docs/README.md

In udel-cbcb/iPTMnetR: Interface to the 'iPTMnet' API

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")

1. Load devtools

library(devtools)

1. Install from github

install_github("udel-cbcb/iptmnetr")

1. 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

udel-cbcb/iPTMnetR documentation built on Nov. 14, 2021, 9:16 p.m.