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
nwilson@mbl.edu
2 Tetherless World Constellation, Rensselaer Polytechnic Institute, 110 8th Street Troy, NY 12180, USA
wangh17@rpi.edu
3 Tetherless World Constellation, Rensselaer Polytechnic Institute, 110 8th Street Troy, NY 12180, USA
dlm@cs.rpi.edu
For Example…
Candidate Names:
Pine Spike California, USA
© 1993 Nathan Wilson CC-BY
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•
•
•
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Chroogomphus vinicolor
Chroogomphus rutilus
Chroogomphus ochraceus
Chroogomphus
Pine Spike
Chroogomphus vinicolor California,
USA
© 2007 Darvin DeShazer CC-BY-NC
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1
Motivation
• Take advantage of the crowd to
understand the world’s biodiversity.
• Clarify connection between
observations and scientific literature.
• Provide accurate and machineinterpretable definitions for groups of
organisms.
• Build a central repository for semantic
descriptions of groups of organisms.
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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
Latin Name
Reference
Type
Circumscription
Cap: overlapping, wavy;
multicolored concentric
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Problem: Circumscriptions
change frequently
4
Definition of a
Scientific Name
Latin Name
Reference
Type
Cap: overlapping, wavy;
multicolored concentric
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Cap: 2-10cm wide;
overlapping, also rosette;
can be flat to wavy;
multicolored concentric;
zones alternate
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
Multiple Circumscriptions
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
5
Scientific Names
& Observations
Circumscription(s)
People
Observations
Genetic Barcode
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Scientific Names
Type
6
Semantic Vernacular
Description (SVD)
SVD
Identifier
Scientific Name(s)
e.g. SV1234
e.g.
Chroogomphus rutilus
Chroogomphus vinicolor
Chroogomphus ochraceus
Name
Description
e.g. PineSpike
e.g.
EquivalentTo:
Fungus
and (hasOverallShape some StipitateAgaric)
and (hasHymenophoreShape some Gilled)
and ((hasPileusDiscColor some Brown)
...
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Definition of a
Scientific Name
Reference
Latin Name
Specimen
SV2345
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SV3456
SV4567
Multiple Circumscriptions
SV5678
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SVDs
Circumscription(s)
People
Observations
SVDs
Genetic Barcode
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Scientific Names
Type
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Fungal Ontology
• 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.
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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 "2012-07-03T12:00:0005:00"^^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
• 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?
Acknowledgements
Katie Dunn
Jason Hollinger
Encyclopedia of Life
Tetherless World Constellation
Marine Biological Laboratory
Rensselaer Polytechnic Institute
Mushroom Observer Community
11/12/2012
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