{"id":"https://openalex.org/W2057240659","doi":"https://doi.org/10.1093/nar/gkn317","title":"BioLit: integrating biological literature with databases","display_name":"BioLit: integrating biological literature with databases","publication_year":2008,"publication_date":"2008-05-19","ids":{"openalex":"https://openalex.org/W2057240659","doi":"https://doi.org/10.1093/nar/gkn317","mag":"2057240659","pmid":"https://pubmed.ncbi.nlm.nih.gov/18515836"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn317","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W385/7629842/gkn317.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W385/7629842/gkn317.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074966371","display_name":"J. Lynn Fink","orcid":"https://orcid.org/0000-0003-2912-6048"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. L. Fink","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA"],"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045021735","display_name":"Sergii Kushch","orcid":"https://orcid.org/0000-0002-5908-7169"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Kushch","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA"],"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036395860","display_name":"Paul Williams","orcid":"https://orcid.org/0000-0001-6259-0390"},"institutions":[{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. R. Williams","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA"],"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. E. Bourne","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA"],"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074966371"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I6750721"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.6278,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.89822788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"Web Server","first_page":"W385","last_page":"W389"},"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":0.9926000237464905,"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":0.9868999719619751,"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/metadata","display_name":"Metadata","score":0.8262869119644165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.677950382232666},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.6661748886108398},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6128929257392883},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5392907857894897},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5310837626457214},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.5071642398834229},{"id":"https://openalex.org/keywords/database-catalog","display_name":"Database catalog","score":0.48771747946739197},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.47197848558425903},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.4647049009799957},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.45319023728370667},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.44612306356430054},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1694578230381012},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14778313040733337}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8262869119644165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.677950382232666},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6661748886108398},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6128929257392883},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5392907857894897},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5310837626457214},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.5071642398834229},{"id":"https://openalex.org/C65610166","wikidata":"https://www.wikidata.org/wiki/Q5227399","display_name":"Database catalog","level":4,"score":0.48771747946739197},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.47197848558425903},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.4647049009799957},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.45319023728370667},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.44612306356430054},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1694578230381012},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14778313040733337},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"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":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkn317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn317","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W385/7629842/gkn317.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18515836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18515836","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:200781","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2447735","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447735","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn317","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W385/7629842/gkn317.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.5,"id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G69765774","display_name":"BioLit: Open Source Tools for Integrating Biological Literature and Databases","funder_award_id":"0544575","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2057240659.pdf","grobid_xml":"https://content.openalex.org/works/W2057240659.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1618455174","https://openalex.org/W2013607137","https://openalex.org/W2053673723","https://openalex.org/W2055436717","https://openalex.org/W2074872734","https://openalex.org/W2079509905","https://openalex.org/W2079691202","https://openalex.org/W2089604928","https://openalex.org/W2096432317","https://openalex.org/W2096525273","https://openalex.org/W2103017472","https://openalex.org/W2103477204","https://openalex.org/W2113142309","https://openalex.org/W2122174694","https://openalex.org/W2126276057","https://openalex.org/W2132784310","https://openalex.org/W2166744107","https://openalex.org/W2168866167","https://openalex.org/W2230062173","https://openalex.org/W4239678514"],"related_works":["https://openalex.org/W2374379029","https://openalex.org/W2394393789","https://openalex.org/W2253738291","https://openalex.org/W2325085362","https://openalex.org/W1503116306","https://openalex.org/W1504835998","https://openalex.org/W2391915033","https://openalex.org/W2354596657","https://openalex.org/W2388609536","https://openalex.org/W2360250168"],"abstract_inverted_index":{"BioLit":[0,47,141,174,179],"is":[1,180],"a":[2,60,91,102,114,123],"web":[3],"server":[4],"which":[5,18],"provides":[6,66],"metadata":[7,32,50],"describing":[8],"the":[9,22,41,45,52,70,77,88,134,146,155,159,168,173],"semantic":[10],"content":[11],"of":[12,44,54,105,122,126,133,148,158,167,176],"all":[13],"open":[14],"access,":[15],"peer-reviewed":[16],"articles":[17],"describe":[19],"research":[20],"from":[21],"major":[23],"life":[24,149],"sciences":[25],"literature":[26],"archive,":[27],"PubMed":[28],"Central.":[29],"Specifically,":[30],"these":[31,49],"include":[33],"database":[34,117,175],"identifiers":[35],"and":[36,58,172],"ontology":[37],"terms":[38],"found":[39],"within":[40],"full":[42],"text":[43],"article.":[46],"delivers":[48],"in":[51,95,151],"form":[53],"XML-based":[55],"article":[56,63,177],"files":[57,171],"as":[59],"custom":[61],"web-based":[62,160],"viewer":[64],"that":[65,145],"context-specific":[67],"functionality":[68],"to":[69,75,93,101],"metadata.":[71],"This":[72],"resource":[73],"aims":[74],"integrate":[76],"traditional":[78],"scientific":[79],"publication":[80],"directly":[81],"into":[82],"existing":[83],"biological":[84,116],"databases,":[85],"thus":[86],"obviating":[87],"need":[89],"for":[90,98,107],"user":[92],"search":[94],"multiple":[96],"locations":[97],"information":[99],"relating":[100],"specific":[103],"item":[104],"interest,":[106],"example":[108,121],"published":[109],"experimental":[110],"results":[111],"associated":[112],"with":[113,140],"particular":[115],"entry.":[118],"As":[119],"an":[120,131],"possible":[124],"use":[125,166],"BioLit,":[127],"we":[128],"also":[129],"present":[130],"instance":[132],"Protein":[135],"Data":[136],"Bank":[137],"fully":[138],"integrated":[139],"data.":[142,178],"We":[143],"expect":[144],"community":[147],"scientists":[150],"general":[152],"will":[153,164],"be":[154],"primary":[156],"end-users":[157],"viewer,":[161],"while":[162],"biocurators":[163],"make":[165],"metadata-containing":[169],"XML":[170],"available":[181],"at":[182],"http://biolit.ucsd.edu.":[183]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"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":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
