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New BioCyc Search Tools Suzanne Paley Pathway Tools Workshop 2018

Organism Properties DNA Sites. New BioCyc Search Tools Suzanne Paley Pathway Tools Workshop 2018. Source of Organism Properties Data. Parsed from Genome Annotation GenBank File Imported from NCBI BioSample or other DB Computed from PGDB

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New BioCyc Search Tools Suzanne Paley Pathway Tools Workshop 2018

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  1. Organism Properties DNA Sites New BioCyc Search ToolsSuzanne PaleyPathway Tools Workshop 2018

  2. Source of Organism Properties Data • Parsed from Genome Annotation GenBank File • Imported from NCBI BioSample or other DB • Computed from PGDB Organism Properties represented in Pathway Tools are a hand-picked subset of MIGS properties – not intended to be comprehensive.

  3. Organism Property Types • Properties of Organism itself • Genome size • Relationship to Oxygen (aerobe, anaerobe, etc) • Temperature Range (mesophile, thermophile, psychrophile) • Properties of Sample • Collection Date, Location • Human Microbiome Body Site • Properties of Database • # Pathways • # GO Terms • # Transcriptional Regulatory Interactions

  4. Constructing Queries • Numbers next to property type and value count organisms w/ data for that property or w/ that value • Select by specific value(s) or any that have value (or the reverse) • Different selection options for numeric, CV, free text properties • Combine multiple constraints w/ AND or OR • Same interface for selecting single organism vs selecting multiple organisms for comparison ops

  5. DNA or mRNA Site Search

  6. Search Options

  7. Example Search

  8. Example Search Results

  9. Caveats • Most site types must be curated or imported manually (exception: RegTransBase imports) • For most Tier 3 databases, only available site type will be Transcription-Units

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