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Posts tagged ‘taxonomy’

Weekly reading: Balhoff et al. on a semantic model for wasp species description

Following Daduhl et al. and Vogt et al., our third paper in the phenotype ontologies Weekly Discussion series will dive into an applied example by Balhoff and co-authors (mainly of the Deans Lab) with a clear taxonomic emphasis. Already we have seen that different scientific orientations draw on phenotype ontologies with the expectation of reframing and solving specific problem complexes.

Daduhl et al.‘s focus was firmly within the bounds of evolutionary and phylogenetic analyses of phenotypes across broader and deeper taxonomic scales. Implementation challenges notwithstanding, there was an underlying agreement that the legacy of phenotype-centric systematic work could be appropriated towards the outlined representation and inference goals.

Vogt et al., in turn, emphasized a need for consistent, machine-processable standards with regards to phenotype syntactics, semantics, etc.; including a separation of descriptive and evolutionary/explanatory elements in our morphological terminology. This has the makings of a potentially divergent paradigm in relation to Daduhl et al.‘s program and perspective.

Another interesting development is the Phenoscape team’s exploration of homology relations in ontologies, outlined here: http://phenoscape.org/wiki/Reasoning_over_homology_statements.

In light of these different lines of research, we set ourselves two immediate questions to address:

1. What are actual applications that utilize phenotype ontologies and (optionally) reasoning for (a) multi-taxon studies with (b) an evolutionary/systematic orientation?

2. Suppose we had the “awesome ontology & reasoning” infrastructure on hand, where current technological limits no longer apply. What kinds of questions would  we ask this infrastructure to solve for us (that cannot be addressed otherwise)?

The paper for next week applies directly to these questions.

Balhoff, J.P., I. Mikó, M.J. Yoder, P.L. Mullins & A.R. Deans. 2013. A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639–659. Available on-line here.

ESA 2014 presentation – Aligning insect phylogenies: Perelleschus and other cases

Slides are up for the Euler/X Perelleschus (+) presentation at Entomology 2014.

Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases from taxonbytes

Knowledge Representation in Systematic Biology – Edited book proposal seeking comments, contributions

I have an opportunity to edit a new book in the series “Species and Systematics” (originally UC Press; now CRC Press). The draft outline is below, but is subject to change and expansion as deemed appropriate.

I am looking for suggestions, and for potential contributors (naturally, while reserving standard/common sense rights to kindly accept or decline). The book will to collect a number of strong, diverse chapters on various projects and directions in this still very young field. Lead authors of chapters will coordinate with co-authors as preferred. I also intend to give authors much freedom to do and say things they maybe could not express using different publication outlets (while keeping things fair and high-minded).

Another key issue is (of course) – who may have time and motivation to contribute an original and impactful chapter in the coming six months? Either way, I am open to suggestions, contact me on- or off-line.

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BIGCB Workshop at UC Berkeley: Tackling the Taxon Concept Problem

November 7-9, 2014. Coolest workshop theme, like, ever. Organized by Brent Mishler and Staci Markos of the UC Berkeley Jepson Herbarium.

Understanding Taxon Ranges in Space and Time: Tackling the Taxon Concept Problem

A Workshop Sponsored by the Berkeley Initiative in Global Change Biology

Friday, November 7, 2014, 1002 VLSB, open to all who are interested.

1:00 pm: Brent Mishler  –  Introduction to the themes and goals of this workshop.

1:10 pm: Edward Gilbert  –  Ideas for incorporating taxonomic concepts into Symbiota.

1:40 pm: Robert Guralnick  –  Map of Life and the challenge of heterogeneous names data for determining species ranges.

2:10 pm: Gaurav Vaidya  –  Tracking taxonomic changes: how, where and why, with examples from the Avibase database of taxon concepts. Link & PDF

2:40 pm: Coffee Break.

3:00 pm: Robert Peet  –  Taxon concepts as essential infrastructure for large-scale data integration: lessons from VegBank, SEEK and BIEN. PDF

3:30 pm: Nico Franz  –  Tracking taxonomic change across classifications and phylogenies. PDF

4:00 pm: Alan Weakley  –  Applying concept maps to 7100 vascular plants of the Southeastern United States, and some thoughts on ‘atomic concepts’ and their utility at the specimen level.  PDF

4:30 pm: Nico Cellinese  –  Thoughts on the right approach to query trees based on phyloreferences (ontologized phylogenetic definitions).


Additional Workshop Notes

  • Communicated by Robert Peet  –  Taxonomic concept infrastructure-related entities requiring identifiers. PDF

2014 UC Boulder Meaning of Names Conference in Review

A relatively short review of the timely conference “The Meaning of Names: Naming Diversity in the 21st Century”, held on September 30 to October 2nd, 2014, and organized by Rob Guralnick and the University of Colorado at Boulder Museum of Natural History.

I have uploaded the Conference Program for reference. I gave an update on Euler/X, the slides are shared again here. Some photos of the conference participants are posted on Flickr.

Having had an opportunity to present for 30 minutes allowed me to review some general ideas about names and concepts and apparently (given positive reactions) made the presentation more accessible. A number of engaging and thematically diverse presentations were in the line-up, although the diversity of domains of application did not necessarily mean immediate directional friction. Names – the “right ones” – remain essential to information transmission that employs human cognition and memorization. Among other fleeting observations, it seemed clear to me that the standard OBO Foundry approach to fixating the meaning of terms is not all that biodiversity informatics needs to integrate taxonomically annotated data. I also think we are at the cusp of separating more clearly and consistently what conventional taxonomic names can achieve for human communication, and what they need to achieve in addition to support scalable computational integration. Two Global Names Architecture presentations (Ellinor Michel and David Patterson, respectively) pointed that way. To what extent the “additional layer” for logic integration is needed, and justified by apparent representational and infrastructural costs, was an underlying theme of the conference. In other words – progress.

Franz. 2014. Explaining taxonomy’s legacy to computers – how and why? from taxonbytes

Conference presentation: Explaining taxonomy’s legacy to computers – how and why?

I will give an updated presentation on the Euler/X project and concept taxonomy at the conference “The Meaning of Names: Naming Diversity in the 21st Century”, held at the Museum of Natural History, University of Colorado – Boulder, on September 29 to October 01, 2014. Slides are posted on Slideshare, and linked here. Thanks to Rob Guralnick for the invitation!

Franz. 2014. Explaining taxonomy’s legacy to computers – how and why? from taxonbytes

Weekly reading: Witteveen on naming and contingency – the type method

This week: part II of our interim series of “new and interesting though not (yet) Next Generation Sequencing” papers. Joeri Witteveen is taking a new look at how the Codes of Nomenclature enforce contingent assignments of types to taxonomic names. Awesome!

Witteveen, J. 2014. Naming and contingency: the type method of biological taxonomy. Biology & Philosophy. Available on-line here.

Weevil Course 2014 – Running Notes

A running post with links to literature and on-line resources, presentations, identification support, and other information accompanying The Weevil Course 2014 (second installment) held from August 05-13 at the Southwestern Research Station in Portal, Arizona. Course related photos are posted on Flickr here.

1. Links to key course/identification resources

2. Miscellaneous course presentations

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