Our group is giving a regular and a virtual poster on weevils at the 2013 Annual Meeting of the Entomological Society of America, held in Austin, TX. The corresponding PDFs are posted here (click on the titles). Andrew Jansen and Guanyang Zhang are also presenting on southwest U.S. and Cuban entimine weevils, respectively. An ESA 2013 meeting review will be forthcoming. The image shows Pachyrhinus californicus (Horn, 1976).
February, 2015. The first fleshed-out use case of reasoning over taxonomic concepts with the Euler/X toolkit is now published.
Franz, N.M., M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. doi:10.1371/journal.pone.0118247. Available on-line here.
An overview – initiated in early November, 2013 and regularly updated (throughout 2015) – of papers and presentations related to the taxonomic concept approach. Since the Fall/Winter of 2013 we have a working Python toolkit Euler/X (openly available on-line) that can read in two taxonomies (T1,T2), a set or articulations (A), and additional constraints (C). The toolkit then calls up Answer Set Programming reasoners to infer and visualize an alignment among the taxonomies that satisfies the constraints. A short video is posted here.
Euler/X merge of two Hominoidea classifications sec. Groves 1993/2005.
- See also the Euler Project website.
- Euler/X code is available here.
- David Thau et al.‘s work prior to Euler: listing and PDFs.
- Update February, 2014 (I): Analysis of the Andropogon use case.
- Update February, 2014 (II): Analysis of two weevil classifications.
- Update February, 2014 (III): Using the Euler/X toolkit to align taxonomies – introductory notes.
- Update March, 2014 (I): Alignment of two classifications of the Monotremata.
- Update April, 2014 (I): Perelleschus reasoning manuscript submitted to PLoS ONE. Abstract.
- Update April, 2014 (II): Progress in aligning the 1993/2005 Mammal Species of the World – Order Primates.
- Update May, 2014 (I): Names, identifications, and concepts (post related to GBIF Guidelines).
- Update June, 2014 (I): Perelleschus concept paper receives Outstanding Paper for 2013 Award.
- Update June, 2014 (II): We now have a completely aligned, consistent merge taxonomy for 317 x 483 concepts of Primates, sec. Groves (2003) and sec. Groves (2005), respectively. Manuscript in preparation.
- Update July, 2014 (I): TaPP 2014 – 6th USENIX Workshop on the Theory and Practice of Provenance – Poster by Chen et al.: Provenance for Explaining Taxonomy Alignments.
- Update July, 2014 (II): The new Euler/X server is set up at: http://euler.asu.edu/
- Update July, 2014 (III): Euler/X demonstration video.
- Update July, 2014 (IV): Zhang & Franz presentation on concept changes in the Heteroptera (5th Quadrennial Meeting of Heteropterists’ Society).
- Update August, 2014: Ludäscher et al. presentation at RuleML 2014.
- Update September,2014 (I): Revision – Franz et al. 2014. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE. PDF
- Update September, 2014 (II): 2014 Colorado “The Meaning of Names” Conference Presentation – Explaining taxonomy’s legacy to computers.
- Update September, 2014 (III): Euler server is now functional (internally) at http://euler.asu.edu/, we are working on increasing accessibility to external users.
- Update, November, 2014 (I): Perelleschus reasoning paper at arXiv
- Update, November, 2014 (II): BIGCB 2014 Workshop presentation.
- Update, November, 2014 (III): Entomological Society of America presentation.
- Update, December, 2014 (I): Primate alignment manuscript at arXiv.
- Update, January, 2015 (I): Radford, Ahles & Bell 1968 translated as Euler/X input tree.
- Update, January, 2015 (II): Euler source is migrating to GitHub at https://github.com/EulerProject.
Another weekly reading, an empirical paper focusing on a Mediterrranean tenebrionid beetle radiation – genus Blaps Fabricius – using the DEC model by Ree et al. Reference: Condamine, F.L., L. Laurent Soldati, A.-L. Clamens, J.-Y. Rasplus & G.J. Kergoat. 2013. Diversification patterns and processes of wingless endemic insects in the Mediterranean Basin: historical biogeography of the genus Blaps (Coleoptera: Tenebrionidae). Journal of Biogeography 40: 1899–1913. Available here.
This paper’s group leader Gael Kergoat participated in the Third International Tenebrionoidea Symposium held earlier this year at ASU.
This week’s reading, diving into geographic patterns below the species level: Lemey, P., A. Rambaut, A.J. Drummond & M.A. Suchard. 2009. Bayesian phylogeography finds its roots. PLoS Computational Biology 5(9): e1000520. Available here.
TDWG 2013 in Florence, Italy, has ended, and it was a great meeting at a gorgeous location. Shown on the photo (left to right): Hilmar Lapp of Phenoscape (NESCent), Mark Schildhauer of NCEAS, and Cynthia Parr of EOL. Our group presented 5 talks and chaired the “Formal Models” section of the Semantics for Biodiversity Symposium. Talks presented by Nico Franz are here; and some impressions from the Conference are posted here. There will be a guest edited Special Issue of the Semantic Web Journal with select papers given at the Symposium. Biodiversity informatics is a truly global discipline, and one of the interesting subcontexts of attending a TDWG meeting is to understand how different regions and initiatives around the world aim for creating a sustained, useful, modern informatics infrastructure for biodiversity data at both local and global scales.
Additional relevant links: