{"id":"https://openalex.org/W4296700195","doi":"https://doi.org/10.1093/bioinformatics/btac640","title":"BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals","display_name":"BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals","publication_year":2022,"publication_date":"2022-09-20","ids":{"openalex":"https://openalex.org/W4296700195","doi":"https://doi.org/10.1093/bioinformatics/btac640","pmid":"https://pubmed.ncbi.nlm.nih.gov/36130260"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5137/47153767/btac640.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5137/47153767/btac640.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101640724","display_name":"Dandan Sun","orcid":"https://orcid.org/0000-0003-4703-821X"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dandan Sun","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China"],"raw_orcid":"https://orcid.org/0000-0003-4703-821X","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073275197","display_name":"Shaozhen Ding","orcid":"https://orcid.org/0000-0002-5581-8403"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shaozhen Ding","raw_affiliation_strings":["Wuhan LifeSynther Science and Technology Co. Limited , Wuhan 430000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wuhan LifeSynther Science and Technology Co. Limited , Wuhan 430000, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071379782","display_name":"Pengli Cai","orcid":"https://orcid.org/0000-0002-7910-6558"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengli Cai","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101469520","display_name":"Dachuan Zhang","orcid":"https://orcid.org/0000-0003-2467-6286"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Dachuan Zhang","raw_affiliation_strings":["Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich , 8093 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2467-6286","affiliations":[{"raw_affiliation_string":"Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich , 8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003999551","display_name":"Mengying Han","orcid":"https://orcid.org/0000-0002-5473-3432"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengying Han","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China"],"raw_orcid":"https://orcid.org/0000-0002-5473-3432","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101770220","display_name":"Qian\u2010Nan Hu","orcid":"https://orcid.org/0000-0001-5213-472X"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qian-Nan Hu","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101770220"],"corresponding_institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0866,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43293834,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"38","issue":"22","first_page":"5137","last_page":"5138"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.7480000257492065,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.7480000257492065,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.0471000000834465,"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/T13180","display_name":"Chemistry and Chemical Engineering","score":0.031700000166893005,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/production","display_name":"Production (economics)","score":0.6763328909873962},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5457004308700562},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.5222721695899963},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.5098618268966675},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.44310617446899414},{"id":"https://openalex.org/keywords/commodity-chemicals","display_name":"Commodity chemicals","score":0.4422365725040436},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35901689529418945},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32210689783096313},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24126550555229187},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11801838874816895},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11369043588638306}],"concepts":[{"id":"https://openalex.org/C2778348673","wikidata":"https://www.wikidata.org/wiki/Q739302","display_name":"Production (economics)","level":2,"score":0.6763328909873962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5457004308700562},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.5222721695899963},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.5098618268966675},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.44310617446899414},{"id":"https://openalex.org/C179720865","wikidata":"https://www.wikidata.org/wiki/Q1550480","display_name":"Commodity chemicals","level":3,"score":0.4422365725040436},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35901689529418945},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32210689783096313},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24126550555229187},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11801838874816895},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11369043588638306},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.0},{"id":"https://openalex.org/C139719470","wikidata":"https://www.wikidata.org/wiki/Q39680","display_name":"Macroeconomics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5137/47153767/btac640.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36130260","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36130260","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5137/47153767/btac640.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1434053985","display_name":null,"funder_award_id":"2019YFA0904300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G1846444229","display_name":null,"funder_award_id":"2020YFA0908300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4528197620","display_name":null,"funder_award_id":"2018YFA0900700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2048465561","https://openalex.org/W2116976883","https://openalex.org/W2606199419","https://openalex.org/W2783658781","https://openalex.org/W2949078105","https://openalex.org/W2989585088","https://openalex.org/W3016452877","https://openalex.org/W3040258020","https://openalex.org/W3110776987","https://openalex.org/W3138458927","https://openalex.org/W3154258817","https://openalex.org/W4213314063"],"related_works":["https://openalex.org/W796285933","https://openalex.org/W2057263938","https://openalex.org/W2302077272","https://openalex.org/W2387486206","https://openalex.org/W2208076193","https://openalex.org/W1850452918","https://openalex.org/W2334293709","https://openalex.org/W3092335715","https://openalex.org/W4211015925","https://openalex.org/W2510469884"],"abstract_inverted_index":{"SUMMARY:":[0],"Advances":[1],"in":[2,13,28],"metabolic":[3],"engineering":[4],"have":[5],"boosted":[6],"the":[7,29,44,62,72,89,97,124],"production":[8,16,30],"of":[9,15,18,34,64,75,88,92,100],"bulk":[10,20,35,77,93],"chemicals,":[11,105],"resulting":[12],"tons":[14],"volumes":[17],"some":[19],"chemicals":[21,36,94],"with":[22,107],"very":[23],"low":[24],"prices.":[25],"A":[26],"decrease":[27],"cost":[31],"and":[32,40,56,111],"overproduction":[33],"makes":[37],"it":[38],"necessary":[39],"desirable":[41],"to":[42,46,60,70,102],"explore":[43,61],"potential":[45,91],"synthesize":[47,103],"higher-value":[48],"products":[49],"from":[50],"them.":[51],"It":[52],"is":[53],"also":[54],"useful":[55],"important":[57],"for":[58],"society":[59],"use":[63],"design":[65],"methods":[66],"involving":[67],"synthetic":[68],"biology":[69],"increase":[71],"economic":[73,112],"value":[74],"these":[76],"chemicals.":[78],"Therefore,":[79],"we":[80],"developed":[81],"'BioBulkFoundary',":[82],"which":[83],"provides":[84],"an":[85],"elaborate":[86],"analysis":[87],"biosynthetic":[90],"based":[95],"on":[96,123],"state-of-art":[98],"exploration":[99],"pathways":[101],"value-added":[104],"along":[106],"associated":[108],"comprehensive":[109],"technology":[110],"database":[113],"into":[114],"a":[115],"user-friendly":[116],"framework.":[117],"AVAILABILITY":[118],"AND":[119],"IMPLEMENTATION:":[120],"Freely":[121],"available":[122,133],"web":[125],"at":[126,134],"http://design.rxnfinder.org/biobulkfoundary/.":[127],"SUPPLEMENTARY":[128],"INFORMATION:":[129],"Supplementary":[130],"data":[131],"are":[132],"Bioinformatics":[135],"online.":[136]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
