Package: pyiptmnet
A simple and lightweight client library for iPTMnet.What is itpyiPTMnet 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.InstallationPlease not this package is only available for python 3.0+Install from PyPIpipinstallpyiptmnetInstall from Githubpipinstallgit+https://github.com/udel-cbcb/pyiptmnet.git#egg=pyiptmnetQuick startThe API consists of functions that mirror the functionality of the iPTMNet rest api. Below you can find a few examples of the functions provided by the API.InfoRetriving information for an entry with an iPTMnet ID -Q15796#importsimportpyiptmnet.apiasapi# get the information for Q15796api.get_info("Q15796")ResultType :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"}}SearchTo search the iPTMnet database for entries related to the genesmad2, you can use thesearchfunction as follows.#importsimportpyiptmnet.apiasapifrompyiptmnet.enumsimport*# search the databaseapi.search("smad2",Termtype.ProteinGeneName,Role.EnzymeOrSubstrate)ResultType :dataframeiptm_idprotein_namegene_namesynonymsorganism_taxon_codeorganism_speciesorganism_common_namesubstrate_rolesubstrate_numenzyme_roleenzyme_numptm_dependent_ppi_roleptm_dep_ppi_numsitesisoformsO70436Mothers against decapentaplegic homolog 2;Smad2Madh210116Rattus norvegicusRatTrue0False0False060Q1W668Mothers against decapentaplegic homolog 2;SMAD29913Bos taurusBovineTrue0False0False040BulkTo perform a bulk query for ptm enzymes on the database with a list of PTM sites in a csv file -sites.csvyou can useget_ptm_enzymes_from_filefunction.#importsimportpyiptmnet.apiasapifrompyiptmnet.enumsimport*# search the databaseapi.get_ptm_enzymes_from_file("sites.csv")ResultType :dataframeptm_typesitesite_positionscoresourcepmidenz_nameenz_idsub_namesub_idPhosphorylationS222HPRD8898866,20068231PRKCBP05771ANXA2P07355PhosphorylationS774HPRD,neXtPro20166139,12773393,20089855,17924679,11438671RPS6KA5O75582HMGN1P05114PhosphorylationT60604neXtProt,PSP21355052,16081417SGK1O00141WNK1Q9H4A3Running testspython -m unittest test.testsCitationIf you like our work and it helps you in your research, please cite us using the following citation.@article{10.1093/database/baz157,
    author = {Gavali, Sachin and Cowart, Julie and Chen, Chuming and Ross, Karen E and Arighi, Cecilia and Wu, Cathy H},
    title = "{RESTful API for iPTMnet: a resource for protein post-translational modification network discovery}",
    journal = {Database},
    volume = {2020},
    year = {2020},
    month = {05},
    abstract = "{iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways.}",
    issn = {1758-0463},
    doi = {10.1093/database/baz157},
    url = {https://doi.org/10.1093/database/baz157},
    note = {baz157},
    eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baz157/33205374/baz157.pdf},
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