@article{franz2015reasoning,
  title = {Reasoning over {{Taxonomic Change}}: {{Exploring Alignments}} for the {{Perelleschus Use Case}}},
  volume = {10},
  issn = {1932-6203},
  shorttitle = {Reasoning over {{Taxonomic Change}}},
  doi = {10.1371/journal.pone.0118247},
  abstract = {Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz \& Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.},
  number = {2},
  urldate = {2017-04-11},
  url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118247},
  journal = {PLOS ONE},
  author = {Franz, Nico M. and Chen, Mingmin and Yu, Shizhuo and Kianmajd, Parisa and Bowers, Shawn and Lud\"ascher, Bertram},
  month = feb,
  year = {2015},
  keywords = {EulerProject,Taxonomy,Phylogenetics,Reasoning,Ontologies,Multiple alignment calculation,Phylogenetic analysis,Biodiversity,Controlled vocabularies},
  pages = {e0118247},
  file = {/Users/ludaesch/Dropbox/zotero/storage/CVRXFHVF/franz2015reasoning.pdf;/Users/ludaesch/Dropbox/zotero/storage/D9EBMMBV/article.html}
}

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Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. 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