{"id":"https://openalex.org/W3048161085","doi":"https://doi.org/10.1093/database/baaa056","title":"FLUTE: Fast and reliable knowledge retrieval from biomedical literature","display_name":"FLUTE: Fast and reliable knowledge retrieval from biomedical literature","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3048161085","doi":"https://doi.org/10.1093/database/baaa056","mag":"3048161085","pmid":"https://pubmed.ncbi.nlm.nih.gov/32761077"},"language":"en","primary_location":{"id":"doi:10.1093/database/baaa056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa056","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa056/33571972/baaa056.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","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/database/article-pdf/doi/10.1093/database/baaa056/33571972/baaa056.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085646049","display_name":"Emilee Holtzapple","orcid":"https://orcid.org/0000-0003-3907-1597"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emilee Holtzapple","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061349447","display_name":"Cheryl A. Telmer","orcid":"https://orcid.org/0000-0002-7649-3134"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheryl A Telmer","raw_affiliation_strings":["Molecular Biosensor and Imagining Center, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biosensor and Imagining Center, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017141796","display_name":"Nata\u0161a Mi\u0161kov-\u017divanov","orcid":"https://orcid.org/0000-0003-1110-3403"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Natasa Miskov-Zivanov","raw_affiliation_strings":["Department of Bioengineering, University of Pittsburgh, 300 Technology Dr, Pittsburgh 15213, USA","Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA","Department of Electrical and Computer Engineering, University of Pittsburgh, 3700 O\u2019Hara St, Pittsburgh, Pennsylvania 15261, USA","Department of Electrical and Computer Engineering, University of Pittsburgh, 3700 O'Hara St, Pittsburgh, Pennsylvania 15261, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Pittsburgh, 300 Technology Dr, Pittsburgh 15213, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, Pennsylvania 15213, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Pittsburgh, 3700 O\u2019Hara St, Pittsburgh, Pennsylvania 15261, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Pittsburgh, 3700 O'Hara St, Pittsburgh, Pennsylvania 15261, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5017141796"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.254,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.79151568,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2020","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9970999956130981,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9965999722480774,"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/computer-science","display_name":"Computer science","score":0.8358392715454102},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.666126549243927},{"id":"https://openalex.org/keywords/flute","display_name":"Flute","score":0.6388171911239624},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5920381546020508},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4769110679626465},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4131016135215759},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40699318051338196},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3941463232040405},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.11126992106437683},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.09395846724510193}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8358392715454102},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.666126549243927},{"id":"https://openalex.org/C4060165","wikidata":"https://www.wikidata.org/wiki/Q11405","display_name":"Flute","level":2,"score":0.6388171911239624},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5920381546020508},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4769110679626465},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4131016135215759},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40699318051338196},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3941463232040405},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.11126992106437683},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.09395846724510193},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","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":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baaa056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa056","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa056/33571972/baaa056.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:32761077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32761077","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7408180","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7408180","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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baaa056","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa056","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa056/33571972/baaa056.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.9100000262260437,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G1906022076","display_name":null,"funder_award_id":"W911NF-17-1-0135","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3048161085.pdf","grobid_xml":"https://content.openalex.org/works/W3048161085.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1597108195","https://openalex.org/W1604098861","https://openalex.org/W1606860353","https://openalex.org/W1871096589","https://openalex.org/W1893336375","https://openalex.org/W1978370150","https://openalex.org/W1989277387","https://openalex.org/W1997956758","https://openalex.org/W2031966872","https://openalex.org/W2043274355","https://openalex.org/W2096173332","https://openalex.org/W2103017472","https://openalex.org/W2103320915","https://openalex.org/W2116423958","https://openalex.org/W2123500593","https://openalex.org/W2125129191","https://openalex.org/W2140601463","https://openalex.org/W2147714160","https://openalex.org/W2154139219","https://openalex.org/W2177317049","https://openalex.org/W2224056471","https://openalex.org/W2251392452","https://openalex.org/W2251677685","https://openalex.org/W2537623931","https://openalex.org/W2581118114","https://openalex.org/W2604808360","https://openalex.org/W2626218535","https://openalex.org/W2626882937","https://openalex.org/W2737480027","https://openalex.org/W2789084399","https://openalex.org/W2790532175","https://openalex.org/W2885911173","https://openalex.org/W2898746416","https://openalex.org/W2917858269","https://openalex.org/W2950595506","https://openalex.org/W2952755768","https://openalex.org/W4210702584","https://openalex.org/W4233698560","https://openalex.org/W4253381305","https://openalex.org/W4287868167","https://openalex.org/W4293374413","https://openalex.org/W6685545510","https://openalex.org/W6773631693"],"related_works":["https://openalex.org/W409076290","https://openalex.org/W2332573710","https://openalex.org/W4295242234","https://openalex.org/W2362989621","https://openalex.org/W435349687","https://openalex.org/W2408862895","https://openalex.org/W274676238","https://openalex.org/W2359595350","https://openalex.org/W653986334","https://openalex.org/W2389148684"],"abstract_inverted_index":{"State-of-the-art":[0],"machine":[1,110],"reading":[2],"methods":[3,39],"extract,":[4],"in":[5,83,103,120],"hours,":[6],"hundreds":[7],"of":[8,10,18,31,34,126],"thousands":[9],"events":[11],"from":[12,72],"the":[13,19,84,101,104,114],"biomedical":[14],"literature.":[15],"However,":[16],"many":[17],"extracted":[20,69,107],"biomolecular":[21,105],"interactions":[22,65,85,106],"are":[23,40],"incorrect":[24],"or":[25],"not":[26],"relevant":[27],"for":[28,52,80,87],"computational":[29],"modeling":[30],"a":[32,118],"system":[33],"interest.":[35],"Therefore,":[36],"rapid,":[37],"automated":[38],"required":[41],"to":[42,63],"filter":[43,64],"and":[44,47,77,89,112],"select":[45],"accurate":[46,90],"useful":[48],"information.":[49],"The":[50],"FiLter":[51],"Understanding":[53],"True":[54],"Events":[55],"(FLUTE)":[56],"tool":[57],"uses":[58],"public":[59],"protein":[60],"interaction":[61,121],"databases":[62,73],"that":[66],"have":[67],"been":[68],"by":[70,108,123],"machines":[71],"such":[74],"as":[75],"PubMed":[76],"score":[78],"them":[79],"accuracy.":[81],"Confidence":[82],"allows":[86],"rapid":[88],"model":[91],"assembly.":[92],"As":[93],"our":[94],"results":[95],"show,":[96],"FLUTE":[97],"can":[98],"reliably":[99],"determine":[100],"confidence":[102],"fast":[109],"readers":[111],"at":[113],"same":[115],"time":[116],"provide":[117],"speedup":[119],"filtering":[122],"three":[124],"orders":[125],"magnitude.":[127],"Database":[128],"URL:":[129],"https://bitbucket.org/biodesignlab/flute.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
