 12180, USA
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For Example…
• Chroogomphus vinicolor• Chroogomphus rutilus• Chroogomphus ochraceus• Chroogomphus• Pine Spike
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Candidate Names:
Chroogomphus vinicolor California, USA
© 2007 Darvin DeShazer CC-BY-NC
Pine Spike California, USA
© 1993 Nathan Wilson CC-BY
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• Take advantage of the crowd to understand the world’s biodiversity.
• Clarify connection between observations and scientific literature.
• Provide accurate and machine-interpretable definitions for groups of organisms.
• Build a central repository for semantic descriptions of groups of organisms.
Motivation
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What is a Species?
• Concept: “A group of organisms capable of interbreeding and producing fertile offspring”
• Definition: Type specimen, a name, and a circumscription that is believed to describe the species that specimen belongs to
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Definition of a Scientific Name
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Latin NameReference
Type
Circumscription
Problem: Circumscriptions change frequently
Cap: overlapping, wavy; multicolored concentric
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Definition of a Scientific Name
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Latin NameReference
Type
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
Multiple Circumscriptions
Cap: 2-10cm wide; overlapping or in a row or a rosette; kidney shaped, also described as fan shaped; can be flat to wavy; multicolored concentric
Cap: 2-10cm wide; overlapping, also rosette; can be flat to wavy; multicolored concentric; zones alternate
Cap: overlapping, wavy; multicolored concentric
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Scientific Names & Observations
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Scientific NamesObservations
Type
Circumscription(s)
People
Genetic Barcode
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Semantic Vernacular Description (SVD)
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SVD
Identifiere.g. SV1234
Namee.g. PineSpike
Descriptione.g.EquivalentTo: Fungus and (hasOverallShape some StipitateAgaric) and (hasHymenophoreShape some Gilled) and ((hasPileusDiscColor some Brown)...
Scientific Name(s)e.g. Chroogomphus rutilusChroogomphus vinicolorChroogomphus ochraceus
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Definition of a Scientific Name
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Latin NameReference
Specimen
SV5678SV4567SV3456SV2345
Multiple Circumscriptions
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SVDs
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SVDs Scientific NamesObservations
Type
Circumscription(s)
People
Genetic Barcode
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• Provides a controlled vocabulary for describing an observation.
• Associates an observation to one or more scientific names.
• Starts with macroscopic features.• Moving into microscopic, chemical, and
molecular features.• Generated by an open collaborative
process.
Fungal Ontology
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Observational Features
ObjectProperty: 'has surface color’ Annotations: label "has surface color"^^Literal SubPropertyOf: 'has color’ Domain: Fungus and (('has overall shape' some earthstar) or ('has overall shape' some gasteroid)) Range: 'Color Value Partition'
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Descriptions
Class: SV1112 Annotations: hasID "1112"^^positiveInteger EquivalentTo: Fungus and (('has surface color' some white) or ('has surface color' some gray) or ('has surface color' some off-white)) and ('has hymenophore shape' some 'spore mass') and ('has overall shape' some gasteroid) and ('has substrate attachment' some pileate-sessile)
SubClassOf: 'proposed at' value "2012-07-03T12:00:00-
05:00"^^dateTime, 'Vernacular Feature Description', 'proposed by' value SV1090
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SVDs
Class: SV1012 Annotations: hasID "1012"^^positiveInteger SubClassOf: 'has SVD name' value WhitePuffball, 'Semantic Vernacular Description', 'has definition' some SV1112, 'has associated scientific name' some 'Bovista pila', 'has associated scientific name' some 'Lycoperdon
perlatum'
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Fungal Ontology
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Highlights
• Explicit, fixed collection of observational features
• ‘Duck’ Typing: If it ‘looks’ like a PineSpike, it is a PineSpike
• Amenable to peer review/codification• Inherently unique• Stable for observers
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Peer-review Process
• Every SVD needs review before use• Alternative names and definitions can
be proposed• Discussion/voting happens where there
are alternatives• Votes are weighted according to users’
past contributions to the process
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Implementation Prototype
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• A Ruby on Rails application
• Triple store powered by Jena TDB
• RESTful web service ready for use
http://mushroomobserver.org/semantic_vernacular
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Questions? Comments?
