How to retreive all GO daughter terms of a particular Gene Ontology term (e.g. GO:0007275- Multicellular organism development)?

Question

[debarunacharya]

Hi,

I want to know How to retreive all GO child terms of a particular Gene Ontology term (e.g. GO:0007275- Multicellular organism development)? please provide me the details of databases(if any), or the methodology to follow.

Thanks in advance

Answer 1

[Guangchuang Yu]

In R:

require(GO.db)
get("GO:0007275", GOBPCHILDREN)

Here is the output:

     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009790" "GO:0007349" "GO:0007389" "GO:0007538" "GO:0007545" "GO:0007562"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0007566" "GO:0009791" "GO:0009835" "GO:0009838" "GO:0010259" "GO:0018992"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0018993" "GO:0030237" "GO:0030238" "GO:0035188" "GO:0035212" "GO:0035295"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0042335" "GO:0043581" "GO:0045137" "GO:0046660" "GO:0046661" "GO:0048229"
     part_of      part_of      part_of    regulates
"GO:0048647" "GO:0048731" "GO:0048736" "GO:2000026"

[Guangchuang Yu]

even more, we can write a small function:

library(GO.db)
library(clusterProfiler)

go_children <- function(goid) {
  ont <- go2ont(goid)$Ontology
  GOCHILDREN <- switch(ont, 
                    BP = GOBPCHILDREN,
                    CC = GOCCCHILDREN,
                    MF = GOMFCHILDREN)
  get(goid, GOCHILDREN)
}  

# Your case in Biological Process
> goid <- "GO:0007275"
> go_children(goid)
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009790" "GO:0007349" "GO:0007389" "GO:0007538" "GO:0007545" "GO:0007562"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0007566" "GO:0009791" "GO:0009835" "GO:0009838" "GO:0010259" "GO:0018992"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0018993" "GO:0030237" "GO:0030238" "GO:0035188" "GO:0035212" "GO:0035295"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0042335" "GO:0043581" "GO:0045137" "GO:0046660" "GO:0046661" "GO:0048229"
     part_of      part_of      part_of    regulates
"GO:0048647" "GO:0048731" "GO:0048736" "GO:2000026"

## Cellular Component term
> go_children("GO:0005886")
     part_of      part_of         is_a      part_of      part_of      part_of
"GO:0000222" "GO:0000223" "GO:0001533" "GO:0043190" "GO:0046658" "GO:0005887"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009897" "GO:0009898" "GO:0016323" "GO:0016324" "GO:0016327" "GO:0019897"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0030094" "GO:0031226" "GO:0031253" "GO:0031520" "GO:0033181" "GO:0042383"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0044214" "GO:0044459" "GO:0044853" "GO:0045258" "GO:0045260" "GO:0045262"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0045264" "GO:0045266" "GO:0045268" "GO:0045270" "GO:0045272" "GO:0045274"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0045276" "GO:0045278" "GO:0045282" "GO:0045284" "GO:0060170" "GO:0060342"
        is_a      part_of      part_of      part_of      part_of      part_of
"GO:0097524" "GO:0098590" "GO:0098797" "GO:0098802" "GO:1990154" "GO:1990176"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:1990191" "GO:1990193" "GO:1990199" "GO:1990203" "GO:1990222" "GO:1990374"
     part_of      part_of
"GO:1990712" "GO:1990851"

[Carlo Yague]

Your answer is much better than mine ! I like it.

Answer 2

[Carlo Yague]

Go to the amigo page for the GO term, then go to the "neighborhood" tab, then look at the "Children of multicellular organism development (GO:0007275)"