Python client for iPTMNet REST API - https://research.bioinformatics.udel.edu/iptmnet/
Project description
iPTMnet is a bioinformatics resource for integrated understanding of protein post-translational modifications (PTMs) in systems biology context. It connects multiple disparate bioinformatics tools and systems of text mining, data mining, analysis and visualization tools, and databases and ontologies into an integrated cross-cutting research resource to address the knowledge gaps in exploring and discovering PTM networks.
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
#imports
import pyiptmnet.api as api
# get the information for Q15796
api.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.
#imports
import pyiptmnet.api as api
from pyiptmnet.enums import *
# search the database
api.search("smad2", Termtype.ProteinGeneName, 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.
#imports
import pyiptmnet.api as api
from pyiptmnet.enums import *
# search the database
api.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 |
Running tests
python -m unittest test.tests
Citations of the underlying Sources
# | Name | Publication | PubMed |
---|---|---|---|
1 | HPRD | Prasad, T. S. K. et al. (2009) Human Protein Reference Database - 2009 Update. Nucleic Acids Research. 37, D767-72. | 18988627 |
2 | phospho.ELM | Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Nucleic Acids Res. 2011 Jan;39(Database issue) 261-7. doi: 10.1093/nar/gkq1104. | 21062810 |
3 | p3DB | Yao Q, Ge H, Wu S, Zhang N, Chen W, Xu C, Gao J, Thelen JJ, Xu D. (2013) P3DB 3.0: From plant phosphorylation sites to protein networks. Nucleic Acids Res 2013. 42(Database issue):D1206-D1213 | 24243849 |
4 | PhosphoGrid | Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. 2006; 34:D535-9. | 16381927 |
5 | PomBase | Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG. PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res. 2012;40(Database issue):D695-9. Epub 2011 | 22039153 |
6 | neXtProt | Gaudet P, Michel PA, Zahn-Zabal M, Britan A, Cusin I, Domagalski M, Duek PD, Gateau A, Gleizes A, Hinard V, Rech de Laval V, Lin JJ, Nikitin F, Schaeffer M, Teixeira D, Lane L, Bairoch A. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res. 2017; 45(D1):D177-D182 doi:10.1093/nar/gkw1062 | 27899619 |
7 | Signor | Perfetto L, Briganti L, Calderone A, Cerquone Perpetuini A, Iannuccelli M, Langone F, Licata L, Marinkovic M, Mattioni A, Pavlidou T, Peluso D, Petrilli LL, Pirrò S, Posca D, Santonico E, Silvestri A, Spada F, Castagnoli L, Cesareni G. SIGNOR: a database of causal relationships between biological entities. Nucleic Acids Res. 2016;44(D1):D548-54. doi: 10.1093/nar/gkv1048 | 26467481 |
8 | dbSNO | Chen YJ, Lu CT, Su MG, Huang KY, Ching WC, Yang HH, Liao YC, Chen YJ, Lee TY. dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic Acids Res. 2015;43(Database issue):D503-11. doi: 10.1093/nar/gku1176. | 25399423 |
9 | PhosphoSitePlus | Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43(Database issue):D512-20. doi: 10.1093/nar/gku1267. | 25514926 |
10 | PhosPhAt | Durek P, Schmidt R, Heazlewood JL, Jones A, Maclean D, Nagel A, Kersten B, Schulze WX. PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res. 38: D828-D834 (2010) | 17984086 |
11 | UniProt | The UniProt Consortium. UniProt: the universal protein knowledgebase Nucleic Acids Res. 45: D158-D169 (2017) | 27899622 |
12 | PRO | Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K,Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res.2017;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. | 27899649 |
13 | RLIMS-P | Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH. RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database (Oxford).2014. pii: bau081. doi: 10.1093/database/bau081. | 25122463 |
14 | eFIP | Wang Q, Ross KE, Huang H, Ren J, Li G, Vijay-Shanker K, Wu CH, Arighi CN. Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature. Methods Mol Biol. 2017;1558:213-232. doi: 10.1007/978-1-4939-6783-4_10. | 28150240 |
15 | SGD | Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM. Curated protein information in the Saccharomyces genome database. Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax011 | 28365727 |
16 | Biomuta | Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancerbiomarker discovery. Nucleic Acids Res. 2018 Jan 4;46(D1):D1128-D1136. doi:10.1093/nar/gkx907 | 30053270 |
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