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Posts tagged ‘Euler/X’

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

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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