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Posts tagged ‘concept taxonomy’

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

Presentations and posters at ECN and ESA 2014

Our lab has had an eventful joint ECN/ESA 2014 meeting and presentation/poster schedule of activities. Most presentations are now posted. Great meetings – even won recognition for our Twitter contributions.

ECN 2014

Symposium – Harvesting the fruits of our labor: Utilizing collections databases to advance 21st century entomology.

1. Neil Cobb, Katja Seltmann & Nico Franz. 2014. The current state of arthropod biodiversity data: Addressing impacts of global change. Presentation.

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Taxonomic concept identification, reconciliation, and the Open Tree of Life – Part 1

“Part 1” – allowing for subsequent parts (e.g., for the blue/non-blue use case; now added at end of post). The relevant OpenTree background discussion is here:

https://github.com/OpenTreeOfLife/muriqui/issues/15

There as several interesting and generally closely overlapping issues and views here. I will pick just (or mainly) the one introduced by Jonathan Rees (November 02, 2014).

“Here’s another example I’m struggling with: there are currently a couple of species in OTT that are misclassified as crustaceans instead of molluscs. When we fix this problem, there will be an incompatible ‘change’ in the membership of Arthropoda. Does this mean that the new group should get a new identifier? – after all its identity in some sense has changed. If so, annotations and OTU mappings linked to the old id have no home in the tree. It doesn’t get a new id with the current taxonomy generator, which assumes that names are tied uniquely to taxon concepts (with some exceptions), but with a more principled system where groups are defined by membership or phylogenetic hypotheses, it might. This would have an impact on OTU mappings and annotation carryover. I don’t have a good answer to this one, but am working on ways to anchor the semantics of ids.”
 

I am attempting to reproduce this under varying scenarios in the Euler/X toolkit. Starting simple, then expanding. I have created an initial scenario with two phylogenetic perspectives of the Ecdysozoa (molting animals) sec. ott1 (= OpenTree Topology at time =1; the later version) versus Ecdysozoa sec. ott0 (OTT at time = 0; the earlier version. Initially, an alignment with complete taxonomic congruence.

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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

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

Ludäscher et al. presentation at RuleML 2014

Presentation slides are up for the latest (August, 2014) presentation on Euler/X concept taxonomy alignment, given by Bertram Ludäscher at “RuleML 2014” – The 8th International Web Rule Symposium held Prague, Czech Republic, August 18-20, 2014.

  • Chen, M., S. Yu, N. Franz, S. Bowers & B. Ludäscher. 2014. A hybrid diagnosis approach combining black-box and white-box approaches. RuleML 2014.

Bertram’s talk on Hybrid (Black-box + White-box) Diagnosis at RuleML’14 in Prague from ludaesch

THE bug meeting – International Heteropterists’ Society Meeting

Postdoctoral researcher Guanyang Zhang attended the 5th Quadrennial Meeting of the Heteropterists’ Society. The meeting took place at the Smithsonian National Museum of Natural History from July 21 to 25, 2014. Meeting program can be found here. The meeting was attended by more than 100 participants from several continents. There were about 50 talks and more than 20 posters. Topics centered around taxonomy and phylogenetics, but also included behavior, evolution and ecology. Click this link to see some meeting pictures and tweets: IHS meeting pictures and tweets.

Zhang & Franz 2014 – Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera from taxonbytes

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Overview of Euler/X toolkit commands

An overview of Euler/X toolkit commands, with examples of how and when to use. This post expands on the Euler/X introduction and demonstration video which show a linear pathway to producing a logically consistent multi-taxonomy alignment. Post in development.

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