{"id":"https://openalex.org/W4395467502","doi":"https://doi.org/10.1093/bioinformatics/btae275","title":"BTR: a bioinformatics tool recommendation system","display_name":"BTR: a bioinformatics tool recommendation system","publication_year":2024,"publication_date":"2024-04-24","ids":{"openalex":"https://openalex.org/W4395467502","doi":"https://doi.org/10.1093/bioinformatics/btae275","pmid":"https://pubmed.ncbi.nlm.nih.gov/38662583"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae275","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae275","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae275/57334065/btae275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae275/57334065/btae275.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083340498","display_name":"Ryan Green","orcid":null},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Green","raw_affiliation_strings":["Department of Computer Science, University of Cincinnati , Cincinnati 45219, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cincinnati , Cincinnati 45219, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049950700","display_name":"Xufeng Qu","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xufeng Qu","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond 23284, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond 23284, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102842945","display_name":"Jinze Liu","orcid":"https://orcid.org/0000-0003-0555-9412"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinze Liu","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond 23284, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond 23284, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072070511","display_name":"Tingting Yu","orcid":"https://orcid.org/0000-0002-9461-4251"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tingting Yu","raw_affiliation_strings":["School of Computing, University of Connecticut , Storrs 06269, United States","Department of Computer Science and Engineering, University of Connecticut, Storrs, 06269, USA"],"raw_orcid":"https://orcid.org/0000-0002-9461-4251","affiliations":[{"raw_affiliation_string":"School of Computing, University of Connecticut , Storrs 06269, United States","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5072070511","https://openalex.org/A5102842945"],"corresponding_institution_ids":["https://openalex.org/I140172145","https://openalex.org/I184840846"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6662,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.88911671,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"40","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6413999795913696,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6413999795913696,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.08889999985694885,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.07339999824762344,"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":0.6873076558113098},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4103752374649048},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3931583762168884},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37902167439460754},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3322160542011261},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22227796912193298},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16564464569091797}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6873076558113098},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4103752374649048},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3931583762168884},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37902167439460754},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3322160542011261},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22227796912193298},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16564464569091797}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae275","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae275","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae275/57334065/btae275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38662583","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38662583","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:pubmedcentral.nih.gov:11091741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11091741","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11091741/pdf/btae275.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae275","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae275","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae275/57334065/btae275.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4382038412","display_name":"CAREER: Testing Evolving Complex Software Systems","funder_award_id":"2152340","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"},{"id":"https://openalex.org/F4320310017","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97"},{"id":"https://openalex.org/F4320310256","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4395467502.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1527772862","https://openalex.org/W2097154153","https://openalex.org/W2102619694","https://openalex.org/W2109419450","https://openalex.org/W2116341502","https://openalex.org/W2141541659","https://openalex.org/W2145374174","https://openalex.org/W2155574916","https://openalex.org/W2296335794","https://openalex.org/W2605897695","https://openalex.org/W2618530766","https://openalex.org/W2747329762","https://openalex.org/W2899457523","https://openalex.org/W2917207851","https://openalex.org/W3036158206","https://openalex.org/W3046375318","https://openalex.org/W3101707147","https://openalex.org/W3118447688","https://openalex.org/W3122109253","https://openalex.org/W3160531185","https://openalex.org/W3194856818","https://openalex.org/W3200776886","https://openalex.org/W4210644165","https://openalex.org/W4226051960","https://openalex.org/W4360591931","https://openalex.org/W4385741486","https://openalex.org/W6631439307","https://openalex.org/W6697144307","https://openalex.org/W6783827371"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,139],"rapid":[2],"expansion":[3],"of":[4,12,55],"Bioinformatics":[5,36,68],"research":[6],"has":[7],"led":[8],"to":[9,52,78,101,131],"a":[10,24,73,83,99],"proliferation":[11],"computational":[13],"tools":[14,57,81],"for":[15,82],"scientific":[16,133],"analysis":[17],"pipelines.":[18],"However,":[19],"constructing":[20],"these":[21],"pipelines":[22],"is":[23,143],"demanding":[25],"task,":[26],"requiring":[27],"extensive":[28],"domain":[29],"knowledge":[30],"and":[31,42],"careful":[32],"consideration.":[33],"As":[34],"the":[35,53,67,96,122],"landscape":[37],"evolves,":[38],"researchers,":[39],"both":[40],"novice":[41],"expert,":[43],"may":[44],"feel":[45],"overwhelmed":[46],"in":[47,90],"unfamiliar":[48],"fields,":[49],"potentially":[50],"leading":[51],"selection":[54],"unsuitable":[56],"during":[58],"workflow":[59,97,134],"development.":[60],"RESULTS:":[61],"In":[62],"this":[63],"article,":[64],"we":[65],"introduce":[66],"Tool":[69],"Recommendation":[70],"system":[71],"(BTR),":[72],"deep":[74],"learning":[75],"model":[76],"designed":[77],"recommend":[79],"suitable":[80],"given":[84],"workflow-in-progress.":[85],"BTR":[86,120],"leverages":[87],"recent":[88],"advances":[89],"graph":[91,100],"neural":[92],"network":[93],"technology,":[94],"representing":[95],"as":[98],"capture":[102],"essential":[103],"context.":[104],"Natural":[105],"language":[106],"processing":[107],"techniques":[108],"enhance":[109],"tool":[110,115,125],"recommendations":[111],"by":[112],"analyzing":[113],"associated":[114],"descriptions.":[116],"Experiments":[117],"demonstrate":[118],"that":[119],"outperforms":[121],"existing":[123],"Galaxy":[124],"recommendation":[126],"system,":[127],"showcasing":[128],"its":[129],"potential":[130],"streamline":[132],"construction.":[135],"AVAILABILITY":[136],"AND":[137],"IMPLEMENTATION:":[138],"Python":[140],"source":[141],"code":[142],"available":[144],"at":[145],"https://github.com/ryangreenj/bioinformatics_tool_recommendation.":[146]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}