Stefan Seifert’s research while affiliated with Bavarian Natural History Collections and other places

Description: This subset of the LIAS light database focuses on lichens found in Switzerland, providing comprehensive data for ecological research and taxon identification purposes. Not all taxa and only categorical (but 2 numerical) characters (descriptors) of the recorded taxa are covered. Updates and additional data will be published subsequently.

There is a growing demand for monitoring pests in natural history collections (NHCs) and establishing integrated pest management (IPM) solutions (Crossman and Ryde 2022). In this context, up-to-date taxonomic reference lists and controlled vocabularies following standard schemes are crucial and facilitate recording organisms detected in collections. The data pipeline described here results in the publication of a taxon reference list based on information from online resources and standard IPM literature. Most of the over 140 pest taxa on species level and above are insects, the rest belong to other animal groups and fungi. The complete taxon names, synonyms, English and German common names, and the hierarchical classification (parent-child relationships) are organised in a client-server installation of DiversityTaxonNames (DTN) at the Bavarian Natural History Collections (SNSB). DTN is a Microsoft Structured Query Language (MS SQL) database tool of the Diversity Workbench (DWB) framework with a published Entity Relation (ER) diagram (Hagedorn et al. 2019). The management is done using the Global Biodiversity Information Facility (GBIF) backbone taxonomy as external name resource, with linkage to the respective Wikidata Q item ID as a external persistent identifier (PID). Moreover, information on pest occurrence in NHCs is given, distinguishing the Consortium of European Taxonomic Facilities (CETAF) major NHC collection types affected (i.e., heritage sciences, life sciences and earth sciences) and the object categories, e.g., natural objects/specimens damaged. The data management in DTN enables the long-running curation, done by list curators. The generic data pipeline for the management and publication of a Global Taxonomic Reference List of Pests in NHCs is based on the DTN taxon lists concept and architecture and described under About "Taxon list of pest organisms for IPM at natural history collections compiled at the SNSB". It includes four steps (A–D) with significant results for best practices of data processing (Fig. 1). A. The data is managed and processed for publication by list curators in the database DiversityTaxonNames (DTN). As a result, the list can be kept up-to-date and is—without transformation—ready to be used for IPM solutions at any NHC with a DiversityCollection installation and as part of the DWB cloud services. B. The up-to-date data is publicly available via the DTN REST Webservice for Taxon Lists with machine-readable Application Programming Interface (API). As a result, the dynamic list publication service can be used as a reference backbone for establishing IPM solutions for pest monitoring at any NHC. C. The data is provided via the GBIF checklist data publication pipeline of the SNSB through GBIF validation tools and Darwin Core Archive in DwC-A (zip format) for GBIF. As a result, the checklist information becomes part of the GBIF network with GBIF ChecklistBank and GBIF Global Taxonomy. This ensures future compliance of data with the Findability, Accessibility, Interoperability, and Reuse (FAIR) guiding principles. D. The DTN REST Web service for Taxon Lists (currently 60 lists) is registered and accessible through the German Federation for Biological Data (GFBio) Terminology service. As a result, the lists with external PIDs and other information are available as a service (see DTN lists overview). In the upcoming Research Data Commons of the German National Research Data Infrastructure (NFDI) Initiative (Diepenbroek et al. 2021), it will be part of a standardized layer of APIs with an agreed interface scheme for improved accessibility. The provided tools, API and data are part of the upcoming NFDI4Biodiversity service portfolio. Future scenarios include the use of the list items and properties as classes for diagnosis purposes with DiversityNaviKey (Triebel et al. 2021) including the publication of images for identifying pests.

The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest. In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.

