gene ontology in pathway tools internals
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Gene Ontology in Pathway Tools: Internals. Relationship between GO and a PGDB. GO is stored in its own Ocelot KB Class-subclass relationship defines the GO is-a hierarchy Additional slots PARTS, PART-OF define the GO part-of hierarchy Each PGDB has a class Gene-Ontology-Terms

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relationship between go and a pgdb
Relationship between GO and a PGDB
  • GO is stored in its own Ocelot KB
    • Class-subclass relationship defines the GO is-a hierarchy
    • Additional slots PARTS, PART-OF define the GO part-of hierarchy
  • Each PGDB has a class Gene-Ontology-Terms
    • Slots GO-TERMS, TERM-MEMBERS encode annotations
  • When annotated a gene product to a GO term, term and its parents are imported into the PGDB
    • Searching for gene/product by GO term only requires access to terms in PGDB
    • Editing GO terms for gene/product requires access to full GO KB
where does go ocelot kb come from
Where does GO Ocelot KB come from?
  • Parsing tool generates Ocelot KB from .obo-xml
  • GO KB is built into Pathway Tools runtime distributions

BUT…

  • GO is updated much more frequently than Pathway Tools software releases
  • How to incorporate new terms into a PGDB?
updating go ocelot kb
Updating GO Ocelot KB
  • Download new .obo-xml file
  • (update-go-kb :input-file <filename>)
    • Checks to see if input-file is more recent than currently installed GO KB
    • Saves file aic-export/go/beta/go.ocelot
  • At startup time, Pathway Tools looks for file and loads it, overriding GO KB in memory
  • Consistency Checker validates PGDB to match the GO KB
    • Updates hierarchy, importing new terms as necessary
    • Deletes terms w/ no subs, parts, or annotated gene products
    • Reports on obsolete terms that have gene products annotated to them – curator should reassign these
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