The document discusses using algorithmic and semantic approaches to improve next-generation taxonomic descriptions of microbial eukaryotes. It presents examples of using ontologies and semantic phenotype descriptions to represent taxonomic characteristics in a computable way. The goal is to apply data-driven techniques to microbial eukaryote taxonomy and allow phenotypic data to be integrated into analyses to provide new insights.

1. Next-Gen Taxonomic Descriptions
for Microbial Eukaryotes
Anne E Thessen
annethessen@gmail.com
http://www.slideshare.net/athessen
The Data Detektiv

2. Acknowledgements
• Hong Cui
• Jim Balhoff
• David Patterson
• Shauna Murray

3. Data-Driven Discovery
• “Data Deluge”
• Large-scale problems
• Maturation of the
internet
• Increased investment
(e.g., EOL, NSF)
• Importance of
microbial eukaryotes

4. Apply Data-Driven Discovery to
Microbial Eukaryote Taxonomy

5. Using Algorithmic Approaches in
Taxonomy

6. Using Algorithmic Approaches in
Taxonomy

7. Using Semantics in Microbial
Eukaryote Taxonomy
• Example: Gymnodinium

8. Using Semantics in Microbial
Eukaryote Taxonomy

9. Using Semantics in Microbial
Eukaryote Taxonomy
• Gene Ontology
• Ontology of Biological Attributes
• Phenotype and Trait Ontology
• Environment Ontology
Dinoflagellate Cingulum
http://purl.obolibrary.org/obo/GO_0097611

10. Using Semantics in Microbial
Eukaryote Taxonomy
• Exploring Taxon Concepts, Hong Cui, University of
Arizona
Cell Surface Texture
http://purl.obolibrary.org/obo/OBA_1000084
Striated
http://purl.obolibrary.org/obo/PATO_0001410
Cingulum Type
http://eol.org/schema/terms/CingulumType
Descending Cingulum
http://eol.org/schema/terms/descendingCingulum

11. Using Semantics in Microbial
Eukaryote Taxonomy
• Semantic Taxon Descriptions
Character Description Semantic Phenotype
1. Cell Surface Texture
Striated has part some (cell surface texture and (is bearer of some stria))
2. Cingulum Type
Descending has part some (cingulum type and (is bearer of some descending))
Cell Surface Texture
http://purl.obolibrary.org/obo/OBA_1000084
Striated
http://purl.obolibrary.org/obo/PATO_0001410
Cingulum Type
http://eol.org/schema/terms/CingulumType
Descending Cingulum
http://eol.org/schema/terms/descendingCingulum
“Body covered with longitudinal striæ” and “transverse groove conspicuously left-handed”

12. Phenotype -> Character State -> Character -> Specimen
Balhoff et al. 2013. A semantic model for species description applied to the ensign wasps
(hymenoptera: evaniidae) of New Caledonia. Syst. Biol.

13. Using Semantics in Microbial
Eukaryote Taxonomy

14. Why Use Semantics?
• Computable phenome data

15. Why Use Semantics?
• Computable phenome data
• Fill in gaps in genomic data
– Fossil taxa
– Gymnodinium (2012)
• 7% of described species have a sequence in GenBank
• 70% are ambiguous Gymnodinium sp.

16. Conclusion
• Apply benefits of data-driven discovery to
microbial eukaryote taxonomy and
systematics
• Difficult transition from human-readable to
machine-readable
• Phenomic data made first-class analytical
citizens
• New insights from old data

17. Questions?
Interested in applying these methods to your
favorite taxon? annethessen@gmail.com

18. Semantics in Taxonomy Example
• Encyclopedia of Life,
TraitBank

19. Semantics in Taxonomy Example
• Which members of Corvidae have a body mass
less than 500g?

20. Gymnodinium
Cingulum Type
Descending