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.
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.
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:
Presentation slides are now posted for the TDWG 2013 ASP Taxonomy Nomenclature talk.
Using Answer Set Programming to Simulate the Interplay of Taxonomic and Nomenclatural Change
Nico Franz, Joohyung Lee & Chao Zhang
Date: 2013-11-01 10:03 AM – 10:11 AM
Presentation slides are now posted for the TDWG 2013 Global Names talk.
Presentation slides are now posted for the TDWG 2013 Symbiota LBCC Crowd Sourcing talk. Thanks to Ed Gilbert, Ben Brandt, and Corinna Gries for timely feedback. An overview of the new crowd sourcing module’s functions and “rules for engagement” for prospective contributors and collection managers is here.
Presentation slides are now posted for the TDWG 2013 SCAN talk.
Date: 2013-10-29 02:45 PM – 02:50 PM
SCAN – the Southwest Collections of Arthropods Network (http://symbiota1.acis.ufl.edu/scan/portal/) – is the first regional arthropod biodiversity data network that utilizes the Symbiota software platform (http://symbiota.org/tiki/tiki-index.php). Since its origin in 2012 SCAN has unified and newly created specimen-level occurrence records on-line pertaining to nearly 15 south-western United States arthropod collections; including more than 515,000 records that represent some 18,000 species. However, due to the disproportionately mismatched diversity versus taxonomic expertise for the region and focal taxa, at least one third of the specimens are not identified (authoritatively or otherwise) to the level of species, with concomitant limitations for derivative taxonomic or evolutionary/ecological research. The member collections are typically separated from each other geographically by distances that prohibit frequent interactions with regional or global experts, except in virtual realm. SCAN has therefore implemented a Filtered Push (FP) based service (http://wiki.filteredpush.org/wiki/) whose primary purpose is to connect high-quality imaged of yet insufficiently identified specimens with suitable experts who can provide identifications remotely. This is achieved through the FP-server system which both records these contributions externally and pushes them back into the source Symbiota platform for review, acceptance, or rejection by the respective collection/node leaders. SCAN is therefore primed to utilize FP at a large scale and with a well circumscribed focal purpose that is relevant to the specific needs of this collections network. We illustrate the SCN/FP workflow, underlying concepts and technology, and current state of implementation and usage. FP allows experts to gradually accumulate credit and “reputations” for their identification contributions, and thus represents a promising means to improve data quality through transparent and distributed expert involvement and attribution.