{"id":"https://openalex.org/W2755605206","doi":"https://doi.org/10.1142/s0219720017400054","title":"MPTM: A tool for mining protein post-translational modifications from literature","display_name":"MPTM: A tool for mining protein post-translational modifications from literature","publication_year":2017,"publication_date":"2017-09-12","ids":{"openalex":"https://openalex.org/W2755605206","doi":"https://doi.org/10.1142/s0219720017400054","mag":"2755605206","pmid":"https://pubmed.ncbi.nlm.nih.gov/28982288"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720017400054","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017400054","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100732036","display_name":"Dongdong Sun","orcid":"https://orcid.org/0000-0002-9077-1866"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongdong Sun","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100376902","display_name":"Minghui Wang","orcid":"https://orcid.org/0000-0002-5788-894X"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minghui Wang","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100359729","display_name":"Ao Li","orcid":"https://orcid.org/0000-0001-9910-8967"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ao Li","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100376902"],"corresponding_institution_ids":["https://openalex.org/I126520041"],"apc_list":null,"apc_paid":null,"fwci":0.8745,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.73260948,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"05","first_page":"1740005","last_page":"1740005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9674999713897705,"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"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9340999722480774,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7116495370864868},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.6716426014900208},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5373228192329407},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.447440505027771},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4309905171394348},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4294835925102234},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.42585915327072144},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4232904016971588},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4176817536354065},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3753209412097931},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.33633488416671753},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.31523841619491577},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3006565570831299},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2276257574558258},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1336933970451355},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09118717908859253}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7116495370864868},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6716426014900208},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5373228192329407},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.447440505027771},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4309905171394348},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4294835925102234},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.42585915327072144},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4232904016971588},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4176817536354065},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3753209412097931},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.33633488416671753},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31523841619491577},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3006565570831299},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2276257574558258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1336933970451355},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09118717908859253},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720017400054","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017400054","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:28982288","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28982288","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.5400000214576721,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1995286508","https://openalex.org/W2013245499","https://openalex.org/W2023193162","https://openalex.org/W2030644393","https://openalex.org/W2041053370","https://openalex.org/W2053039860","https://openalex.org/W2058483961","https://openalex.org/W2079056345","https://openalex.org/W2082340690","https://openalex.org/W2097960255","https://openalex.org/W2098203835","https://openalex.org/W2100627415","https://openalex.org/W2105217514","https://openalex.org/W2106830745","https://openalex.org/W2123939104","https://openalex.org/W2131520733","https://openalex.org/W2132178599","https://openalex.org/W2133431243","https://openalex.org/W2143733560","https://openalex.org/W2144133357","https://openalex.org/W2152869996","https://openalex.org/W2158577092","https://openalex.org/W2166057395","https://openalex.org/W2177299352","https://openalex.org/W2211826787","https://openalex.org/W2408260152","https://openalex.org/W2417424288","https://openalex.org/W2557399158","https://openalex.org/W2572369686","https://openalex.org/W2583901045","https://openalex.org/W2593930842","https://openalex.org/W2726439135","https://openalex.org/W4233334497"],"related_works":["https://openalex.org/W2803753687","https://openalex.org/W2793278779","https://openalex.org/W3185751515","https://openalex.org/W1479703980","https://openalex.org/W2749535755","https://openalex.org/W1553529581","https://openalex.org/W4206039273","https://openalex.org/W4232119327","https://openalex.org/W2911489562","https://openalex.org/W4386625831"],"abstract_inverted_index":{"Due":[0],"to":[1,47,97,168,189],"the":[2,18,22,149,203,226,251,262],"importance":[3],"of":[4,27,29,75,80],"post-translational":[5],"modifications":[6],"(PTMs)":[7],"in":[8,17,50,95,133],"human":[9,218],"health":[10],"and":[11,24,38,100,105,123,143,161,176,195,198,223,229,242,261],"diseases,":[12,219],"PTMs":[13,130,173],"are":[14,70,83,248,265],"regularly":[15],"reported":[16],"biomedical":[19],"literature.":[20],"However,":[21],"continuing":[23],"rapid":[25],"pace":[26],"expansion":[28],"this":[30],"literature":[31,155],"brings":[32],"a":[33,44,59,66,76,115,144,243],"huge":[34],"challenge":[35],"for":[36,72,158],"researchers":[37,99],"database":[39,101,236],"curators.":[40],"Therefore,":[41],"there":[42],"is":[43,148,165,255],"pressing":[45],"need":[46],"aid":[48],"them":[49,201],"identifying":[51],"relevant":[52],"PTM":[53,107,179,240],"information":[54,74,108,180,241],"more":[55],"efficiently":[56],"by":[57,135,181],"using":[58,136],"text":[60,116,183,187,228],"mining":[61,73,117,156],"system.":[62],"So":[63],"far,":[64],"only":[65],"few":[67],"web":[68,151],"servers":[69],"available":[71,110,257],"very":[77],"limited":[78],"number":[79],"PTMs,":[81],"which":[82,121],"based":[84],"on":[85,172,250,267],"simple":[86],"pattern":[87],"matching":[88],"or":[89],"pre-defined":[90],"rules.":[91],"In":[92,232],"our":[93],"work,":[94],"order":[96],"help":[98],"curators":[102],"easily":[103],"find":[104,169],"retrieve":[106],"from":[109,131,139,174,225],"text,":[111],"we":[112],"have":[113],"developed":[114],"tool":[118,164],"called":[119],"MPTM,":[120],"extracts":[122],"organizes":[124],"valuable":[125],"knowledge":[126],"about":[127],"11":[128],"common":[129],"abstracts":[132],"PubMed":[134,175],"relations":[137],"extracted":[138,239],"dependency":[140],"parse":[141],"trees":[142],"heuristic":[145],"algorithm.":[146],"It":[147],"first":[150],"server":[152],"that":[153],"provides":[154],"service":[157],"hydroxylation,":[159],"myristoylation":[160],"GPI-anchor.":[162],"The":[163],"also":[166,212],"used":[167],"new":[170],"publications":[171],"uncovers":[177],"potential":[178],"large-scale":[182],"analysis.":[184],"MPTM":[185,245,252,254],"analyzes":[186],"sentences":[188],"identify":[190],"protein":[191,205],"names":[192],"including":[193],"substrates":[194],"protein-interacting":[196],"enzymes,":[197],"automatically":[199],"associates":[200],"with":[202,238],"UniProtKB":[204],"entry.":[206],"To":[207],"facilitate":[208],"further":[209],"investigation,":[210],"it":[211],"retrieves":[213],"PTM-related":[214],"information,":[215],"such":[216],"as":[217],"Gene":[220],"Ontology":[221],"terms":[222],"organisms":[224],"input":[227],"related":[230],"databases.":[231],"addition,":[233],"an":[234],"online":[235,258],"(MPTMDB)":[237],"local":[244],"Lite":[246],"package":[247],"provided":[249],"website.":[253],"freely":[256],"at":[259],"http://bioinformatics.ustc.edu.cn/mptm/":[260],"source":[263],"codes":[264],"hosted":[266],"GitHub:":[268],"https://github.com/USTC-HILAB/MPTM":[269],".":[270]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
