Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal
Authors: Franz Nico , Gilbert Edward , Ludäscher Bertram , Weakley Alan 
Published: September 2016

Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1) representation of taxonomic concept labels (TCLs: name sec. source) to precisely identify name usages and meanings, (2) use of parent/child relationships to assemble separate taxonomic perspectives, and (3) expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion) that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records.
Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1) We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2). We will leverage RCC–5 data from the Weakley Flora and further development of the Euler/X logic reasoning toolkit to provide comprehensive genus- to variety-level concept alignments for at least 10 major flora treatments with highest relevance to SERNEC. The visualizations and estimated &gt; 1 billion inferred concept-to-concept relations will effectively drive specimen data integration in the transformed portal. (3) We will expand Symbiota's taxonomy and occurrence schemas and related user interfaces to support the new concept data, including novel batch and map-based specimen determination modules, with easy output options in Darwin Core Archive format. (4) Through combinations of the new technology, enlisted taxonomic expertise, and SERNEC's large image resources, we will upgrade minimally 80% of all SERNEC specimen identifications from names to the narrowest suitable TCLs, or add "uncertainty" flags to specimens needing further study. (5) We will utilize the novel tools and data to demonstrate how controlling for the taxonomic variable in 12 use cases variously drives the outcomes of evolutionary, ecological, and conservation-based research hypotheses.
Broader impacts. Our project is focused on just one herbarium network, but the potential impact is as wide as Darwin Core or even comparative biology. We believe that trust in networked biodiversity data depends on open and dynamic system designs, allowing expert access and resolution of multiple conflicting views that reflect the complex realities of ongoing taxonomic research. Taking well over 1 million SERNEC records from name- to TCL-resolution will show that "big" specimen data can pass the credibility threshold needed to validate the substantive data mobilization investment. We will mentor one postdoctoral researcher (UNC), two Ph.D. students (ASU, UIUC), and at least 15 undergraduate students (ASU). Each of our workshops will capacitate 10-15 SERNEC experts, who in turn can recruit colleagues and students at their home collections. We will incorporate the project theme and use cases into undergraduate courses taught at six institutions and reaching an estimated 300-500 students annually (10-40% minority students). At each institution, project members will make a systematic effort to recruit new students from underrepresented groups. Our group's leadership of Symbiota (with close ties to iDigBio), SERNEC, and local biodiversity projects and centers will further promote the new data culture. We will create a feature story "Where do plant species occur?" for ASU's popular "Ask A Biologist" website, and a series of undergraduate student-led "How-To" videos that illustrate the use case workflows, including the creation of multi-taxonomy alignments.