Biodiversity in Knowledge Graphs Topics co-occurring with biodiversity in the scholarly literature, as visualized using SPARQL queries to Wikidata (left) and to MaRDI (right). Biodiversity in NFDI Knowledge Graphs Daniel Mietchen, Leibniz-IGB FU Berlin & Leibniz-FIZ & MaRDI & Wikidata DOI: 10.5281/zenodo.10997504 Abstract: Knowledge graphs are a mechanism to address the challenge of leveraging data from diverse sources for use cases not served by the individual sources alone. Already well established in some specific parts of the research ecosystem, they are currently experiencing a trend towards broader adoption, including in the context of the German National Research Data Infrastructure (NFDI). A number of knowledge graphs are run by or otherwise closely associated with NFDI consortia or their members. This work provides an overview of the landscape of NFDI-associated Knowledge Graphs and explores it from the perspective of biodiversity-related use cases. Knowledge Graphs used in NFDI contexts See also Shigapov et al. (2023) Dataset: an overview of knowledge graphs in NFDI 10.5281/zenodo.8124286 . Knowledge Graphs for NFDI4Biodiversity? Potential paths forward ●Leverage internal expertise, e.g. iKnow ●Consider use cases ●Leverage existing NFDI KGs ●Leverage existing biodiversity KGs ●Identify gaps in coverage/ usability ●Set up one or more NFDI4Biodiversity KGs? ●Curation by experts and/ or crowd? Key issues ●Ontology gaps ●Ontology mapping ●Licensing ●Consistency across use cases ●Scalability ●Sustainability of KGs and related infrastructures Knowledge Graphs covering biodiversity KG name KG URL Sample user FactGrid database.factgrid.de NFDI4Objects NFDI4Culture KG nfdi4culture.de/resour ces/knowledge-graph NFDI4Culture Wikidata wikidata.org NFDI4DS MaRDI portal portal.mardi4nfdi.de MaRDI ORKG orkg.org NFDI4Chem NFDI4Earth KG nfdi4earth-knowledge hub.geo.tu-dresden.de NFDI4Earth EU Data Portal data.europa.eu KonsortSWD KGI4NFDI@ BASE4NFDI base4nfdi.de/projects/ kgi4nfdi NFDI4 Microbiota See also Babalou et al. (2023) Reproducible Domain-Specific Knowledge Graphs in the Life Sciences: a Systematic Literature Review KG name Sample content OpenBioDiv publications, taxa, journals, people Plazi taxonomic treatments, publications UniProt taxa, proteins, protein functions Ozymandias taxa, publications, people, journals GloBI taxa, biotic interactions Gene Ontology taxa, genes, gene functions Wikidata taxa, genes, publications, expeditions ORKG publications, methods, people DBpedia taxa, people, processes, genes SPARQL Microservices taxa, publications, images MeSH diseases, taxa, genes, processes Knowledge graphs can be queried in several ways, and some query types can be federated across KGs. Multiple queries involving the same entity types can then be combined into a profile for that entity type, as demoed here with a Wikidata-based taxon profile for Caenorhabditis elegans at https://scholia.toolforge.org/taxon/Q91703. See also Nielsen et al. (2017) Scholia and scientometrics with Wikidata. The work presented here was supported by the enKORE project under VolkswagenStiftung grant number 97 863, by the MaRDI project under DFG grant number 460135501 and in general terms by the Knowledge Graph community.