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Gene Ontology in Pathway Tools: Internals

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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  1. Gene Ontology in Pathway Tools: Internals

  2. 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

  3. 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?

  4. 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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