"IndExs—Index of Exsiccatae" is an online database with bibliographic information on exsiccatae and exsiccata-like series launched in 2001 (Triebel and Scholz 2022). This type of series is a specific system in botany and mycology to create, publish and distribute well identified and documented reference material. In most cases the distributed specimens are numbered and each number consists of uniform material (herbarium duplicates) from a single collection event. Exsiccatal series are regularily published with small booklets containing the printed labels/ schedae of each numbered entity. The title of the series often shows the geographic and taxonomic focus of the series, e.g., "Delogne & Gravet, Hépat. Ardenne" and "Hertel, Lecideaceae Exs.". The persons editing the series are specialists, often recognized botanists and taxonomists. They are mostly not identical with the persons collecting and identifying the specimens distributed. Examples are E. M. Fries with "Fries, Herb. Norm. Pl. Suec.", G. L. Rabenhorst who published 24 series with more than 6,000 numbered entities and K. H. Rechinger with "Rechinger & Polunin, Exs. Herb. Baghdad". In the minority of cases the editors are anonymous persons and organisations devoted to plant exchange like "Société Dauphinoise pour l'échange des plantes". The more than 2.200 known series are widely distributed in public herbaria, either kept separately or integrated in the main collection. We estimate that more than 10 million specimens belong to such a series with printed labels. Approximately 70 series are running. The eldest exsiccata might be that of Johann Balthasar Ehrhart (from 1732 see here). It is followed by the better known exsiccatae edited by Jakob Friedrich Ehrhart, e.g., the series "Ehrhart, Pl. Crypt. Linn." starting with 1785. The two newest series started in 2020 and are bryophyte series from Taiwan and Vietnam. The online database IndExs categorizes the series according to the group of organisms distributed and delivers editors, full title, standard abbreviation, editing institution, place of publication, range of (suggested) publication dates, range of numbered entities, examplary images of printed label as well as information sources and literature (Triebel et al. 2004). A stable and persistent exsiccata identifier, so-called "IndExs Exsiccata ID" is given. This set of standardized information is available via the IndExs search interface, and ready to be downloaded via several formats (csv, xls, xml). A machine readable REST web service is under development. IndExs information and services with stable IndExs Exsiccata ID are used by data portals like the Macroalgal Herbarium Consortium Portal powered by Symbiota, the JACQ herbarium management system and integrated in collection management systems like DiversityCollection, a module of the Diversity Workbench (DWB) tool suite. It is envisaged to be included in future terminology services like the GFBio Terminology Service. IndExs is appropriate to build the curated reference list for exsiccatae in the frame of herbarium digitization approaches (Borsch et al. 2020). IndExs is storing information on the work of 1,300 editors of exsiccatae who are persons from nearly 300 years. According to the data models of DiversityAgents (Weiss et al. 2016) and DiversityExsiccatae (Hagedorn et al. 2008) the information is managed in freely accessible interlinked instances of SQL RDBMS DiversityAgents and DiversityExsiccatae. The applications are installed as part of the data network at the SNSB IT Center. In 2012, the Wikidata project started and acts as central storage for the structured data of its Wikimedia sister projects (Anonymous 2022, Vrandečić and Krötzsch 2014). The content of Wikidata is available under a free license, exported using standard formats, and can be interlinked to other open data sets on the linked data web including life sciences (Anonymous 2022, Mitraka et al. 2015). The study will use existing IndExs services for the 1,300 IndExs editors and 2,200 disambiguated exsiccata series and expand them for linked data / semantic web approaches. It will explore the usability of Wikidata: for disambiguation of person names (=editors) in IndExs by adapting Wikidata Identifiers, for adding information to existing Wikidata person Q-entities (items) via statements on persons´ work, for integrating IndExs information in Wikidata with URI for "IndExs Exsiccata ID" via a newly proposed P-entity (property) for this special kind of creative work in natural science, for adding new Q-entities in Wikidata for IndExs editors. for disambiguation of person names (=editors) in IndExs by adapting Wikidata Identifiers, for adding information to existing Wikidata person Q-entities (items) via statements on persons´ work, for integrating IndExs information in Wikidata with URI for "IndExs Exsiccata ID" via a newly proposed P-entity (property) for this special kind of creative work in natural science, for adding new Q-entities in Wikidata for IndExs editors. These editors of published booklet series with distributed physical material fulfill the Wikidata criteria of notability. They are often more or less well-known botanists and mycologists. By their published work they might even more fulfill the criteria than certain persons categorized as botanical collectors with assignment of a Wikidata ID through activities of CETAF, DiSSCo and COST MOBILISE.