Difference between revisions of "Updating go.ace file"
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| Definition || def: || Add corresponding value including double quotes. Omit information in brackets at the end of the definition. | | Definition || def: || Add corresponding value including double quotes. Omit information in brackets at the end of the definition. | ||
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+ | | Status || is_obsolete: || If tag is not present, Status should be set to Valid. If tag is present, Status should be set to Obsolete. | ||
|- | |- | ||
| Term || name: || Add corresponding value in double quotes. | | Term || name: || Add corresponding value in double quotes. |
Revision as of 18:32, 20 June 2013
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? Also, what to do with synonyms?
WormBase ?GO_term Model:
?GO_term Name ?Text Status UNIQUE Valid Obsolete Definition ?Text Term ?Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?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 Attribute_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 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 in double quotes. |
Definition | def: | Add corresponding value including double quotes. Omit information in brackets at the end of the definition. |
Status | is_obsolete: | If tag is not present, Status should be set to Valid. If tag is present, Status should be set to Obsolete. |
Term | name: | Add corresponding value in double quotes. |
Type | namespace: | Make first letter upper case and add corresponding value. |
Instance | is_a: | In each is_a: tag, look for corresponding GO Name. Fill in .ace tag with corresponding id: in double quotes. |
Component | relationship: part_of | In each relationship: part_of tag, look for GO Name. Fill in .ace tag with corresponding id: in double quotes. |
Instance_of | is_a: | For GO Name, look at is_a tag. Fill in .ace with corresponding value(s) in double quotes. |
Component_of | relationship: part_of | For GO Name, look at relationship: part_of. Fill in .ace with corresponding value(s) in double quotes. |
Ancestor | is_a: and relationship: part_of | For each GO Name, look at is_a: and relationship: part_of. Fill in .ace with each corresponding value in double quotes. Then, for each value filled in, iterate and look at their 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. Remove any redundant values from list. |
Descendent | 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: in double qutoes. 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. Remove any redundant values from list. |
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
I found it helpful to use the GOOSE query tool to check the ancestors and descendents: http://berkeleybop.org/goose
For the term 'nuclear envelope' GO:0005635
.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 adenylate cyclase-activating serotonin receptor signaling pathway GO:0007192
.obo [Term] id: GO:0007192 name: adenylate cyclase-activating serotonin receptor signaling pathway namespace: biological_process def: "The series of molecular signals generated as a consequence of a serotonin receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb] synonym: "activation of adenylate cyclase activity by serotonin receptor signalling pathway" RELATED [GOC:mah] synonym: "serotonin receptor, adenylate cyclase activating pathway" RELATED [GOC:dph, GOC:tb] synonym: "serotonin receptor, adenylyl cyclase activating pathway" EXACT [] is_a: GO:0007189 ! adenylate cyclase-activating G-protein coupled receptor signaling pathway is_a: GO:0007210 ! serotonin receptor signaling pathway
.ace GO_term : "GO:00007192" Definition "The series of molecular signals generated as a consequence of a serotonin receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." Term "adenylate cyclase-activating serotonin receptor signaling pathway" Namespace Biological_process Instance_of "GO:0007189" Instance_of "GO:0007210" Ancestor "GO:0007189" Ancestor "GO:0007210" Ancestor "GO:0007188" Ancestor "GO:0007186" Ancestor "GO:0007166" Ancestor "GO:0007165" Ancestor "GO:0007187" Ancestor "GO:0050794" Ancestor "GO:0051716" Ancestor "GO:0050789" Ancestor "GO:0044763" Ancestor "GO:0050896" Ancestor "GO:0009987" Ancestor "GO:0044699" Ancestor "GO:0008150" Ancestor "GO:0065007" Ancestor "GO:0007154" Ancestor "GO:0044700" Ancestor "GO:0023052"
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" Instance_of "GO:0044707" Component_of "GO:0010259" Ancestor "GO:0010259" Ancestor "GO:0007275" Ancestor "GO:0007568" Ancestor "GO:0044707" Ancestor "GO:0044767" Ancestor "GO:0032501" Ancestor "GO:0044699" Ancestor "GO:0032502" Ancestor "GO:0008150" Descendent "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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