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Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

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.

SUBMITTER: Franz NM

PROVIDER: S-EPMC4336294 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

Franz Nico M NM Chen Mingmin M Yu Shizhuo S Kianmajd Parisa P Bowers Shawn S Ludäscher Bertram B

PloS one 20150220 2

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 ...[more]

PMID: 25700173

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Project description:Background and aim: 'Reasoning 4 Change' (R4C) is a newly developed instrument, including four domains (D1-D4), to assess clinical practitioners' and students' clinical reasoning with a focus on clients' behaviour change in a physiotherapy context. To establish its use in education and research, its psychometric properties needed to be evaluated. The aim of the study was to generate criterion scores and evaluate the reliability and construct validity of a web-based version of the R4C instrument. Methods: Fourteen physiotherapy experts and 39 final-year physiotherapy students completed the R4C instrument and the Pain Attitudes and Beliefs Scale for Physiotherapists (PABS-PT). Twelve experts and 17 students completed the R4C instrument on a second occasion. The R4C instrument was evaluated with regard to: internal consistency (five subscales of D1); test-retest reliability (D1-D4); inter-rater reliability (D2-D4); and construct validity in terms of convergent validity (D1.4, D2, D4). Criterion scores were generated based on the experts' responses to identify the scores of qualified practitioners' clinical reasoning abilities. Results: For the expert and student samples, the analyses demonstrated satisfactory internal consistency (? range: 0.67-0.91), satisfactory test-retest reliability (ICC range: 0.46-0.94) except for D3 for the experts and D4 for the students. The inter-rater reliability demonstrated excellent agreement within the expert group (ICC range: 0.94-1.0). The correlations between the R4C instrument and PABS-PT (r range: 0.06-0.76) supported acceptable construct validity. Conclusions: The web-based R4C instrument shows satisfactory psychometric properties and could be useful in education and research. The use of the instrument may contribute to a deeper understanding of physiotherapists' and students' clinical reasoning, valuable for curriculum development and improvements of competencies in clinical reasoning related to clients' behavioural change.

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Dataset Information

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

Publications

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

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