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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Gene Ontology in Pathway Tools: Internals

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Gene ontology in pathway tools internals

Gene Ontology in Pathway Tools: Internals


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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