{"id":"https://openalex.org/W2104965688","doi":"https://doi.org/10.1093/bioinformatics/bti1011","title":"Beyond the clause: extraction of phosphorylation information from medline abstracts","display_name":"Beyond the clause: extraction of phosphorylation information from medline abstracts","publication_year":2005,"publication_date":"2005-06-01","ids":{"openalex":"https://openalex.org/W2104965688","doi":"https://doi.org/10.1093/bioinformatics/bti1011","mag":"2104965688"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti1011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1011","pdf_url":null,"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"],"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/A5051261629","display_name":"Meenakshi Narayanaswamy","orcid":null},"institutions":[{"id":"https://openalex.org/I33585257","display_name":"Anna University, Chennai","ror":"https://ror.org/01qhf1r47","country_code":"IN","type":"education","lineage":["https://openalex.org/I33585257"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"M. Narayanaswamy","raw_affiliation_strings":["AU\u2010KBC Research Centre Anna University Chennai India"],"affiliations":[{"raw_affiliation_string":"AU\u2010KBC Research Centre Anna University Chennai India","institution_ids":["https://openalex.org/I33585257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111754779","display_name":"K. E. Ravikumar","orcid":null},"institutions":[{"id":"https://openalex.org/I33585257","display_name":"Anna University, Chennai","ror":"https://ror.org/01qhf1r47","country_code":"IN","type":"education","lineage":["https://openalex.org/I33585257"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"K. E. Ravikumar","raw_affiliation_strings":["AU\u2010KBC Research Centre Anna University Chennai India"],"affiliations":[{"raw_affiliation_string":"AU\u2010KBC Research Centre Anna University Chennai India","institution_ids":["https://openalex.org/I33585257"]}]},{"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, University of Delaware , Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051261629"],"corresponding_institution_ids":["https://openalex.org/I33585257"],"apc_list":null,"apc_paid":null,"fwci":1.4768,"has_fulltext":false,"cited_by_count":69,"citation_normalized_percentile":{"value":0.80743815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"Suppl 1","first_page":"i319","last_page":"i327"},"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9952999949455261,"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/T10028","display_name":"Topic Modeling","score":0.9941999912261963,"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/medline","display_name":"MEDLINE","score":0.6122410893440247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5930272936820984},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5055129528045654},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.411862850189209},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11759832501411438},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06200087070465088}],"concepts":[{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.6122410893440247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5930272936820984},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5055129528045654},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.411862850189209},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11759832501411438},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06200087070465088}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/bti1011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1011","pdf_url":null,"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"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320767","display_name":"University Grants Commission","ror":"https://ror.org/04p800546"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1790194223","https://openalex.org/W1980860611","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/W2093618552","https://openalex.org/W2104768328","https://openalex.org/W2114277790","https://openalex.org/W2115880858","https://openalex.org/W2117400858","https://openalex.org/W2151598682","https://openalex.org/W2154139219","https://openalex.org/W2158505321","https://openalex.org/W2166057395","https://openalex.org/W2166884712","https://openalex.org/W2314420468"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Motivation:":[0],"Phosphorylation":[1],"is":[2,31,38,84],"an":[3,87],"important":[4],"biochemical":[5],"reaction":[6],"that":[7,75],"plays":[8],"a":[9,70,82],"critical":[10],"role":[11],"in":[12,56,59,111,119],"signal":[13],"transduction":[14],"pathways":[15],"and":[16,44,48,64],"cell-cycle":[17],"processes.":[18],"A":[19],"text":[20],"mining":[21],"system":[22,68],"to":[23,46,98,108],"extract":[24],"the":[25,29,40,60,67,77,91,114],"phosphorylation":[26,54],"relation":[27],"from":[28,103],"literature":[30],"reported.":[32],"The":[33,62,94],"focus":[34],"of":[35,51,66,76,101],"this":[36],"paper":[37],"on":[39],"new":[41,95],"methods":[42,78,96],"developed":[43,97],"implemented":[45],"connect":[47],"merge":[49,99],"pieces":[50,100],"information":[52,102],"about":[53],"mentioned":[55],"different":[57,104],"sentences":[58,105],"text.":[61],"effectiveness":[63],"accuracy":[65],"as":[69,72,74],"whole":[71],"well":[73],"for":[79],"extraction":[80],"beyond":[81],"clause/sentence":[83],"evaluated":[85],"using":[86],"independently":[88],"annotated":[89],"dataset,":[90],"Phospho.ELM":[92],"database.":[93],"are":[106],"shown":[107],"be":[109],"effective":[110],"significantly":[112],"raising":[113],"recall":[115],"without":[116],"much":[117],"difference":[118],"precision.":[120],"Contact:vijay@cis.udel.edu":[121]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
