GOTerms search GO.db and R

Question

[mzezza]

Hello,

I'm using GO.db package to download a GO Terms list with this:

  var <- as.list(GOTERM)
if(length(var) > 0){
  GOID(var[[1]])
  Term(var[[1]])
  Synonym(var[[1]])
  Secondary(var[[1]])
  Definition(var[[1]])
  Ontology(var[[1]])
}

I want to have the possibility of search in this list with a keyword like, for example, "dopamine". (Doesn't exist a term "dopamine" but exist "dopamine catabolic process" for example ..).

Thanks and sorry for my english.

Answer 1

[Guangchuang Yu]

> require(GO.db)
> tbl=toTable(GOTERM)
> tbl[grep("dopamine", tbl$Definition),] -> x
> dim(x)
[1] 461   7
> x[1:2,]
          go_id      go_id
2212 GO:0001588 GO:0001588
2213 GO:0001588 GO:0001588
                                                            Term Ontology
2212 dopamine neurotransmitter receptor activity, coupled via Gs       MF
2213 dopamine neurotransmitter receptor activity, coupled via Gs       MF
                                                                                                                                  Definition
2212 Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gs to initiate a change in cell activity.
2213 Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gs to initiate a change in cell activity.
                           Synonym Secondary
2212 dopamine D1 receptor activity      <NA>
2213 dopamine D5 receptor activity      <NA>

> x[x$Ontology == "BP", ] %>% head
           go_id      go_id
3016  GO:0001963 GO:0001963
15819 GO:0006585 GO:0006585
15820 GO:0006585 GO:0006585
15821 GO:0006585 GO:0006585
17182 GO:0007191 GO:0007191
17183 GO:0007191 GO:0007191
                                                                  Term Ontology
3016                               synaptic transmission, dopaminergic       BP
15819                      dopamine biosynthetic process from tyrosine       BP
15820                      dopamine biosynthetic process from tyrosine       BP
15821                      dopamine biosynthetic process from tyrosine       BP
17182 adenylate cyclase-activating dopamine receptor signaling pathway       BP
17183 adenylate cyclase-activating dopamine receptor signaling pathway       BP
                                                                                                                                                                                                                                                                                                     Definition
3016                                                                                                                                                                                         The process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine.
15819 The chemical reactions and pathways resulting in the formation of dopamine (3,4-dihydroxyphenylethylamine) from L-tyrosine, via the metabolic precursor 3,4-dihydroxy-L-phenylalanine (L-dopa). Dopamine is a catecholamine neurotransmitter and a metabolic precursor of norepinephrine and epinephrine.
15820 The chemical reactions and pathways resulting in the formation of dopamine (3,4-dihydroxyphenylethylamine) from L-tyrosine, via the metabolic precursor 3,4-dihydroxy-L-phenylalanine (L-dopa). Dopamine is a catecholamine neurotransmitter and a metabolic precursor of norepinephrine and epinephrine.
15821 The chemical reactions and pathways resulting in the formation of dopamine (3,4-dihydroxyphenylethylamine) from L-tyrosine, via the metabolic precursor 3,4-dihydroxy-L-phenylalanine (L-dopa). Dopamine is a catecholamine neurotransmitter and a metabolic precursor of norepinephrine and epinephrine.
17182                                                The series of molecular signals generated as a consequence of a dopamine 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).
17183                                                The series of molecular signals generated as a consequence of a dopamine 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).
                                                                               Synonym
3016                                                                              <NA>
15819                                                 dopamine anabolism from tyrosine
15820                                                 dopamine formation from tyrosine
15821                                                 dopamine synthesis from tyrosine
17182  activation of adenylate cyclase activity by dopamine receptor signaling pathway
17183 activation of adenylate cyclase activity by dopamine receptor signalling pathway
      Secondary
3016       <NA>
15819      <NA>
15820      <NA>
15821      <NA>
17182      <NA>
17183      <NA>

Answer 2

[EagleEye]

You can retrieve all GO terms with corresponding gene list as simple table format (tab-delimited) using GeneSCF,

Example,

A: Gene ontology in sheep