During the Taxonomic Database Working Group (TDWG) 2013 meeting in Florence, Italy, results of an early-state logic reasoning toolkit were presented. The toolkit is called "Euler/X", and is openly available atÂ
https://github.com/EulerProject/EulerX. Euler/X uses the syntax and semantics of the TDWG-ratified Taxonomic Concept Transfer Schema (
https://github.com/tdwg/tcs). It is a multi-hierarchy alignment reasoning tool that represents all
intra-hierarchy components as taxonomic concepts with parent/child relationships, and the
inter-hierarchy relationships as set constraints (Region Connection Calculus [RCC-5]: congruence, [inverse] inclusion, overlap, and exclusion). The use case presented at TDWG 2013 is now published at
http://dx.doi.org/10.1371/journal.pone.0118247.
Over the past three years we have worked broadly and deeply at the intersection of TCS syntax and semantics, logic reasoning with Euler/X, and the heterogeneous primary systematic literature. This work strongly indicates that we are achieving a novel, widely compatible way to represent and reconcile systematic progress and persistent conflict in ways that are more powerful than the Linnaean system yet entirely compatible with it, and are readily interpretable by humans and actionable by machines.
Progress with use cases - spanning angiosperm floras, primate classifications, insect revisions, and bird phylogenies - will be reviewed, showing that the foundations for linking systematic advancement to logic reasoning are well established. Former scalability bottlenecks are being resolved increasingly through custom reasoning solutions. At present, reconciling two input hierarchies, each with 1,500 taxonomic concept labels, is feasible on a desktop.
The TCS approach and related reasoning tools have profound implications for the development of biodiversity informatics. We will argue that this approach is ready now for direct integration with voucher-based biodiversity data portals, allowing systematic expert contributors to regain recognition for critical contributions to quality data packages, and users to control for the robustness of data-driven analyses while recognizing that taxonomic or phylogenetic structure is almost never a "constant", but instead a variable that we can logically represent and control for.
Because the TCS offers critical services to this field that the Darwin Core (DwC) standard alone is not designed to offer, our results also point to the need to eventually augment or replace DwC with a more suitable standard that achieves the semantics we need to reliably integrate biodiversity data at scale.
Reference:
Franz, N.M, N.M. Pier, D.M. Reeder, M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2016. Two influential primate classifications logically aligned. Systematic Biology 65(4): 561–582. doi:10.1093/sysbio/syw023
