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Posts tagged ‘integration’

ICE 2016 Orlando Symposium proposal – Building the Biodiversity Knowledge Graph for Insects

Calls are going out currently to submit Symposium proposals for the XXV International Congress of Entomology (ICE 2016) in Orlando. Here is the summary for one such proposal led by Nico Franz and Katja Seltmann and intended for the category: Biodiversity, Biogeography and Conservation Biology. If you would like to contribute as potential speaker to this Symposium proposal, please contact Nico Franz (s0on).

Title: Building the Biodiversity Knowledge Graph for Insects – Components, Progress, Challenges.
Presentation Type: Combination Oral and Poster Presentations.

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Weekly reading: Daduhl et al. on the Teleost Anatomy Ontology

Last semester’s Weekly Discussion series dealt with Next Generation Sequencing technologies and related informatics challenges and advances. A review of what we read and discussed remains pending. Meanwhile we have selected a topic for the coming Spring 2014 semester:

Phenotype ontologies – origins, theory, applications, prospects, and challenges.

As usual we will place an emphasis on the utility of ontology-centered approaches for systematics – phylogenetics, taxonomy – in particular. The series starts off with a helpful paper that covers a lot of ground and is closely aligned with the OBO Foundry community.

Dahdul, W.M., J.G. Lundberg, P.E. Midford, J.P. Balhoff, H. Lapp, T.J. Vision, M.A. Haendel, M. Westerfield & P.M. Mabee. 2010. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology 59: 369-383. Available on-line here.

Prior work on concept taxonomy – 2013 onwards

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.

Hominoidea1993-2005

Euler/X merge of two Hominoidea classifications sec. Groves 1993/2005.


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