{"id":"https://openalex.org/W2166057395","doi":"https://doi.org/10.1093/bioinformatics/bti390","title":"Literature mining and database annotation of protein phosphorylation using a rule-based system","display_name":"Literature mining and database annotation of protein phosphorylation using a rule-based system","publication_year":2005,"publication_date":"2005-04-06","ids":{"openalex":"https://openalex.org/W2166057395","doi":"https://doi.org/10.1093/bioinformatics/bti390","mag":"2166057395","pmid":"https://pubmed.ncbi.nlm.nih.gov/15814565"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti390","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2759/48971277/bioinformatics_21_11_2759.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2759/48971277/bioinformatics_21_11_2759.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000004912","display_name":"Zhengyong Hu","orcid":null},"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":true,"raw_author_name":"Z. Z. Hu","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA. zh9@georgetown.edu"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA. zh9@georgetown.edu","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051261629","display_name":"Meenakshi Narayanaswamy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Narayanaswamy","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111754779","display_name":"K. E. Ravikumar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. E. Ravikumar","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027009667","display_name":"K. Vijay\u2010Shanker","orcid":"https://orcid.org/0000-0003-0958-3073"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Vijay-Shanker","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. H. Wu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000004912"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"],"apc_list":null,"apc_paid":null,"fwci":3.7973,"has_fulltext":false,"cited_by_count":123,"citation_normalized_percentile":{"value":0.93991597,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"11","first_page":"2759","last_page":"2765"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.987500011920929,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9761999845504761,"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":0.6962976455688477},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6841399669647217},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5227387547492981},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.5189237594604492},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.5052900910377502},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4837084412574768},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.4813157320022583},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4609426259994507},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4369159936904907},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34289315342903137},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2499476969242096},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13249734044075012},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13137269020080566},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09512332081794739},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.062467366456985474}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6962976455688477},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6841399669647217},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5227387547492981},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.5189237594604492},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.5052900910377502},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4837084412574768},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.4813157320022583},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4609426259994507},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4369159936904907},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34289315342903137},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2499476969242096},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13249734044075012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13137269020080566},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09512332081794739},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.062467366456985474}],"mesh":[{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","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":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016239","descriptor_name":"MEDLINE","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti390","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2759/48971277/bioinformatics_21_11_2759.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15814565","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15814565","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.92.5252","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.92.5252","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://pir.georgetown.edu/pirwww/about/doc/RLIMS-P.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti390","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2759/48971277/bioinformatics_21_11_2759.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.4399999976158142}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166057395.pdf","grobid_xml":"https://content.openalex.org/works/W2166057395.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W27076413","https://openalex.org/W1505057322","https://openalex.org/W1667964228","https://openalex.org/W1790194223","https://openalex.org/W1981933378","https://openalex.org/W1983453172","https://openalex.org/W1987146951","https://openalex.org/W1999117234","https://openalex.org/W2004620268","https://openalex.org/W2008085355","https://openalex.org/W2020459598","https://openalex.org/W2023736097","https://openalex.org/W2093618552","https://openalex.org/W2114277790","https://openalex.org/W2117400858","https://openalex.org/W2130260860","https://openalex.org/W2131924932","https://openalex.org/W2133431243","https://openalex.org/W2139259976","https://openalex.org/W2141172196","https://openalex.org/W2152183901","https://openalex.org/W2152698860","https://openalex.org/W2154139219","https://openalex.org/W2158505321","https://openalex.org/W2166884712"],"related_works":["https://openalex.org/W2169425537","https://openalex.org/W4312158493","https://openalex.org/W2033835987","https://openalex.org/W4248750016","https://openalex.org/W4205092877","https://openalex.org/W1824784554","https://openalex.org/W2086443788","https://openalex.org/W3141940143","https://openalex.org/W1561860948","https://openalex.org/W1979295894"],"abstract_inverted_index":{"A":[0],"rule-based":[1],"system,":[2],"RLIMS-P":[3,48,85],"(Rule-based":[4],"LIterature":[5],"Mining":[6],"System":[7],"for":[8,34,58,66,76,82],"Protein":[9],"Phosphorylation),":[10],"was":[11,28],"used":[12,29],"to":[13,30],"extract":[14],"protein":[15,93],"phosphorylation":[16,36,40],"information":[17,83],"from":[18,46],"MEDLINE":[19],"abstracts.":[20,47],"An":[21],"annotation-tagged":[22],"literature":[23,87],"corpus":[24],"developed":[25],"at":[26],"PIR":[27],"evaluate":[31],"the":[32,73],"system":[33],"finding":[35],"papers":[37],"and":[38,44,52,56,61,64,70,79,89],"extracting":[39],"objects":[41],"(kinases,":[42],"substrates":[43,69],"sites)":[45],"achieved":[49],"a":[50],"precision":[51,81],"recall":[53,75],"of":[54,62,68,92],"91.4":[55],"96.4%":[57],"paper":[59,77],"retrieval,":[60],"97.9":[63],"88.0%":[65],"extraction":[67],"sites.":[71],"Coupling":[72],"high":[74,80],"retrieval":[78],"extraction,":[84],"facilitates":[86],"mining":[88],"database":[90],"annotation":[91],"phosphorylation.":[94]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":28},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":9}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}