Fetching GO terms based on gene IDs using Entrez e-utilities

Question

[Shraddha]

Hello all,

I'm trying to access GO terms for a list of genes, but they're not easily available. Manually, these are the steps I'd take:

1. Search gene ID on NCBI; find protein ID
2. Search protein ID on Uniprot/Uniparc; find Pfam ID
3. Search Pfam ID on Pfam; switch to InterPro tab, get GO terms

I have seen the e-utilities functionality by Entrez , but I'm having trouble understanding how to use it. When I try a command such as

esearch -db gene -query 'LOC115705987' | elink -target protfam | esearch -db protein -query [PROT]

I get a response like

<ENTREZ_DIRECT>
  <Db>protein</Db>
  <WebEnv>MCID_61e013e99059043a7d58ece9</WebEnv>
  <QueryKey>3</QueryKey>
  <Count>1001315687</Count>
  <Step>3</Step>
</ENTREZ_DIRECT>

My question is, how can I use this information to get (at first) the protein ID, and subsequently the GO terms?

Thanks in advance!

Answer 1

[GenoMax]

how can I use this information to get (at first) the protein ID, and subsequently the GO terms?

Using EntrezDirect:

$ esearch -db gene -query 'LOC115705987' | elink -target protein | esummary | xtract -pattern DocumentSummary -element Caption,Title
XP_030489337    probable serine/threonine-protein kinase At1g09600 [Cannabis sativa]

This is a predicted record so information here on out may not be available. There are references to CDD that may be useful.

$ esearch -db gene -query 'LOC115705987' | elink -target protein | efetch -format ft
>Feature ref|XP_030489337.1|
1   234 Protein
            product probable serine/threonine-protein kinase At1g09600
<11 233 Region
            region  PKc_like
            note    Protein Kinases, catalytic domain
            db_xref CDD:389743
37  37  Site
75  75
77  77
96  96
109 109
111 114
116 116
154 155
            site_type   other
            note    polypeptide substrate binding site [polypeptide binding]
            db_xref CDD:270870
92  103 Site
108 116
            site_type   other
            note    activation loop (A-loop)
            db_xref CDD:270870
1   234 CDS
            product probable serine/threonine-protein kinase At1g09600
            protein_id  ref|XP_030489337.1|
            db_xref GeneID:115705987

[Shraddha]

Thank you! Do you know if uniprot, pfam, and interpro can also be accessed through this? Here I don't see any corresponding databases.