SRI International Bioinformatics 1 Gene Ontology in Pathway Tools: Internals

SRI International Bioinformatics 2 Relationship between GO and a PGDB GO is stored in its own Ocelot KB l Class-subclass relationship defines the GO is-a hierarchy l Additional slots PARTS, PART-OF define the GO part-of hierarchy Each PGDB has a class Gene-Ontology-Terms l 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 l Searching for gene/product by GO term only requires access to terms in PGDB l Editing GO terms for gene/product requires access to full GO KB

SRI International Bioinformatics 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?

SRI International Bioinformatics 4 Updating GO Ocelot KB Download new.obo-xml file (update-go-kb :input-file ) l Checks to see if input-file is more recent than currently installed GO KB l 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 l Updates hierarchy, importing new terms as necessary l Deletes terms w/ no subs, parts, or annotated gene products l Reports on obsolete terms that have gene products annotated to them – curator should reassign these