{"id":"https://openalex.org/W2120564292","doi":"https://doi.org/10.1186/2041-1480-6-1","title":"Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles","display_name":"Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2120564292","doi":"https://doi.org/10.1186/2041-1480-6-1","mag":"2120564292","pmid":"https://pubmed.ncbi.nlm.nih.gov/25789152"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-6-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-6-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-6-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-6-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069397549","display_name":"\u015eenay Kafkas","orcid":"https://orcid.org/0000-0001-7509-5786"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"\u015eenay Kafkas","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","institution_ids":[]},{"raw_affiliation_string":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016481961","display_name":"Jee-Hyub Kim","orcid":"https://orcid.org/0000-0002-0359-2887"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jee-Hyub Kim","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","institution_ids":[]},{"raw_affiliation_string":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055642256","display_name":"Xingjun Pi","orcid":"https://orcid.org/0000-0003-3137-3363"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Xingjun Pi","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","institution_ids":[]},{"raw_affiliation_string":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055576279","display_name":"Johanna McEntyre","orcid":"https://orcid.org/0000-0002-1611-6935"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Johanna R McEntyre","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK","institution_ids":[]},{"raw_affiliation_string":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5069397549"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":3.3128,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.92761837,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8046000003814697,"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":0.8046000003814697,"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/T11937","display_name":"Research Data Management Practices","score":0.060499999672174454,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T13607","display_name":"Academic Publishing and Open Access","score":0.03590000048279762,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.74583500623703},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.7300392389297485},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.7084249258041382},{"id":"https://openalex.org/keywords/citation","display_name":"Citation","score":0.6133618354797363},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5439801216125488},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5369002819061279},{"id":"https://openalex.org/keywords/accession-number","display_name":"Accession number (library science)","score":0.48581552505493164},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.44412657618522644},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3307762145996094},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.31039708852767944},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19717636704444885},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.09116929769515991}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.74583500623703},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.7300392389297485},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7084249258041382},{"id":"https://openalex.org/C2778805511","wikidata":"https://www.wikidata.org/wiki/Q1713","display_name":"Citation","level":2,"score":0.6133618354797363},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5439801216125488},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5369002819061279},{"id":"https://openalex.org/C15190224","wikidata":"https://www.wikidata.org/wiki/Q1417099","display_name":"Accession number (library science)","level":4,"score":0.48581552505493164},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.44412657618522644},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3307762145996094},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.31039708852767944},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19717636704444885},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.09116929769515991},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/2041-1480-6-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-6-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-6-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:25789152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25789152","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 biomedical semantics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4363206","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4363206","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-6-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-6-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-6-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120564292.pdf","grobid_xml":"https://content.openalex.org/works/W2120564292.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2045657963","https://openalex.org/W2053901275","https://openalex.org/W2057240659","https://openalex.org/W2097052916","https://openalex.org/W2111303602","https://openalex.org/W2128863362","https://openalex.org/W2142741334"],"related_works":["https://openalex.org/W1489267134","https://openalex.org/W2107691364","https://openalex.org/W1412967071","https://openalex.org/W2404565489","https://openalex.org/W2915827701","https://openalex.org/W4306399392","https://openalex.org/W2141132558","https://openalex.org/W2005601993","https://openalex.org/W2156467546","https://openalex.org/W2120564292"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1],"this":[2,212],"study,":[3],"we":[4,76],"present":[5],"an":[6],"analysis":[7],"of":[8,30,51,70,91,102,107,112,120,138,189,203],"data":[9,21,43,81,154,166,205],"citation":[10,119],"practices":[11],"in":[12,25,115,143,175,179,183,206,208],"full":[13,187],"text":[14],"research":[15,192],"articles":[16,31,108,172],"and":[17,66,94,178,216],"their":[18],"corresponding":[19],"supplementary":[20,42,153,165],"files,":[22],"made":[23],"available":[24],"the":[26,55,79,89,92,100,136,146,152,190,197,201],"Open":[27],"Access":[28],"set":[29],"from":[32,124,151,158],"Europe":[33],"PubMed":[34],"Central.":[35],"Our":[36,161],"aim":[37],"is":[38,133],"to":[39,64,185,199,210],"investigate":[40],"whether":[41],"files":[44,82],"should":[45,167],"be":[46,168],"considered":[47,169],"as":[48,128,141],"a":[49,68,103],"source":[50],"information":[52,180,213],"for":[53],"integrating":[54],"literature":[56],"with":[57,173],"biomolecular":[58],"databases.":[59],"RESULTS:":[60],"Using":[61],"text-mining":[62],"methods":[63],"identify":[65],"extract":[67],"variety":[69],"core":[71],"biological":[72],"database":[73,86,147],"accession":[74,113,148],"numbers,":[75],"found":[77],"that":[78,95,164],"supplemental":[80,204],"contain":[83],"many":[84],"more":[85,214],"citations":[87,97],"than":[88],"body":[90],"article,":[93],"those":[96],"often":[98],"take":[99],"form":[101],"relatively":[104],"small":[105],"number":[106],"citing":[109],"large":[110],"collections":[111],"numbers":[114,149],"text-based":[116],"files.":[117],"Moreover,":[118],"value-added":[121],"databases":[122,126],"derived":[123],"submission":[125],"(such":[127],"Pfam,":[129],"UniProt":[130],"or":[131],"Ensembl)":[132],"common,":[134],"demonstrating":[135],"reuse":[137],"these":[139],"resources":[140],"datasets":[142],"themselves.":[144],"All":[145],"extracted":[150],"are":[155],"publicly":[156],"accessible":[157],"http://dx.doi.org/10.5281/zenodo.11771.":[159],"CONCLUSIONS:":[160],"study":[162],"suggests":[163],"when":[170],"linking":[171],"data,":[174],"curation":[176],"pipelines,":[177],"retrieval":[181],"tasks":[182],"order":[184,209],"make":[186,211],"use":[188],"entire":[191],"article.":[193],"These":[194],"observations":[195],"highlight":[196],"need":[198],"improve":[200],"management":[202],"general,":[207],"discoverable":[215],"useful.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
