{"id":"https://openalex.org/W2096144498","doi":"https://doi.org/10.1093/bioinformatics/bti546","title":"Querying and computing with BioCyc databases","display_name":"Querying and computing with BioCyc databases","publication_year":2005,"publication_date":"2005-06-16","ids":{"openalex":"https://openalex.org/W2096144498","doi":"https://doi.org/10.1093/bioinformatics/bti546","mag":"2096144498","pmid":"https://pubmed.ncbi.nlm.nih.gov/15961440"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/16/3454/573094/bti546.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/16/3454/573094/bti546.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007704760","display_name":"Markus Krummenacker","orcid":"https://orcid.org/0000-0002-2546-3007"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. Krummenacker","raw_affiliation_strings":["SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015212276","display_name":"Suzanne Paley","orcid":"https://orcid.org/0000-0001-5763-8935"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Paley","raw_affiliation_strings":["SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018498646","display_name":"Lukas A. Mueller","orcid":"https://orcid.org/0000-0001-8640-1750"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. Mueller","raw_affiliation_strings":["Cornell University, Department of Plant Breeding and Genetics, Emerson Hall, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cornell University, Department of Plant Breeding and Genetics, Emerson Hall, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005870843","display_name":"Tingting Yan","orcid":"https://orcid.org/0000-0002-6730-2877"},"institutions":[{"id":"https://openalex.org/I196817621","display_name":"Carnegie Institution for Science","ror":"https://ror.org/04jr01610","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I196817621"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Yan","raw_affiliation_strings":["Carnegie Institution of Washington, Dept of Plant Biology, Stanford, CA 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Institution of Washington, Dept of Plant Biology, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I196817621"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. D. Karp","raw_affiliation_strings":["SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5007704760"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":null,"apc_paid":null,"fwci":23.035,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.99334249,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"16","first_page":"3454","last_page":"3455"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9958000183105469,"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":0.9958000183105469,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9731000065803528,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9610000252723694,"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":0.8566643595695496},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.6904979348182678},{"id":"https://openalex.org/keywords/lisp","display_name":"Lisp","score":0.6451554894447327},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6204522848129272},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5823061466217041},{"id":"https://openalex.org/keywords/sql","display_name":"SQL","score":0.522031307220459},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.505174458026886},{"id":"https://openalex.org/keywords/data-access","display_name":"Data access","score":0.44860154390335083},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3983246088027954}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8566643595695496},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6904979348182678},{"id":"https://openalex.org/C190883126","wikidata":"https://www.wikidata.org/wiki/Q132874","display_name":"Lisp","level":2,"score":0.6451554894447327},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6204522848129272},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5823061466217041},{"id":"https://openalex.org/C510870499","wikidata":"https://www.wikidata.org/wiki/Q47607","display_name":"SQL","level":2,"score":0.522031307220459},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.505174458026886},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.44860154390335083},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3983246088027954}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/16/3454/573094/bti546.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15961440","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15961440","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:1450015","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1450015","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/16/3454/573094/bti546.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":[],"awards":[{"id":"https://openalex.org/G210435092","display_name":null,"funder_award_id":"GM75742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G588656828","display_name":null,"funder_award_id":"GM70065","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6432839626","display_name":null,"funder_award_id":"R33 GM070065","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2074906123","https://openalex.org/W2105941683","https://openalex.org/W2133298156","https://openalex.org/W2155201905","https://openalex.org/W2160453515","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2573939812","https://openalex.org/W2120098008","https://openalex.org/W1639806124","https://openalex.org/W2902831276","https://openalex.org/W2540682188","https://openalex.org/W4385834214","https://openalex.org/W3022423983","https://openalex.org/W12347151","https://openalex.org/W2957025774","https://openalex.org/W1575529579"],"abstract_inverted_index":{"Summary:":[0],"We":[1],"describe":[2],"multiple":[3,23],"methods":[4],"for":[5,32],"accessing":[6],"and":[7,11,35,37,50,57],"querying":[8],"the":[9,16,41],"complex":[10],"integrated":[12],"cellular":[13],"data":[14],"in":[15,54],"BioCyc":[17,52,87],"family":[18],"of":[19,70],"databases:":[20],"access":[21,26,39,85],"through":[22,27,40],"file":[24],"formats,":[25],"Application":[28],"Program":[29],"Interfaces":[30],"(APIs)":[31],"LISP,":[33],"Perl":[34],"Java,":[36],"SQL":[38],"BioWarehouse":[42],"relational":[43],"database.":[44],"Availability:":[45],"The":[46],"Pathway":[47],"Tools":[48],"software":[49],"20":[51],"DBs":[53],"Tiers":[55],"1":[56],"2":[58],"are":[59],"freely":[60],"available":[61],"to":[62,67,86],"academic":[63],"users;":[64],"fees":[65],"apply":[66],"some":[68],"types":[69],"commercial":[71],"use.":[72],"For":[73,80],"download":[74],"instructions":[75],"see":[76,89],"http://BioCyc.org/download.shtml":[77],"Supplementary":[78],"information:":[79],"more":[81],"details":[82],"on":[83],"programmatic":[84],"DBs,":[88],"http://bioinformatics.ai.sri.com/ptools/ptools-resources.html":[90],"Contact:":[91],"[email":[92],"protected]":[93]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}