Linked (Open) Data for Microbial Population Biology

Linked (Open) Data for Microbial Population Biology Carsten Fortmann-Grote1 March 12 2024 1ca[email protected] Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 1 / 19 A short tour of the institute Evolutionary Genetics (D. Tautz (Emeritus)) Model organisms: Mus domesticus, mus musculus Behavioural genomics Population genetics credits: https://www.evolbio.mpg.de/ 3039130/group_evolanimalbehpers Microbial Population Biology (P. Rainey) Model organism: Pseudomonas fluorescens, Bacillus sub. Evolution of communities Host-microbe interactions Genetics credits: Theodosiou (left), Schwarz (middle), Grote (right) Theoretical Biology (A. Traulsen) Population Structure and Game Theory Metaorganisms Cancer Evolution Hindersin et al, PLOS Comp. Bio (2019) 10.1371/journal.pcbi.1004437 Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 2 / 19 Research topics in Microbial Population Biology Bacterial communities as Darwinian entities Antibiotica resistance Bacteria and phages Host-microbe interactions (plants, soil) Long term evolution experiments Adaptation to artificial selection pressures Genetic bases for evolutionary processes Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 2 / 19 A typical MPB project Wildtype clone and/or genetically modified strain(s) Timelapse microscopy from growing microbial communities Time resolved whole genome / core gene NGS data Transcription profiles Optical density measurements from plaque assays Functional annotations Need for integrated analysis of multiomics-multimodal data "Find images, ELN entries for ∆mreB strains and annotations for mreB" Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 3 / 19 Integrating data the sparqling way Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 4 / 19 Data integration of internal sources DB API LOD ready? RDF conversion Tripal Genome DB JSON-LD yes SPARQL SPARQL-anything virtualization JSON to RDF serialization OMERO JSON-LD yes omero-rdf OpenBIS JSON ??? ??? ("semantic annotation") StrainDB None no csv dump →csv2rdf Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 5 / 19 CSV2RDF Credits: Sarah Komla-Ebri Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 6 / 19 Genome database P.flu SBW25 Genome Database Organism Database (Tripal) Based on Drupal CMS Implements Chado DB Scheme (SQL) Converts genome annotation into searchable, cross-linked database Integrates Genome Browser (JBrowse) Supports OBO Ontologies & Controlled Vocabularies (Sequence Ontology, Gene Ontology, . . . ) JSON-LD API ⇒In principle ready for consumption by LOD clients Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 7 / 19 Querying a JSON-LD API Direct query SELECT distinct ?s ?p ?o where { ?s a SO:0000316 . ?s ?p ?o . } | s | p | o | |-----------+-------------------------------------------------+------------------------------------| | CDS:11845 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type | so:0000316 | | CDS:11845 | http://www.w3.org/2000/01/rdf-schema#label | CDS:PFLU_0001-0 | | CDS:11845 | http://edamontology.org/data_2091 | 11845 | | CDS:11845 | https://schema.org/name | CDS:PFLU_0001-0 | | CDS:11845 | http://edamontology.org/data_0842 | CDS:PFLU_0001-0 | | CDS:11845 | http://purl.obolibrary.org/obo/OBI_0100026 | Pseudomonas fluorescens | | CDS:11845 | http://www.w3.org/2000/01/rdf-schema#type | CDS | | CDS:11845 | http://edamontology.org/data_2012 | CDS:11845/Sequence+coordinates | | CDS:11845 | http://purl.obolibrary.org/obo/OGI_0000021 | CDS:11845/location+on+map | | CDS:11845 | http://purl.obolibrary.org/obo/SBO_0000374 | CDS:11845/relationship | | CDS:11845 | http://purl.obolibrary.org/obo/SBO_0000554 | CDS:11845/database+cross+reference | | CDS:11845 | http://semanticscience.org/resource/SIO_001166 | CDS:11845/annotation | Object URIs are Graph URIs of linked json-ld documents. Exploring the graph across documents requires dynamic generation of graph URIs, not supported in SPARQL1.1 Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 8 / 19 Our P.flu SBW25 RDF playground Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 15 / 19 Image, genotype, mpb number and straindb columns prefix ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/> prefix mpimap: <http://ome.evolbio.mpg.de/MapAnnotation/> prefix mpiimg: <http://ome.evolbio.mpg.de/Image/> prefix mpi: <http://ome.evolbio.mpg.de/> prefix strains: <http://raineylab.evolbio.mpg.de/straindb/strains/> prefix props: <http://raineylab.evolbio.mpg.de/straindb/properties/> select distinct ?img ?mpbn ?genotype ?phenotype where { ?img <http://www.wikidata.org/prop/direct/P180> ?ann . ?ann ome_core:Map ?map . ?map ome_core:Key ?key . ?map ome_core:Value ?mpb . filter(?key in ("", "MPB")). bind(concat("MPB", ?mpb) as ?mpbn ). service <http://micropop046.evolbio.mpg.de:3030/MPBStrainDB/sparql> { ?strain props:sId ?mpbn . ?strain props:genotype ?genotype . ?strain props:phenotype ?phenotype . } } order by ?img limit 7 img mpbn genotype phenotype http://ome.evolbio.mpg.de/Image/6752778 MPB15447 PFLU0085 del 1309-1374 (del 437-458) Wrinkly Spreader http://ome.evolbio.mpg.de/Image/6752779 MPB15447 PFLU0085 del 1309-1374 (del 437-458) Wrinkly Spreader http://ome.evolbio.mpg.de/Image/6752780 MPB15447 PFLU0085 del 1309-1374 (del 437-458) Wrinkly Spreader http://ome.evolbio.mpg.de/Image/6752781 MPB15456 WsT AwsX delta229-261 Wrinkly Spreader http://ome.evolbio.mpg.de/Image/6752782 MPB15456 WsT AwsX delta229-261 Wrinkly Spreader http://ome.evolbio.mpg.de/Image/6752783 MPB15456 WsT AwsX delta229-261 Wrinkly Spreader https://ome.evolbio.mpg.de/Image/6752855 MPB15455 “22A1” WspF 150bpdel (delta 677-826) Wrinkly Spreader Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 16 / 19 SparNatural for visual query generation file:///home/grotec/Sandbox/pflukg/index.html Graphical query editor Supports federation and customized data sources No support (yet) for BIND and aggregations Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 17 / 19 On omero-rdf select distinct ?key ?val where { # ?ann <http://www.wikidata.org/prop/direct/P180> ?img . ?ann ome_core:Map ?map . ?map ome_core:Key ?key . ?map ome_core:Value ?val . } key val Type still Organism Pseudomonas fluorescens Strain SBW25 MPB 15447 Parent 0 Investigation Deep Learning for MPB Study Segmentation and Classif. . . 5 colony morphotype Assay 0085 Phenotype WS Genotype 0085 omero-rdf stores key, value as bnode property values. would need key as property, value as property value requires loading ontologies, controlled vocabs into omero and exposure in map annotations. Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 18 / 19 Tasks and contributions to NFDI4BI P.flu SBW25 Knowledge Graph as a Use Case Controlled vocabularies for microbial population biology and evolutionary cell biology Contributions to linked open data software, clients, recommendations Carsten Fortmann-Grote Linked (Open) Data for Microbial Population BiologyMarch 12 2024 19 / 19