Difference between revisions of "Updating go.ace file"
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*Output file: go.ace | *Output file: go.ace | ||
+ | |||
+ | *No model change, except....what to do with is_obsolete tag in .obo? | ||
WormBase ?GO_term Model: | WormBase ?GO_term Model: |
Revision as of 19:19, 12 June 2013
Updating the go.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 |
---|---|
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 .ace with corresponding id: |
Index Ancestors | For each GO Name, look at is_a and relationship: part_of. Fill in .ace with corresponding value. Then, for each value, look at is_a and relationship: part_of. Continue to fill in .ace with corresponding value until we reach the root node, for which no is_a or relationship: part_of exists. |
Index Descendents | |
Version |
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