Updating go.ace file

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Updating the GO_term.ace File - Script Specifications

  • Output file: go.ace
  • Model changes - added Status and Synonym tags.
  • Model changes for WS250:
    • Script on tazendra: /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl
      • 'Term' tag was removed from the model; we will now put GO term Name information in the 'Name' tag - needs script change - Line 42
      • We will change how we populate Version information - needs script change - Lines 29 and 52
        • Get version information from GO obo header tag that has the format: 'data-version: releases/YYYY-MM-DD'
        • An example of a new .ace tag value would be: 'Gene Ontology releases/2015-06-13'
      • We added an Alt_id tag which is a new tag for the ?GO_term model - needs script addition
        • In GO obo file, tag name is alt_id
        • In ?GO_term model, tag name is Alt_id
        • We will populate the tag with the exact string in the alt_id field; some terms may have many alt_id

WormBase ?GO_term Model for WS250:

     ?GO_term Name ?Text
              Definition ?Text
              Alt_id ?Text
              Synonym Broad ?Text
                      Exact ?Text
                      Narrow ?Text
                      Related ?Text
              Status UNIQUE Valid
                            Obsolete
              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 // will this replace CDS? [040203 krb]
                            CDS ?CDS XREF GO_term
                            Sequence ?Sequence XREF GO_term // Erich, [011210 krb]
                            Transcript ?Transcript XREF GO_term // [030411 krb]
                            Phenotype ?Phenotype XREF GO_term // Erich, [020128 dl]
                            Index Ancestor ?GO_term XREF Descendent // Lincoln [020709 [krb]
                                  Descendent ?GO_term XREF Ancestor
                            Anatomy_term ?Anatomy_term XREF GO_term // added [031107 krb]
                            Homology_group ?Homology_group XREF GO_term // added [031120 krb]
                            Expr_pattern ?Expr_pattern XREF GO_term
                            Picture ?Picture XREF Cellular_component
                            GO_annotation ?GO_annotation XREF GO_term
              Version 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

Sample GO Header:

format-version: 1.2
data-version: 2013-06-24
date: 23:06:2013 14:54
saved-by: rl
auto-generated-by: TermGenie 1.0
subsetdef: Cross_product_review "Involved_in"
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
subsetdef: virus_checked "Viral overhaul terms"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
default-namespace: gene_ontology
remark: cvs version: $Revision: 9500 $
ontology: go



  • Mapping from .obo file to .ace file:
.ace tag name .obo tag name Action
Object name id: Add corresponding value in double quotes.
Status is_obsolete: If tag is not present, Status should be set to Valid. If tag is present, Status should be set to Obsolete.
Definition def: Add corresponding value including double quotes. Omit information in brackets at the end of the definition.
Name name: Add corresponding value in double quotes.
Broad, Exact, Narrow, or Related synonym: For each synonym, check text after double quotes to populate Broad, Exact, Narrow, or Related. For ?Text add value in double quotes. Ignore information in brackets. Note that a single GO term object can have multiple synonyms.
Type namespace: Make first letter upper case and add corresponding value.
Instance is_a: Take object Name (id:) and look for that value in the is_a: tag for all entries. Fill in .ace tag with corresponding id: from obo file in double quotes. Can have multiple values.
Component relationship: part_of In each relationship: part_of tag, look for Name. Fill in .ace tag with corresponding id: in double quotes. Can have multiple values.
Instance_of is_a: For Name, look at is_a tag. Fill in .ace with corresponding value(s) in double quotes. Can have multiple values.
Component_of relationship: part_of For Name, look at relationship: part_of. Fill in .ace with corresponding value(s) in double quotes. Can have multiple values.
Ancestor is_a: and relationship: part_of For each 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 Name. If 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, data-version: releases/YYYY-MM-DD Gene Ontology followed by value after 'data-version:' tag.


  • 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
    • GO:1900529 regulation of cell shape involved in cellular response to glucose starvation

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"
Status "Valid"
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"
Version         "Gene Ontology Revision: 9500"


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"
Status "Valid"
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"
Related "activation of adenylate cyclase activity by serotonin receptor signalling pathway"
Related "serotonin receptor, adenylate cyclase activating pathway"
Exact "serotonin receptor, adenylyl cyclase activating pathway"
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"
Version     "Gene Ontology Revision: 9500"
	 	


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"
Status "Valid"
Definition "The control of viability and duration in the adult phase of the life-cycle."
Term "determination of adult lifespan"
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"
Version      "Gene Ontology Revision: 9500"


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"
Status "Valid"
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"
Version      "Gene Ontology Revision: 9500"


For the term 'regulation of cell shape involved in cellular response to glucose starvation', GO:1900529

.obo
[Term]
id: GO:1900529
name: regulation of cell shape involved in cellular response to glucose starvation
namespace: biological_process
def: "OBSOLETE. Any regulation of cell shape that is involved in cellular response to glucose starvation." [GOC:al, GOC:TermGenie,  PMID:9135147]
comment: This term was obsoleted at the TermGenie Gatekeeper stage.
is_obsolete: true
created_by: al
creation_date: 2012-05-08T01:43:38Z
.ace
GO_term : "GO:1900529"
Status "Obsolete"
Definition "OBSOLETE. Any regulation of cell shape that is involved in cellular response to glucose starvation."
Term "regulation of cell shape involved in cellular response to glucose starvation"
Biological_process
Version   "Gene Ontology Revision: 9500"





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