{"id":"https://openalex.org/W2768826694","doi":"https://doi.org/10.1093/nar/gkx1104","title":"iPTMnet: an integrated resource for protein post-translational modification network discovery","display_name":"iPTMnet: an integrated resource for protein post-translational modification network discovery","publication_year":2017,"publication_date":"2017-10-24","ids":{"openalex":"https://openalex.org/W2768826694","doi":"https://doi.org/10.1093/nar/gkx1104","mag":"2768826694","pmid":"https://pubmed.ncbi.nlm.nih.gov/29145615"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkx1104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx1104","pdf_url":"https://academic.oup.com/nar/article-pdf/46/D1/D542/23162331/gkx1104.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/46/D1/D542/23162331/gkx1104.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027838788","display_name":"Hongzhan Huang","orcid":"https://orcid.org/0000-0001-9594-9304"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongzhan Huang","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001355963","display_name":"Cecilia N. Arighi","orcid":"https://orcid.org/0000-0002-0803-4817"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecilia N Arighi","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010355751","display_name":"Karen Ross","orcid":"https://orcid.org/0000-0003-4633-6055"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen E Ross","raw_affiliation_strings":["Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020539776","display_name":"Jia Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jia Ren","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042712921","display_name":"Gang Li","orcid":"https://orcid.org/0000-0003-0621-2779"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Li","raw_affiliation_strings":["Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084831565","display_name":"Sheng\u2010Chih Chen","orcid":"https://orcid.org/0000-0003-1550-5418"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sheng-Chih Chen","raw_affiliation_strings":["Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432294","display_name":"Qinghua Wang","orcid":"https://orcid.org/0000-0002-4557-5989"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qinghua Wang","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005968346","display_name":"Julie Cowart","orcid":"https://orcid.org/0000-0003-1916-4649"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie Cowart","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027009667","display_name":"K. Vijay\u2010Shanker","orcid":"https://orcid.org/0000-0003-0958-3073"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K Vijay-Shanker","raw_affiliation_strings":["Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cathy H Wu","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA","Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5027838788"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.8348,"has_fulltext":false,"cited_by_count":188,"citation_normalized_percentile":{"value":0.98036726,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"46","issue":"D1","first_page":"D542","last_page":"D550"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9750999808311462,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9642999768257141,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.658352255821228},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5884753465652466},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5536577701568604},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.43806105852127075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37193095684051514},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3292251229286194},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17512205243110657}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.658352255821228},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5884753465652466},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5536577701568604},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.43806105852127075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37193095684051514},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3292251229286194},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17512205243110657},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkx1104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx1104","pdf_url":"https://academic.oup.com/nar/article-pdf/46/D1/D542/23162331/gkx1104.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:29145615","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29145615","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5753337","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5753337","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkx1104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx1104","pdf_url":"https://academic.oup.com/nar/article-pdf/46/D1/D542/23162331/gkx1104.