Agreeing to disagree: Reconciling conflicting taxonomic views using a logic‐based approach

Abstract

Taxonomy alignment is a way to integrate two or more taxonomies. Semantic interoperability between datasets, information systems, and knowledge bases is facilitated by combining the different input taxonomies into merged taxonomies that reconcile apparent differences or conflicts. We show how alignment problems can be solved with a logic-based region connection calculus (RCC-5) approach, using five base relations to compare concepts: congruence, inclusion, inverse inclusion, overlap, and disjointness. To illustrate this method, we use different "geo-taxonomies", which organize the United States into several, apparently conflicting, geospatial hierarchies. For example, we align T CEN , a taxonomy derived from the Census Bureau's regions map, with T NDC , from the National Diversity Council (NDC), and with T TZ , a taxonomy capturing the U.S. time zones. Using these case studies, we show how this logicbased approach can reconcile conflicts between taxonomies. We have implemented these case studies with an open source tool called Euler/X which has been applied primarily for solving complex alignment problems in biological classification. In this paper, we demonstrate the feasibility and broad applicability of this approach to other domains and alignment problems in support of semantic interoperability.

Through the magnifying glass: Exploring aggregations of COVID‐19 datasets by county, state, and taxonomies of U.S. regions

“…Figure 1 shows how the overview dataset is converted into two dataset D 1 and D 2 : D 1 uses T CEN , while D 2 uses T NDC . 2.4 | Reconciliation of taxonomies T CEN and T NDC are aligned and reconciled into a combined or "merged" taxonomy via a logic-based taxonomy alignment approach (Cheng et al, 2017). The method uses a qualitative reasoning approach (RCC-5), in which concepts in T CEN are mapped to T NDC using one of five base relations: equivalence, overlap, disjointness, inclusion, and inverse inclusion.…”

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

“…For complex alignment challenges, the toolkit workflow favors a partitioned, bottom-up approach [29]. The large problem of aligning all concepts is broken down into multiple smaller alignment problems, e.g.…”

“…4. Under the default logic reasoning constraint of parent coverage, differential child-level sampling will propagate up to yield incongruent relationships among the respective parent-level clade concepts [14,26,29]. Local relaxation of the coverage constraint can mitigate this effect.…”

“…Here we propose a solution to the phylogenomic conflict representation challenge. The solution is an extension of prior concept taxonomy research [14,25,26], and deploys logic reasoning to align tree hierarchies based on Region Connection Calculus (RCC-5) assertions of node congruence [27,28,29]. We demonstrate the feasibility of this approach by aligning subregions and entire phylogenomic trees of the 2015./2014.Neornithes as inferred by 2015.PEA and 2014.JEA.…”

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

“…This solution requires collaboration between systematic experts, platform designers, and users of phylogenomic information. It is an extension of prior "concept taxonomy" research [14, 25, 26], and deploys logic reasoning to align tree hierarchies based on Region Connection Calculus (RCC–5) assertions of node congruence [27, 28, 29]. We demonstrate the feasibility of this approach by aligning subregions and entire phylogenomic trees inferred by 2015.PEA and 2014.JEA.…”