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Vorstellung eines NFDI4Biodiversity-Kooperationsprojekts zwischen der Generaldirektion der staatlichen Archive Bayerns (GDA) und den Staatlichen Naturwissenschaftlichen Sammlungen Bayerns (SNSB) über die Langzeitarchivierung einer Datenbank der SNSB zum Management der Sammlung von Mehltaupilz-Objekten.

Ein zentrales Ziel des NFDI4Biodiversity Konsortiums ist, einen einheitlichen Zugang zu heterogenen Biodiversitätsdaten zu ermöglichen. Dafür arbeiten wir zurzeit an drei konkrete Themen: Daten aus heterogenen Quellen einheitlich in die cloud-basierte Infrastruktur, namens Research Data Commons, importieren. Datenprovidern ermöglichen standardisierte Schnittstellen (APIs) für Data Harvesting zu implementieren. Notwendige Prozesse für die Extraktion, ggf. Transformation und für das Laden (ETL) der Daten implementieren.

Das NFDI4Biodiversity-Konsortium besteht aus einem Netzwerk von Ressourcen-Anbietern, welche u.a. Datenanbieter, Datenzentren und Serviceanbieter umfassen. In Task Area 3 Measure 3 werden diese Partner adressiert, damit sie ihre Dienste, Software und Daten unabhängig von Task Area 1 Use Cases für NFDI konsolidieren, weiterentwickeln und für die Research Data Commons (RDC) Cloud erschließen können. So werden Forschungsdaten für die Nationale Forschungsdateninfrastruktur (NFDI) mobilisiert und der gemeinsame Ausbau von Werkzeugen und IT Services vorangetrieben.

"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.

MOBILISE WG3 WIKI

Poster GFBio-04from the GFBio General Assembly 2021 of"Work Package 2 - Data Submission, Ingest, Archiving & Publication" of the GFBio Project summarizing the projects and subtasks work and outcome between 2013 and 2021. The ecological and environmental research community relies on theEcological Markup Language(EML) as metadata exchange standard. It allows for providing information packages with XML-based EML files and assignedtabular CSV data filesstructured according user-specific proprietary content schemas, often matrices with measurement data (EML-CSV). The biological systematics, nature observation and conservation domain focus on structuring descriptive and trait data acording community agreed vocabularies, internal data schemas and classifications. A combination of EML metadata and research data in the XML-based TDWG approved standardSDD(Structured Descriptive Data) is appropriate to create wellstructured trait data (EML-SDD).

Poster GFBio-01fromthe GFBio General Assembly 2021 of the Work Package 1 - PR & Outreach of the GFBio Project summarizing the projects work and outcome between 2013and 2021. The overarching aim of Outreach and User Engagement (WP1) was to raise awareness for research data management among reasearchers and increase data literacy by providing support, training and teaching.

Poster GFBio-03 from the GFBio General Assembly 2021 of the "Work Package 2 - Data Submission, Ingest, Archiving & Publication" of the GFBio Project summarizing the projects and subtasks work and outcome between 2013 and 2021. ABCDis a well recognized TDWG community standard and XML schema for collection and occurrence data. It is appropriate to exchange primary biodiversity data records that document digital specimens and species' occurrences in time and space. TheGFBio Submission Systemis supporting data producers to submit such data for FAIR access guided by the data centers at natural science collections.

Poster GFBio-06 from the GFBio General Assembly 2021 of "Work Package 2 - Data Submission, Ingest, Archiving & Publication" of the GFBio Project summarizing the projects and subtasks work and outcome between 2013 and 2021. In a selection process, CoreTrustSeal was chosen as the certification authority. Subsequently, the GFBio data Centers workedtowards certification, including the required documentation of the technical and data management workflows.

Poster GFBio-02from the GFBio General Assembly 2021 of the Work Package 1 - PR & Outreach of the GFBio Project summarizing the projects and subtaskswork and outcome between 2013 and 2021. The GWDG is an infrastructure and services provider for science. With its mission, it is offering services to the GFBio Community and supports the development of NFDI. Together with the SNSB developing and delivering Diversity Workbench (DWB) software, a cloud-based service featuring browser- based individual access to a DWB virtual working environment was developed. The approach is comfortable because the users avoid local software installations and administration with admin rights, and are prevented from data loss due to cloud based storage and automated backups.

DiversityNaviKey is designed as a diagnostic tool in the field of biology and related sciences to identify organisms as well as to interactively select other entities and objects related to research based on a set of predefined properties. It allows queries on structured sources of descriptive data (trait data) to diagnose groups of objects based on combinations of optionally modified descriptor-states or values that are selected consecutively during the diagnostic process. The Web App is implemented as a single-page application and contains the entire presentation logic to dynamically change a pre-generated HTML page in the browser. The content data is accessed via a web service as JSON packages. DiversityNaviKey is a progressive web application that uses caching mechanisms of browsers, such as Service Worker and IndexedDB. Thus, the main tasks are also available in offline mode. The current set up uses the SNSB technical infrastructure and data pipelines with PostgreSQL Cache Database and the data management tool DiversityDescriptions as backend. The exemplary data sources are from various domains, two of them are large datasets from the long-term projects DEEMY and LIAS.

Biodiversity is more than just the diversity of living species. It includes genetic and phenotypic diversity of organisms, functional diversity, interactions and the diversity of populations and whole ecosystems. The recent Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report confirmed that our planet experiences a rapid loss of biodiversity with dramatic consequences for mankind. Answers to scientifically and societal relevant questions can only be found based on the availability of data integrated from multiple sources and building on different knowledge domains in science and society. The FAIR data principles provide a framework towards such integration. To foster access to interoperable data, NFDI4BioDiversity focuses on the following six objectives: 1) Promoting research data management as an integral part of biodiversity research, 2) Enabling FAIRness of data, 3) Consolidating FAIRness with quality, 4) Embedding NFDI4BioDiversity into the (inter-)national landscape, 5) Addressing NFDI-wide cross-cutting topics and 6) Promoting collaborative governance, viability and sustainability of data infrastructure services and science. These objectives are implemented by the NFDI4BioDiversity work programme and its five task areas: Task Area 1 - Community engagement (2involve): This task area will integrate across different knowledge holders and take care of research data management requests related to biodiversity data. A large part of all species data is collected by volunteers in natural history societies, NGOs, museums and citizen science projects as well as collected by different authorities This task area includes 23 use cases with community-driven topics and cross-domain user groups. Task Area 2 - National and international networking (2connect): This task area ensures that any cross-domain activities and developments of NFDI4BioDiversity are coordinated and in-line with the overall development of the NFDI as well as international activities. Task Area 3 - Long-term data, tools and service preservation, certification (2consolidate): This task area consolidates existing German infrastructures and data pipelines for long-term FAIR data preservation, archiving and publication and guides them towards certification. Task Area 4 - Data integration, exploration, and exploitation - the NFDI-Research Data Commons (NFDI-RDC, 4all & 4future): This task area develops a Cloud-based research infrastructure that provides scientists, providers and users with the technical baseline for exchanging data and services in a collaborative research environment. This facilitates the integration, use, and export of biodiversity data as well as the joint development and reuse of services and data. Task Area 5 - Coordination, collaborative governance & sustainability: This task area implements the governance model and coordination of NFDI4BioDiversity. It includes sustainability aspects and long-term maintenance.

Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of ‘FAIR++’ digital objects is introduced.