openBIS for Evolutionary Biology

openBIS for Evolutionary Biology Kristian Ullrich & Carsten Fortmann-Grote Sept. 22 2025 openBIS User Group Meeting, Berlin This work is published under Creative Commons Attribution License CC-BY-4.0 International. Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 1 / 17 Our Institute in Plön (SH) MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE Departments Research Groups Fellow Groups Other Groups Microbial Populations Rainey Theoretical Biology Traulsen Polytraits Barghi Biological Clocks Kaiser Development Dynamics Kaucka Behavioural Genomics Liedvogel Evo Cell Biology Lopez Garrido Bioinformatics Haubold Antibiotic Resistance Schulenburg Environmental Stukenbrock Lise Meitner Groups Diversification and Innovation Feiner EvoMed Baines Research Areas of the Institute •Classical research laboratory (culture, DNA/RNA/protein, Q-PCR, …) MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE Research Areas of the Institute •Classical research laboratory (culture, DNA/RNA/protein, Q-PCR, …)" •Phenotyping (Microscopy, CT/MRT-Images, …) MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE Research Areas of the Institute •Classical research laboratory (culture, DNA/RNA/protein, Q-PCR, …)" •Phenotyping (Microscopy, CT/MRT-Images, …)" •Simulation and Modelling MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE Data management policy centered on openBIS Data sources Data Management at MPI EvolBioJune 22 2021 5 Data Sources ●Image data –Microscopes –CT scanners –X-ray imagers –Cameras ●Sequence data –Inhouse sequencers –Offsite (Kiel, Cologne) ●Model & Simulation data –Wallace cluster –Ada cluster –GWDG cluster –MPCDF cluster Data publication and archiving Doc Internal External Seq. Data openBIS Isilon storage ENA Images OMERO Isilon storage BIA Code Gitlab Gitlab Gitlab/Github Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 2 / 17 openBIS - Instance at MPI PLOEN Hardware/Software and Storage setup at MPI PLOEN 3rd copy goes to (2026???) 22.04.5 LTS PostgreSQL 11.22 v20.10.11.1 3.3 PB openBIS - Instance at MPI PLOEN Multigroup setup MAX-PLANCK-INSTITUT FÜR EVOLUTIONSBIOLOGIE NGS order submission system NGS Request Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 6 / 17 NGS order submission system NGS Run •multiple runs per order (splitting) •multiple orders per run (pooling) Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 7 / 17 NGS order submission system NGS Dataset Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 8 / 17 NGS order submission system Outlook Postprocessing Request standardized postprocessing •Quality control •Genome assembly •Reference alignment •Variant calling Data brokering Deposit NGS data+metadata on public repositories •SRA •ENA •invenio (e.g. zenodo) •datacite (e.g. edmond) Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 9 / 17 Data integration and knowledge graphs related work by BAM and Fraunhofer Materials Open Laboratory •OpenBISmantic @ github •OpenBIS-Ontology @ github Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 10 / 17 Virtualization turns openBIS into a Linked Data Resource Knowledge Graph construction USER Query R2RML Endpoint ontology mappings openBIS postgresql DB SQL to RDF SPARQL to SQL Virtualization •R2RML: Relational to RDF mapping languagea •SPARQL query optimization (Ontology) •Unfold SPARQL query to SQL (Mappings) •Rewrite SQL results as RDF (Mappings) •implementation: ontop-VKGb aDas, Sundara, and Cyganiak 2012. bCalvanese et al. 2015. Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 11 / 17 Example: Microbial Strains Collection openBIS collection Mapping definition Sample properties 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" Property labels rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label rdfs:label bisp:373 "Strain" bisp:377 "Resistance marker" bisp:402 "Date Created" bisp:372 "sID" bisp:391 "Box" bisp:392 "Position" bisp:375 "Phenotype" bisp:388 "Parent" bisp:390 "Freezer" bisp:378 "Accession" bisp:376 "Construction" bisp:389 "Rack/Drawer" bisp:393 "ID" bisp:374 "Genotype" bisp:2 "Name" Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 12 / 17 Linked graphs 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" Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 13 / 17 Example query How many images are in OMERO for openBIS sample MPB19149? Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 14 / 17 Outlook •Mappings •Project – Experiment – Experimental Step – Collection – Object – Attachment hierarchy •Selective mapping (authorization, group membership, roles) •leverage "Semantic Annotations" •related work: OpenBISmantic (mapping and ontology) @ BAM & Fraunhofer •Caching: dynamic virtualization can be slow, periodically dump entire graph and serve as static KG •Frontend: Graphical query builders, LLM chats •Integration of further resources: Gene & protein resources, orthology DBs, metabolic pathway resources Kristian Ullrich & Carsten Fortmann-Grote openBIS for Evolutionary Biology Sept. 22 2025 openBIS User Group Meeting, Berlin 15 / 17