{"id":"https://openalex.org/W1997387866","doi":"https://doi.org/10.1145/2506583.2506619","title":"Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach","display_name":"Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W1997387866","doi":"https://doi.org/10.1145/2506583.2506619","mag":"1997387866"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506619","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5028161578","display_name":"Manabu Torii","orcid":"https://orcid.org/0000-0002-4825-0696"},"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":"Manabu Torii","raw_affiliation_strings":["Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#","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":["Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432286","display_name":"Qinghua Wang","orcid":"https://orcid.org/0000-0001-8494-8824"},"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":["Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"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":"Cathy H. Wu","raw_affiliation_strings":["Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","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 and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA#TAB#","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028161578"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":0.8773,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.72839123,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"3","issue":null,"first_page":"201","last_page":"210"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9819999933242798,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9639999866485596,"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/annotation","display_name":"Annotation","score":0.769397497177124},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7274323105812073},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.6511964797973633},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5813170075416565},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5585252046585083},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5008845329284668},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.44923219084739685},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4258458614349365},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.4212372303009033},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38524729013442993},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.34355077147483826},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32389217615127563},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30528414249420166},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19009804725646973},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11959618330001831},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11157289147377014},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08121240139007568}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.769397497177124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7274323105812073},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.6511964797973633},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5813170075416565},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5585252046585083},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5008845329284668},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.44923219084739685},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4258458614349365},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.4212372303009033},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38524729013442993},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.34355077147483826},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32389217615127563},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30528414249420166},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19009804725646973},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11959618330001831},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11157289147377014},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08121240139007568},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506619","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7099999785423279,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W303589260","https://openalex.org/W590716758","https://openalex.org/W1483118642","https://openalex.org/W1553529581","https://openalex.org/W1593657456","https://openalex.org/W1986579413","https://openalex.org/W1993755899","https://openalex.org/W2001829063","https://openalex.org/W2003619089","https://openalex.org/W2008085355","https://openalex.org/W2014849717","https://openalex.org/W2019779692","https://openalex.org/W2032566933","https://openalex.org/W2051689038","https://openalex.org/W2061231608","https://openalex.org/W2062163602","https://openalex.org/W2075322787","https://openalex.org/W2099369363","https://openalex.org/W2100644624","https://openalex.org/W2103931447","https://openalex.org/W2104965688","https://openalex.org/W2122496897","https://openalex.org/W2127603354","https://openalex.org/W2130930065","https://openalex.org/W2143892076","https://openalex.org/W2144133357","https://openalex.org/W2144181601","https://openalex.org/W2145383760","https://openalex.org/W2152183901","https://openalex.org/W2152398020","https://openalex.org/W2152869996","https://openalex.org/W2157658519","https://openalex.org/W2158040974","https://openalex.org/W2162172965","https://openalex.org/W2166057395","https://openalex.org/W2236252949","https://openalex.org/W2408260152","https://openalex.org/W2442495973","https://openalex.org/W2914431807","https://openalex.org/W4233334497"],"related_works":["https://openalex.org/W3004288456","https://openalex.org/W4362496998","https://openalex.org/W2184397297","https://openalex.org/W3185751515","https://openalex.org/W1479703980","https://openalex.org/W2810079151","https://openalex.org/W2749535755","https://openalex.org/W1663435917","https://openalex.org/W1496929818","https://openalex.org/W2094989391"],"abstract_inverted_index":{"Literature-based":[0],"annotation":[1],"of":[2,8,18,26,69,144,163],"protein":[3,54,201],"phosphorylation":[4,13,27,55,149,202],"is":[5,14,218],"the":[6,61,67,132,180,195],"focus":[7],"many":[9],"biological":[10],"databases,":[11],"as":[12],"a":[15,46,76,155],"global":[16],"regulator":[17],"cellular":[19],"activity.":[20],"To":[21,84],"speed":[22],"up":[23],"manual":[24],"curation":[25],"information,":[28,203],"text":[29],"mining":[30,194],"technology":[31],"has":[32,100],"been":[33,102,191],"utilized.":[34],"In":[35],"this":[36,86],"paper,":[37],"we":[38,88],"report":[39],"our":[40],"ongoing":[41],"effort":[42,78],"to":[43,52,104,110,113,179],"enhance":[44],"RLIMS-P,":[45,66],"rule-based":[47],"information":[48,56],"extraction":[49,138],"(IE)":[50],"system":[51,80,176],"identify":[53],"in":[57,75,131,193],"scientific":[58],"literature.":[59],"Despite":[60],"high":[62],"accuracy":[63],"attained":[64],"by":[65],"use":[68],"elaborated":[70],"patterns":[71],"and":[72,82,91,108,141,146,151,165,169,171,187],"rules":[73],"resulted":[74],"substantial":[77],"for":[79,117,148,167,173,211],"development":[81],"maintenance.":[83],"mitigate":[85],"challenge,":[87],"redesigned":[89],"RLIMS-P":[90,124,198,215],"integrated":[92],"new":[93,206],"natural":[94],"language":[95],"processing":[96],"(NLP)":[97],"techniques.":[98],"It":[99],"also":[101],"adapted":[103],"mine":[105],"full-text":[106,156,196],"articles":[107],"generalized":[109],"be":[111,209],"able":[112],"exploit":[114],"common":[115],"features":[116],"different":[118],"post-translational":[119],"modifications":[120],"(PTMs).":[121],"The":[122,175],"updated":[123],"(version":[125],"2.0)":[126],"was":[127,177],"evaluated":[128],"on":[129,200],"abstracts":[130],"publicly":[133],"available":[134,219],"BioNLP":[135],"GENIA":[136],"event":[137],"(GE)":[139],"corpus,":[140],"achieved":[142,161],"F-scores":[143,162],"0.92":[145,166],"0.96":[147],"substrate":[150,168],"site,":[152,170],"respectively.":[153],"On":[154],"corpus":[157],"developed":[158],"in-house,":[159],"it":[160],"0.91":[164],"0.88":[172],"kinase.":[174],"applied":[178],"PubMed":[181],"Central":[182],"(PMC)":[183],"Open":[184],"Access":[185],"Subset,":[186],"promising":[188],"results":[189],"have":[190],"obtained":[192],"articles.":[197],"focuses":[199],"but":[204],"its":[205],"design":[207],"would":[208],"generalizable":[210],"other":[212],"PTM":[213],"types.":[214],"version":[216],"2.0":[217],"at:":[220],"http://proteininformationresource.org/rlimsp/.":[221]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}