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1. Artportalen, http://artportalen.se
2. Biodiversity Heritage Library, http://biodiversitylibrary.org
3. Encyclopedia of Life, http://eol.org
4. International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. ASM Press, Washington, DC, USA (1992)
5. International Code of Zoological Nomenclature. The International Trust for Zoological Nomenclature, London, UK, 4th edn. (2000)
6. Burdsall, H.H., Bank, M.T.: The Genus Laetiporus in North America. Harvard Papers in Botany 6(1),43{55 (2001)
7. Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balho, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westereld, M., Mabee, P.M.: The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology 59, 369{383 (2010), doi:10.1093/sysbio/syq013
8. Knapp, S., McNeill, J., Turland, N.J.: Changes to Publication Requirements Made at the XVIII Inter-national Botanical Congress in Melbourne - What Does e-Publication Mean for You? PhytoKeys 6(0),5{11 (2011), doi:10.3897/phytokeys.6.1960
9. Knowlton, N.: Sibling Species in the Sea. Annual Review of Ecology and Systematics 24, 189{216 (1993), doi:10.1146/annurev.es.24.110193.001201
10. Mayr, E.: The Bearing of the New Systematics on Genetical Problems. The Nature of Species. Advances in Genetics 2, 205{237 (1948)
11. McGuinness, D.L., van Harmelen, F.: OWL Web Ontology Language Overview. World Wide Web Consortium (W3C) Recommendation. (2004), http://www.w3.org/TR/owl-features/
12. Miko, I., Deans, A.R.: Masner, a New Genus of Ceraphronidae (Hymenoptera: Ceraphronoidea) Described Using Controlled Vocabularies. ZooKeys 20, 127{153 (2009), doi:10.3897/zookeys.20.119
13. Patterson, D.J., Cooper, J., Kirk, P.M., Pyle, R.L., Remsen, D.P.: Names are Key to the Big New Biology. Trends in Ecology & Evolution 25(12), 686{691 (2010), doi:10.1016/j.tree.2010.09.004
14. Sato, H., Yumoto, T., Murakami, N.: Cryptic Species and Host Specicity in the Ectomycorrhizal Genus Strobilomyces (Strobilomycetaceae). American Journal of Botany 94(10), 1630{1641 (2007)
15. Sullivan, B.L., Wood, C.L., Ili, M.J., Bonney, R.E., Fink, D., Kelling, S.: eBird: a Citizen-based Bird Observation Network in the Biological Sciences. Biological Conservation 142, 2282{2292 (2009),doi:10.1016/j.biocon.2009.05.006
16. Ueda, K., Loarie, S.: iNaturalist, http://inaturalist.org
17. Wilson, E.O.: The Future of Life. Random House Digital, Inc. (2002)
18. Wilson, N., Dunn, K., Wang, H., McGuinness, D.L.: Application of Semantic Technology to Define Names for Fungi. Tech. rep., Tetherless World Constellation at Rensselaer Polytechnic Institute (2012), http://tw.rpi.edu/web/doc/ApplicationofSemanticTechnologytoDefineNamesforFungi
19. Wilson, N., Hollinger, J.: Mushroom Observer, http://mushroomobserver.org
20. Yoder, M.J., Miko, I., Seltmann, K.C., Bertone, M.A., Deans, A.R.: A Gross Anatomy Ontology for Hymenoptera. PLoS ONE 5(12), e15991 (2010), doi:10.1371/journal.pone.0015991
AcknowledgementsKatie Dunn
Jason HollingerEncyclopedia of Life
Tetherless World ConstellationMarine Biological Laboratory
Rensselaer Polytechnic InstituteMushroom Observer Community