Updating go.ace file

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Updating the GO term.ace File - Script Specifications

  • Output file: go.ace
  • No model change, except....what to do with is_obsolete tag in .obo?

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 Action
Name id: Add corresponding value.
Definition def: Add corresponding value. Omit information in brackets at the end of the definition.
Term name: Add corresponding value.
Type namespace: Make first letter upper case and add corresponding value.
Child Instance is_a: In each is_a: tag, look for GO Name. Fill in .ace tag with corresponding id:
Child Component relationship: part_of In each relationship: part_of tag, look for GO Name. Fill in .ace tag with corresponding id:
Parent Instance is_a: For each GO Name, look at is_a tag. Fill in .ace with corresponding value.
Parent Component_of relationship: part_of For each GO Name, look at relationship: part_of. Fill in .ace with corresponding value.
Index Ancestors is_a: and relationship: part_of For each GO Name, look at is_a and relationship: part_of. Fill in .ace with corresponding value. Then, for each value filled in, iterate and look at is_a and relationship: part_of. Continue to fill in .ace with corresponding value until the root node is reached, for which no is_a or relationship: part_of exists.
Index Descendents is_a: and relationship: part_of For each is_a and relationship: part_of, look for GO Name. If GO Name matches value in either tag, fill in .ace with corresponding id:. For each corresponding id:, iterate and look for id: in is_a and relationship: part_of. Continue to iterate until each id: is no longer found in is_a and relationship: part_of.
Version In header, remark: cvs version: Add value in between $ signs after cvs version:.


  • Some possible terms to check:
    • GO:0005635 nuclear envelope
    • GO:0007192 adenylate cyclase-activating serotonin receptor signaling pathway
    • GO:0008340 determination of adult lifespan
    • GO:0003729 mRNA binding

Examples: Terms in .obo and .ace

For the term 'nuclear envelope'

.obo
[Term]
id: GO:0005635
name: nuclear envelope
namespace: cellular_component
alt_id: GO:0005636
def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest 
of the  cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called     
the perinuclear space)." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
xref: Wikipedia:Nuclear_envelope
is_a: GO:0031967 ! organelle envelope
is_a: GO:0044428 ! nuclear part
relationship: part_of GO:0012505 ! endomembrane system

.ace:
GO_term : "GO:0005635"
Definition "The double lipid bilayer enclosing the nucleus and separating its contents from the 
rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm 
(also called the  perinuclear space)."
Term     "nuclear envelope"
Cellular_component
Instance_of      "GO:0044428"
Instance_of      "GO:0031967"
Component_of     "GO:0012505"




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