iPTMnetR

A simple and lightweight client library for iPTMnet.

What is it

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.

Installation

Install from CRAN

install.packages("iptmnetr")

Install from github

1. Install devtools

install.packages("devtools")

2. Load devtools

library(devtools)

3. Install from github

install_github("udel-cbcb/iptmnetr")

4. Load the library

library(iptmnetr)

Quick start

The API consists of functions that mirror the functionality of the iPTMNet rest api.

Info

Retriving information for an entry with an iPTMnet ID - Q15796

# get the information for Q15796 
get_info("Q15796")

Result

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"
  }
}

Search

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)

Result

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

Bulk

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")

Result

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