Knowledge Graphs for NFDI4BIOIMAGE

Knowledge Graph(s) for NFDI4BIOIMAGE Carsten Fortmann-Grote October 16 2025 This work is published under Creative Commons Attribution License CC-BY-4.0 International. Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 1 / 29 Data driven lifescience is multimodal by nature •Experimental •Imaging •Microscopy (>150 file formats), X-ray, Nuclear Magn. Resonance, Electron-Micr., . . . •OMICS •Genomics (DNA), Transcriptomics (RNA), Proteomics (AA), . . . •Flow cytometry •. . . •Theoretical •Simulations •Mathematical models •Computational •High throughput data processing •Structural biology •AI Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 2 / 29 Data driven lifescience is multimodal by nature •Experimental •Imaging •Microscopy (>150 file formats), X-ray, Nuclear Magn. Resonance, Electron-Micr., . . . •OMICS •Genomics (DNA), Transcriptomics (RNA), Proteomics (AA), . . . •Flow cytometry •. . . •Theoretical •Simulations •Mathematical models •Computational •High throughput data processing •Structural biology •AI Standardization of data and metadata is very challenging Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 2 / 29 Life science NFDIs www.nfdi.de/consortia •Domain specific consortia X data specific consortia Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 3 / 29 Inhouse data Image data Sequence data Code & Simulation data 0 20 40 60 80 100 time 0 2000 4000 6000 8000 10000 12000 cell count 95% HDI over 100 gLV solutions for one species 95% HDI run 0 run 1 median Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 4 / 29 Data and software policy Policy Data collection Data analysis DMP Sequence data Materials Notes Protocols Simulation data Image data Code OMERO Storage openBIS GitLab/Hub DMP FDK DMP Library FDK edmondzenodo ENABIA GitLab/Hub PuRe Results Publication Library Reuse Checklist MPI-EvolBio Data Policy •Dedicated solutions per data type •preand post publication repositories •DMP per group and scientist (pilot phase) •Monitored by library and data coordinator (FDK) Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 5 / 29 Data and software policy Repositories Type Documentation Internal Storage External Archive (unpublished) (post published) Seq. Data Electronic Lab Notebook Institute storage European Nucleotide Archive Images OMERO Image Database Institute storage BioImage Archive Code Gitlab Gitlab Gitlab/Github Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 6 / 29 Questions we would like to be able to answer •Find me images of cells with genotype XY and their DNA sequences! •Annotate images with organism, genotype, phenotype metadata! •Provide raw image and sequence data from paper doi:10.1234/abcdef Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 7 / 29 Questions we would like to be able to answer •Find me images of cells with genotype XY and their DNA sequences! •Annotate images with organism, genotype, phenotype metadata! •Provide raw image and sequence data from paper doi:10.1234/abcdef Requirements •In-house data integration •Integration of external (meta)data sources Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 7 / 29 Query response time is a concern for VKGs 1.50 1.75 2.00 2.25 2.50 2.75 3.00 time (s) query = list of attributes 2 3 4 5 6 7 query = group by attribute sort 2 3 4 5 6 7 8 9query = group by attribute avg 2.2 2.4 2.6 2.8 3.0 query = group by attribute other avg 20 25 30 35 40 45 50 query = image properties ontop fuseki virtuoso endpoint 2 3 4 5 6 7 time (s) query = count triples ontop fuseki virtuoso endpoint 10 20 30 40 50 query = construct triples ontop fuseki virtuoso endpoint 2 3 4 5 6 7 query = fulltext search ontop fuseki virtuoso endpoint 2.2 2.4 2.6 2.8 3.0 3.2 3.4 query = regex ontop fuseki virtuoso endpoint 1.6 1.8 2.0 2.2 2.4 2.6 query = filter regex sort Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 14 / 29 Caching strategy to buffer slow response from VKGs USER Query R D F Materialized Knowledge Graph R2RML Virtual Knowledge Graph Endpoint ontology mappings Relational DB SQL to RDF Cache, fast Live query, slow SPARQL to SQL •Live response from virtual KG •can be slow to answer complex queries •RDF dump at regular intervals (≈1/d) •SPARQL frontend serves dumped RDF •fast but lags behind live data Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 15 / 29 OMERO KG Annotated images in OMERO Derived RDF Graph ome_ns:MPB ome_ns:Organism ome_ns:Study ome_core:image rdf:type rdfs:label ome_ns:Strain ome_ns:Investigation ome_core:image ome_core:image ome_core:image rdfs:label ome_core:dataset rdf:type rdfs:label ome_core:dataset ome_core:dataset ome_core:dataset rdf:type