Molecular sequencing data generation is being driven by global and regional efforts to discover, understand and monitor biodiversity. To fully explore this data in biodiversity research we need a network of connected data resources, linking sequence data with natural history collections, taxonomy and literature. The BiCIKL project (Biodiversity Community Integrated Knowledge Library, Penev et al. 2022) has set the groundwork towards creating this network of linked data and fostering FAIR (Findable, Accessible, Interoperable and Reusable) practices in the biodiversity domain. Connecting biodiversity and molecular data along the biodiversity research cycle requires a foundation of well-structured and rich metadata in the molecular sequence databases. Referencing the physical specimens is important as this provides context about the source of the material that was used for generating the molecular sequence data, including information about origin and species identification. To connect biodiversity and molecular data, we developed tools and workflows for improving and standardising metadata, federated searches and validations for specimen reference in sequence data, such as the SpASe tool, which enables the discovery of links between natural history collections and sequences, and the European Nucleotide Archive Source Attribute Helper API, which facilitates the construction of specimen attributes in a structured format. This work was done in close collaboration with DiSSCo (Distributed System of Scientific Collections) and some biodiversity genomics projects (e.g. Biodiversity Genomics Europe, BGE). Furthermore, we enabled community curation of biological source annotations such as specimen references in sequence data through the PlutoF platform and the ELIXIR Contextual Data Clearinghouse (Abarenkov et al. 2021, Balavenkataraman Kadhirvelu et al. 2022) and increased bidirectional linking from sequences in the European Nucleotide Archive (ENA) to collections, taxonomy and literature services (e.g., Plazi TreatmentBank, OpenBioDiv). We also worked closely with the community to enable the structured publication of environmental DNA data, promoting and engaging in the definition of standards and developing tools to facilitate data deposition and retrieval. Overall, the project has contributed significantly to strengthen the connections between the biodiversity and genomics communities towards higher data integration and interoperability. Structured, enriched, accessible and linked sequence data will provide a strong foundation for the application of biodiversity knowledge in the response to global challenges, such as biodiversity loss, ecosystem change and food security. Beyond BiCIKL, we will continue our work as a community to promote a culture of FAIR linked molecular data, towards a fully integrated biodiversity knowledge ecosystem.

Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal.

Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco-evolutionary research, which greatly depends on knowing the precise location where the specimens were collected in order to characterize the environment in which they lived. Yet, only about 55% of the accessible records are georeferenced and only 31% have coordinate uncertainty information, which is critical for conducting rigorous studies. The awareness of this gap of knowledge which hinders the enormous potential of such data in research led to the organization of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented.