Updating go.ace file
From WormBaseWiki
Revision as of 15:03, 13 June 2013 by Vanaukenk (talk | contribs) (→Examples: Terms in .obo and .ace)
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_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 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"
Back to Gene Ontology