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2768826694.pdf","grobid_xml":"https://content.openalex.org/works/W2768826694.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1519266993","https://openalex.org/W1568341953","https://openalex.org/W1894267660","https://openalex.org/W1954914035","https://openalex.org/W1964670939","https://openalex.org/W1987963824","https://openalex.org/W1989962769","https://openalex.org/W1999615477","https://openalex.org/W2004071190","https://openalex.org/W2007805002","https://openalex.org/W2011953977","https://openalex.org/W2033208312","https://openalex.org/W2041053370","https://openalex.org/W2043274355","https://openalex.org/W2051147053","https://openalex.org/W2054285199","https://openalex.org/W2056371507","https://openalex.org/W2063368579","https://openalex.org/W2068947311","https://openalex.org/W2070063830","https://openalex.org/W2071925258","https://openalex.org/W2075319133","https://openalex.org/W2079121387","https://openalex.org/W2092296317","https://openalex.org/W2092847630","https://openalex.org/W2095926488","https://openalex.org/W2105217514","https://openalex.org/W2122863289","https://openalex.org/W2125353047","https://openalex.org/W2134873394","https://openalex.org/W2138319716","https://openalex.org/W2140601282","https://openalex.org/W2154139219","https://openalex.org/W2159675211","https://openalex.org/W2162172965","https://openalex.org/W2164412127","https://openalex.org/W2167350014","https://openalex.org/W2170283197","https://openalex.org/W2560310361","https://openalex.org/W2583901045","https://openalex.org/W2739999456","https://openalex.org/W4210702584"],"related_works":["https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W2612240612","https://openalex.org/W4324018414","https://openalex.org/W4211208250","https://openalex.org/W4211054902","https://openalex.org/W2472351724","https://openalex.org/W3145366215","https://openalex.org/W2170381940"],"abstract_inverted_index":{"Protein":[0,95],"post-translational":[1],"modifications":[2],"(PTMs)":[3],"play":[4],"a":[5,84,181],"pivotal":[6],"role":[7],"in":[8,138],"numerous":[9],"biological":[10],"processes":[11],"by":[12],"modulating":[13],"regulation":[14],"of":[15,77,86,175,189],"protein":[16],"function.":[17],"We":[18],"have":[19],"developed":[20],"iPTMnet":[21,57,128,179],"(http://proteininformationresource.org/iPTMnet)":[22],"for":[23,167,183],"PTM":[24,42,45,53,101,117,136,148,154,190,196],"knowledge":[25],"discovery,":[26],"employing":[27],"an":[28],"integrative":[29],"bioinformatics":[30],"approach-combining":[31],"text":[32,64],"mining,":[33,35],"data":[34,59],"and":[36,52,68,80,93,100,107,110,126,150,164,186,192,198],"ontological":[37],"representation":[38],"to":[39],"capture":[40],"rich":[41],"information,":[43],"including":[44,172],"enzyme-substrate-site":[46,155],"relationships,":[47],"PTM-specific":[48],"protein-protein":[49],"interactions":[50],"(PPIs)":[51],"conservation":[54],"across":[55,111],"species.":[56,112],"encompasses":[58],"from":[60,74],"(i)":[61],"our":[62],"PTM-focused":[63],"mining":[65,76],"tools,":[66],"RLIMS-P":[67],"eFIP,":[69],"which":[70],"extract":[71],"phosphorylation":[72],"information":[73],"full-scale":[75],"PubMed":[78],"abstracts":[79],"full-length":[81],"articles;":[82],"(ii)":[83],"set":[85],"curated":[87],"databases":[88],"with":[89,144],"experimentally":[90],"observed":[91],"PTMs;":[92],"iii)":[94],"Ontology":[96],"that":[97],"organizes":[98],"proteins":[99],"proteoforms,":[102],"enabling":[103,195],"their":[104],"representation,":[105],"annotation":[106],"comparison":[108],"within":[109],"Presently":[113],"covering":[114],"eight":[115],"major":[116],"types":[118],"(phosphorylation,":[119],"ubiquitination,":[120],"acetylation,":[121],"methylation,":[122],"glycosylation,":[123],"S-nitrosylation,":[124],"sumoylation":[125],"myristoylation),":[127],"knowledgebase":[129],"contains":[130],"more":[131,145],"than":[132,146],"654":[133],"500":[134],"unique":[135],"sites":[137],"over":[139,151],"62":[140],"100":[141],"proteins,":[142],"along":[143],"1200":[147],"enzymes":[149],"24":[152],"300":[153],"relations.":[156],"The":[157],"website":[158],"supports":[159],"online":[160],"search,":[161],"browsing,":[162],"retrieval":[163],"visual":[165,184],"analysis":[166,188],"scientific":[168],"queries.":[169],"Several":[170],"examples,":[171],"functional":[173],"interpretation":[174],"phosphoproteomic":[176],"data,":[177],"demonstrate":[178],"as":[180],"gateway":[182],"exploration":[185],"systematic":[187],"networks":[191],"conservation,":[193],"thereby":[194],"discovery":[197],"hypothesis":[199],"generation.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":28},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":7}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}
