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Genome Biology Ontology + Gatekeeper Jasper Koehorst Laboratory of - PowerPoint PPT Presentation

Sep 10, 2022 •368 likes •431 views

Genome Biology Ontology + Gatekeeper Jasper Koehorst Laboratory of Systems and Synthetic Biology Current formats Not designed To store computational annotation meta-data For semantic data mining To query / ask questions

  1. Genome Biology Ontology + Gatekeeper Jasper Koehorst Laboratory of Systems and Synthetic Biology

  2. Current formats ● Not designed – To store computational annotation meta-data – For semantic data mining – To query / ask questions ● Therefore – No database system like query interface – No data provenance of predictions is included 2

  3. Overview of the types in GBOL Provenance Procedures Positions Articles Sample Sequence / Features 3

  4. Code generation: EMPUSA • Linked data graph is free format: Ontology defines structure but does not enforce it. • NEED TO MANTAIN CONSISTENCY • From Ontology (protégé file) • OWL + ShEx • API: Java + R • Instance validation included • > 80.000 lines of code generated • HTML documentation (website) • OWL compatible file

  5. Semantic Annotation Platform with Provenance Conversion types Genetic elements Functional annotation • EMBL / GenBank • Gene prediction • BLAST • FASTA • tRNA/rRNA • Enzyme predictions • GFF • Crispr • Domain annotation • QTL • … • Signal peptides • VCF • Transmembrane • … • Localization • …

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