ome_core:dataset site_image:41697 "19149" "Pseudomonas fluorescens" "cell measurements" site_dataset:989 site_image:42047 ome_core:Image "MPB19149_OD0....tif" site_project:304 "TimeSeries" "SBW25" site_image:42046 site_dataset:852 site_dataset:806 site_image:42048 "cell shape" site_dataset:789 "MPB19149 15.12.20" ome_core:Project site_dataset:790 ome_core:Dataset Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 16 / 29 OpenBIS VKG Samples collection openBIS Graph bisp:375 bisp:376 bisp:391 bisp:393 bisp:374 bisp:400 rdf:type bisp:2 bisp:392 bisp:389 bisp:390 bisp:388 bisp:373 <https://openbis/rdf/Sample/32357> "cell shape defect" "copy of MPB13859 (overnight culture in LB)" "MPB #195" "MPB19149" "SBW25 pbp1a(G1450A)" "PFLU pbp1a(G1450A)" bisc:77 "pbp1a(G1450A)" "A1" "44" "5" "MPB17743" "SBW25" Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 17 / 29 OMERO Graph ome_ns:MPB ome_ns:Organism ome_ns:Study ome_core:image rdf:type rdfs:label ome_ns:Strain ome_ns:Investigation ome_core:image ome_core:image ome_core:image rdfs:label ome_core:dataset rdf:type rdfs:label ome_core:dataset ome_core:dataset ome_core:dataset rdf:type ome_core:dataset site_image:41697 "19149" "Pseudomonas fluorescens" "cell measurements" site_dataset:989 site_image:42047 ome_core:Image "MPB19149_OD0....tif" site_project:304 "TimeSeries" "SBW25" site_image:42046 site_dataset:852 site_dataset:806 site_image:42048 "cell shape" site_dataset:789 "MPB19149 15.12.20" ome_core:Project site_dataset:790 ome_core:Dataset openBIS Graph bisp:375 bisp:376 bisp:391 bisp:393 bisp:374 bisp:400 rdf:type bisp:2 bisp:392 bisp:389 bisp:390 bisp:388 bisp:373 <https://openbis/rdf/Sample/32357> "cell shape defect" "copy of MPB13859 (overnight culture in LB)" "MPB #195" "MPB19149" "SBW25 pbp1a(G1450A)" "PFLU pbp1a(G1450A)" bisc:77 "pbp1a(G1450A)" "A1" "44" "5" "MPB17743" "SBW25" Example How many images are in OMERO for openBIS sample MPB19149? Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 18 / 29 Virtual KG system supports cross-database queries Number of images (OMERO) grouped by sample (openBIS) Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 19 / 29 Connecting local resources to the semantic web Lab Notebook & Inventory AAACCCDGGGANCDGTTTTATAGATTTGGGA TTTTATAAACCCDGGGANCDGAGATTTGGGA AAACCCDGGGANCDGTTTTATAGATTTGGGA AACDGGGANCDGTTGTTTTATAGATTTGGGA AACDGGGANCDGTAAACCCDGGGANCDDGT GTTTTATAGATTTGGGANCDGTTTTATAGATTT Sequence Archive Image Repository Code repository Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 20 / 29 Connecting local resources to the semantic web Lab Notebook & Inventory AAACCCDGGGANCDGTTTTATAGATTTGGGA TTTTATAAACCCDGGGANCDGAGATTTGGGA AAACCCDGGGANCDGTTTTATAGATTTGGGA AACDGGGANCDGTTGTTTTATAGATTTGGGA AACDGGGANCDGTAAACCCDGGGANCDDGT GTTTTATAGATTTGGGANCDGTTTTATAGATTT Sequence Archive Image Repository Code repository Leverage NFDI to •make graphs discoverable (F) •ensure aligned terminologies (I) Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 20 / 29 NFDI4BIOIMAGE Knowledge Graph(s) https://kg.nfdi4bioimage.de/#/datasets/N4BIKG/query <<prefixes>> select distinct ?graph (count(?s)as ?triples)where { graph ?graph {?s ?p ?o} } group by ?graph order by desc(?triples) graph triples https://nfdi4bioimage.de/kg/owl 13887 https://kg.nfdi4bioimage.de/n4bikg/owl 12382 https://kg.nfdi4bioimage.de/n4bikg/n4bi_zenodo_community 3482 https://kg.nfdi4bioimage.de/n4bikg/core 19 https://kg.nfdi4bioimage.de/n4bikg/services 5 Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 21 / 29 Graph of graphs n4bikg:owl Duplicates employed ontologies to support local lookup n4bikg:zenodo Metadata harvested from the "NFDI4BIOIMAGE" zenodo community n4bikg:core Core data on NFDI4BIOIMAGE consortium n4bikg:services Web services and RDF resources maintained by NFDI4BIOIMAGE Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 22 / 29 Thank you •NFDI4BIOIMAGE: Josh Moore, Susanne Kunis •German Bioimaging: Tiago Lubiana + Andra Waagmeester and others •MPI EvolBio: Paul Rainey, Daniel Olvera •FDM-SH: Inken Wohlers (Research Center Borstel) •NFDI Section Metadata KG Working Group: Heike Fliegl, Lozana Rossenova, Fidan Limani, . . . Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 29 / 29 Thank you •NFDI4BIOIMAGE: Josh Moore, Susanne Kunis •German Bioimaging: Tiago Lubiana + Andra Waagmeester and others •MPI EvolBio: Paul Rainey, Daniel Olvera •FDM-SH: Inken Wohlers (Research Center Borstel) •NFDI Section Metadata KG Working Group: Heike Fliegl, Lozana Rossenova, Fidan Limani, . . . •FIZ Karlsruhe for the kind invitation •everyone for your attention! Carsten Fortmann-Grote Knowledge Graph(s) for NFDI4BIOIMAGE October 16 2025 29 / 29