Difference between revisions of "Updating go.ace file"

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| Name || id:
 
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| Definition || def:
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| Term || name:
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| Type || namespace:
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| Child Instance || In each is_a tag, look for GO Name.  Fill in .ace tag with corresponding id:
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| Child Component || In each relationship: part_of tag, look for GO Name.  Fill in .ace tag with corresponding id:
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| Parent Instance || For each GO Name, look at is_a tag.  Fill in .ace with corresponding id:
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| Parent Component_of || For each GO Name, look at relationship: part_of.  Fill in corresponding id:
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Revision as of 19:02, 12 June 2013

Updating the go.ace File - Script Specifications

  • Output file: go.ace

WormBase ?GO_term Model: 

    ?GO_term  Name	  ?Text
              Definition ?Text
              Term	  ?Text
              Type UNIQUE Biological_process
                          Cellular_component
                          Molecular_function
              Child	Instance	?GO_term	XREF	Instance_of
                       Component	?GO_term	XREF	Component_of
              Parent	Instance_of	?GO_term	XREF	Instance
                       Component_of	?GO_term	XREF	Component
              Attributes_of	Cell	?Cell	XREF	GO_term
                               Motif	?Motif	XREF	GO_term
                               Gene	?Gene	XREF	GO_term
                               CDS	?CDS	XREF	GO_term
                               Sequence	?Sequence	XREF	GO_term
                               Transcript	?Transcript	XREF	GO_term
                               Pseudogene	?Pseudogene	XREF	GO_term
                               Phenotype	?Phenotype	XREF	GO_term
                               Index	Ancestor	?GO_term	XREF	Descendent
                                       Descendent	?GO_term	XREF	Ancestor
                               Anatomy_term	?Anatomy_term	XREF	GO_term
                               Homology_group	?Homology_group	XREF	GO_term
                               Expr_pattern	?Expr_pattern	XREF	GO_term
                               Picture	?Picture	XREF	Cellular_component
               Version	UNIQUE	Text	UNIQUE	Text


Sample GO term in .obo file: 

    [Term]
    id: GO:0000003
    name: reproduction
    namespace: biological_process
    alt_id: GO:0019952
    alt_id: GO:0050876
    def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, GOC:isa_complete, ISBN:0198506732]
    subset: goslim_generic
    subset: goslim_pir
    subset: goslim_plant
    subset: gosubset_prok
    synonym: "reproductive physiological process" EXACT []
    xref: Wikipedia:Reproduction
    is_a: GO:0008150 ! biological_process


  • Mapping from .obo file to .ace file:
.ace tag name .obo tag name
Name id:
Definition def:
Term name:
Type namespace:
Child Instance In each is_a tag, look for GO Name. Fill in .ace tag with corresponding id:
Child Component In each relationship: part_of tag, look for GO Name. Fill in .ace tag with corresponding id:
Parent Instance For each GO Name, look at is_a tag. Fill in .ace with corresponding id:
Parent Component_of For each GO Name, look at relationship: part_of. Fill in corresponding id:
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