Collaboratively Creating Computable Species Descriptions

Nathan Wilson Marine Biological Laboratory Director of Biodiversity Informatics for the Encyclopedia of Life

Text and most images are licensed under the Creative Commons Attribution, Share-Alike 3.0 License Images marked with † are licensed under the Creative Commons Attribution, Share-Alike, Non-Commercial 3.0 License Images marked with †† are licensed under the Creative Commons Attribution, Share-Alike, Non-Commercial 2.5 License EOL TraitBank EOL TraitBank Existing Species Descriptions

Species Databases In Text (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) Existing Species Descriptions

Species Databases In Text, but (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) difficult to reliably extract Existing Species Descriptions

Species Databases In Text, but (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) difficult to reliably extract

Computer Id Systems Digital (DELTA, Lucid, DiscoverLife, MatchMaker...) Existing Species Descriptions

Species Databases In Text, but (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) difficult to reliably extract

Computer Id Systems Digital, but hard to scale (DELTA, Lucid, DiscoverLife, MatchMaker...) and maintain Existing Species Descriptions

Species Databases In Text, but (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) difficult to reliably extract

Computer Id Systems Digital, but hard to scale (DELTA, Lucid, DiscoverLife, MatchMaker...) and maintain

Observation Platforms In User’s Heads (GBIF, Artsdatabanken, iNaturalist, eBird, MushroomObserver...) Existing Species Descriptions

Species Databases In Text, but (EOL, BHL, ARKive, Animal Diversity Web, MushroomExpert...) difficult to reliably extract

Computer Id Systems Digital, but hard to scale (DELTA, Lucid, DiscoverLife, MatchMaker...) and maintain

Observation Platforms In User’s Heads, but (GBIF, Artsdatabanken, iNaturalist, eBird, MushroomObserver...) more crowd source-able Identification Processes

Circumscription(s)

People Observations Scientific Names

Barcodes Type

[email protected] - http://mushroomobserver.org - http://eol.org Cryptic Species

PineSpike California, USA © 1993 Nathan Wilson

Chroogomphus ochraceus vinicolor California, USA © 2007 Darvin DeShazer† California, USA © 2013 Ron Pastorino† [email protected] - http://mushroomobserver.org - http://eol.org 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 velvety and smooth; color varies quite a bit, shades

[email protected] - http://mushroomobserver.org - http://eol.org Definition of a Scientific Name

Reference Latin name Type

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; can rosette; kidney shaped, also Cap: 2-10cm wide; be flat to wavy; multicolored described as fan shaped; can be overlapping, also rosette; can concentric zoning on the upper flat to wavy; multicolored be flat to wavy; multicolored surface; zones alternate concentric Cap: 2-10cm wide; concentric; zones alternate between velvety and smooth; ; zones alternate between overlapping, wavy; color varies quite a bit, shades Formal Circumscription(s) [email protected] - http://mushroomobserver.org - http://eol.org Definition of a Scientific Name Informal Descriptions

Field Guides Reference Gray Latin name Literature Type Word of Mouth

Online Cap: 2-10cm wide; usually overlapping or in a row or a Descriptions rosette; kidney shaped, also Cap: 2-10cm wide; described as fan shaped, overlapping or in a row or a sometimes fused laterally; can rosette; kidney shaped, also Cap: 2-10cm wide; be flat to wavy; multicolored described as fan shaped; can be overlapping, also rosette; can concentric zoning on the upper flat to wavy; multicolored be flat to wavy; multicolored surface; zones alternate concentric Cap: 2-10cm wide; concentric; zones alternate between velvety and smooth; ; zones alternate between overlapping, wavy; color varies quite a bit, shades Formal Circumscription(s) [email protected] - http://mushroomobserver.org - http://eol.org Definition of a Scientific Name

Reference Latin name Type

Circumscription(s) SV9876543 SV8756431 SV7564627 SV6643978

[email protected] - http://mushroomobserver.org - http://eol.org Semantic Vernacular Description Identifier: SV1234 SVD Name: PineSpike

EquivalentTo: and (hasOverallShape some StipitateAgaric) and (hasHymenophoreShape some Gilled) and ((hasPileusDiscColor some Brown) ...

Chroogomphus rutilus Chroogomphus ochraceus

[email protected] - http://mushroomobserver.org - http://eol.org Observations & Scientific Names

Circumscription(s)

People Observations SVD Scientific Names

Barcodes Type

[email protected] - http://mushroomobserver.org - http://eol.org 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

✦ Essentially a semantic morpho-species Goals

✦ Formal names for observational experiences

✦ Stabilize observation data

✦ Capture what was observed

✦ Generate stable, computable PineSpike California, USA © 1993 Nathan Wilson descriptions

[email protected] - http://mushroomobserver.org - http://eol.org Prototype http://mushroomobserver.org/semantic_vernacular

[email protected] - http://mushroomobserver.org - http://eol.org Ontology Development

✦ Must be user extensible

✦ Reuse is divine (EnvO, PATO, UBERON...)

✦ Common patterns => Templates

✦ Community-based review/versioning process Review Process

✦ Review should be online & reasonably fast

✦ Need review before official use

✦ Chance for alternative names & semantic definitions

✦ Is there a role for anonymous review? Acknowledgements

✦ Deborah McGuinness

✦ Han Wang

✦ Katie Dunn

✦ Jason Hollinger

✦ Observer Community Cantharellus californicus Arora & Dunham California, USA ✦ EOL & Marine Biological © 2002 Nathan Wilson Laboratory

[email protected] - http://mushroomobserver.org - http://eol.org