A simple and lightweight client library for iPTMnet.
iPTMnetR is a thin wrapper around the rest api of iPTMnet database. It makes it very easy to query iPTMnet database and integrate the results into any existing bioinformatics pipeline.
See the Quick start for more details.
install.packages("iptmnetr")
- Install devtools
install.packages("devtools")
- Load devtools
library(devtools)
- Install from github
install_github("udel-cbcb/iptmnetr")
- Load the library
library(iptmnetr)
The API consists of functions that mirror the functionality of the iPTMNet rest api.
Retriving information for an entry with an iPTMnet ID - Q15796
# get the information for Q15796
get_info("Q15796")
Type : dictionary
{
"uniprot_ac": "Q15796",
"uniprot_id": "SMAD2_HUMAN",
"protein_name": "Mothers against decapentaplegic homolog 2;",
"gene_name": "SMAD2",
"synonyms": [
"MADH2",
"MADR2"
],
"organism": {
"taxon_code": 9606,
"species": "Homo sapiens",
"common_name": "Human"
},
"pro": {
"id": "PR:Q15796",
"name": "mothers against decapentaplegic homolog 2 (human)",
"definition": "A smad2 that is encoded in the genome of human.",
"short_label": "hSMAD2",
"category": "organism-gene"
}
}
To search the iPTMnet database for entries related to the gene smad2
, you can use the search
function as follows.
# search the database
search("Smad2",TermType()$ProteinOrGeneName,Role()$EnzymeOrSubstrate)
Type : dataframe
iptm_id | protein_name | gene_name | synonyms | organism_taxon_code | organism_species | organism_common_name | substrate_role | substrate_num | enzyme_role | enzyme_num | ptm_dependent_ppi_role | ptm_dep_ppi_num | sites | isoforms |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
O70436 | Mothers against decapentaplegic homolog 2; | Smad2 | Madh2 | 10116 | Rattus norvegicus | Rat | True | 0 | False | 0 | False | 0 | 6 | 0 |
Q1W668 | Mothers against decapentaplegic homolog 2; | SMAD2 | 9913 | Bos taurus | Bovine | True | 0 | False | 0 | False | 0 | 4 | 0 |
To perform a bulk query for ptm enzymes on the database with a list of PTM sites in a csv file - sites.csv
you can use get_ptm_enzymes_from_file
function.
# search the database
get_ptm_enzymes_from_file("sites.csv")
Type : dataframe
ptm_type | site | site_position | score | source | pmid | enz_name | enz_id | sub_name | sub_id |
---|---|---|---|---|---|---|---|---|---|
Phosphorylation | S2 | 2 | 2 | HPRD | 8898866,20068231 | PRKCB | P05771 | ANXA2 | P07355 |
Phosphorylation | S7 | 7 | 4 | HPRD,neXtPro | 20166139,12773393,20089855,17924679,11438671 | RPS6KA5 | O75582 | HMGN1 | P05114 |
Phosphorylation | T60 | 60 | 4 | neXtProt,PSP | 21355052,16081417 | SGK1 | O00141 | WNK1 | Q9H4A3 |