Difference between revisions of "Updating go.ace file"
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| Parent Instance || is_a: || For each GO Name, look at is_a tag. Fill in .ace with corresponding value. | | 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 | + | | Parent Component_of || relationship: part_of || For each GO Name, look at relationship: part_of. Fill in .ace with corresponding value. |
|- | |- | ||
| 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 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. | ||
| Line 83: | Line 83: | ||
| Index Descendents || For each is_a and relatinoship: part_of, look for GO Name. If GO Name matches value in either tag, fill in .ace with corresponding id. | | Index Descendents || For each is_a and relatinoship: part_of, look for GO Name. If GO Name matches value in either tag, fill in .ace with corresponding id. | ||
|- | |- | ||
| − | | Version || In header, remark: cvs version: | + | | Version || In header, remark: cvs version: || Add value in between $ signs after cvs version. |
|- | |- | ||
|} | |} | ||
Revision as of 19:56, 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 | 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 | 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 | For each is_a and relatinoship: part_of, look for GO Name. If GO Name matches value in either tag, fill in .ace with corresponding id. | |
| 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
Back to Gene Ontology
