Updating go.ace file

Updating the GO term.ace File - Script Specifications

• Input file: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

• 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_of	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
Component       "GO:0034992"
Component       "GO:0005641'
Component       "GO:0031965"
Component       "GO:0005643"
Component       "GO:0044195"
Instance_of     "GO:0044428"
Instance_of     "GO:0031967"
Component_of    "GO:0012505"
Ancestor        "GO:0005575"
Ancestor        "GO:0005623"
Ancestor        "GO:0044464"
Ancestor        "GO:0012505"
Ancestor        "GO:0031975"
Ancestor        "GO:0031967"
Ancestor        "GO:0005622"
Ancestor        "GO:0044424"
Ancestor        "GO:0043229"
Ancestor        "GO:0043231"
Ancestor        "GO:0005634"
Ancestor        "GO:0044428"
Ancestor        "GO:0044446"
Ancestor        "GO:0043226"
Ancestor        "GO:0043227"
Ancestor        "GO:0044422"
Descendent      "GO:0034992"
Descendent      "GO:0005641"
Descendent      "GO:0031965"
Descendent      "GO:0005643"
Descendent      "GO:0044195"
Descendent      "GO:0034993"
Descendent      "GO:0005637"
Descendent      "GO:0044453"
Descendent      "GO:0005640"
Descendent      "GO:0031229"
Descendent      "GO:0005639"
Descendent      "GO:0002180"
Descendent      "GO:0031316"
Descendent      "GO:0031308"
Descendent      "GO:0031309"
Descendent      "GO:0044613"
Descendent      "GO:0044614"
Descendent      "GO:0044611"
Descendent      "GO:0044612"
Descendent      "GO:0044615"
Descendent      "GO:0031080"
Descendent      "GO:0070762"

For the term determination of adult lifespan GO:0008340

.obo
[Term]
id: GO:0008340
name: determination of adult lifespan
namespace: biological_process
def: "The control of viability and duration in the adult phase of the life-cycle." [GOC:ems]
is_a: GO:0044707 ! single-multicellular organism process
relationship: part_of GO:0010259 ! multicellular organismal aging

.ace
GO_term : "GO:0008340"
Definition "The control of viability and duration in the adult phase of the life-cycle."
Term "determination of adult lifespan"
Namespace Biological_process
Component "GO:1901047"

For the term mRNA binding GO:0003729

.obo
[Term]
id: GO:0003729
name: mRNA binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns." [GOC:kmv, SO:0000234]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003723 ! RNA binding

.ace
GO_term : "GO:0003729"
Definition "Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns."
Term     "mRNA binding"
Molecular _function
Instance     "GO:0030350"
Instance     "GO:0003730"
Instance     "GO:0048027"
Instance     "GO:0008143"
Instance     "GO:0035368"
Instance_of  "GO:0003723"
Ancestor     "GO:0003723"
Ancestor     "GO:0003676"
Ancestor     "GO:1901363"
Ancestor     "GO:0097159"
Ancestor     "GO:0005488"
Ancestor     "GO:0003674"
Descendent   "GO:0030350"
Descendent   "GO:0003730"
Descendent   "GO:0048027"
Descendent   "GO:0008143"
Descendent   "GO:0035368"
Descendent   "GO:0035925"

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