{"id":"https://openalex.org/W4241630616","doi":"https://doi.org/10.1093/bib/bbz104","title":"Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology","display_name":"Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology","publication_year":2019,"publication_date":"2019-07-25","ids":{"openalex":"https://openalex.org/W4241630616","doi":"https://doi.org/10.1093/bib/bbz104"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz104","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/109/40418534/bbz104.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/22/1/109/40418534/bbz104.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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":"Peter D Karp","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049879477","display_name":"Peter Midford","orcid":"https://orcid.org/0000-0001-6512-3296"},"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":"Peter E Midford","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006710775","display_name":"Richard Billington","orcid":"https://orcid.org/0000-0001-7288-8916"},"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":"Richard Billington","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047592210","display_name":"Anamika Kothari","orcid":null},"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":"Anamika Kothari","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","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":false,"raw_author_name":"Markus Krummenacker","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053894822","display_name":"Mario Latendresse","orcid":"https://orcid.org/0000-0002-6292-0158"},"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":"Mario Latendresse","raw_affiliation_strings":["Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050296347","display_name":"Wai Kit Ong","orcid":"https://orcid.org/0000-0003-0972-1499"},"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":"Wai Kit Ong","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016728461","display_name":"Pallavi Subhraveti","orcid":null},"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":"Pallavi Subhraveti","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044919501","display_name":"Ron Caspi","orcid":"https://orcid.org/0000-0002-6113-3590"},"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":"Ron Caspi","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110621263","display_name":"Carol A. Fulcher","orcid":null},"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":"Carol Fulcher","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011903148","display_name":"Ingrid M. Keseler","orcid":"https://orcid.org/0000-0003-1738-6117"},"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":"Ingrid M Keseler","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","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":"Suzanne M Paley","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5049879477"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.6135,"has_fulltext":true,"cited_by_count":229,"citation_normalized_percentile":{"value":0.97693386,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"22","issue":"1","first_page":"109","last_page":"126"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987000226974487,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9976999759674072,"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":0.7098862528800964},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5477610230445862},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5102205276489258},{"id":"https://openalex.org/keywords/cyberinfrastructure","display_name":"Cyberinfrastructure","score":0.4522581100463867},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.4415965676307678},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4187147915363312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2925943434238434},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1923466920852661}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7098862528800964},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5477610230445862},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5102205276489258},{"id":"https://openalex.org/C2776397876","wikidata":"https://www.wikidata.org/wiki/Q1450531","display_name":"Cyberinfrastructure","level":2,"score":0.4522581100463867},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.4415965676307678},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4187147915363312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2925943434238434},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1923466920852661},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbz104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz104","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/109/40418534/bbz104.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:7346730","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8453236","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbz104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz104","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/109/40418534/bbz104.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1167613700","display_name":null,"funder_award_id":"GM080746","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2009364751","display_name":null,"funder_award_id":"GM077678","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2856777376","display_name":null,"funder_award_id":"GM075742","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3144428136","display_name":null,"funder_award_id":"GM07767","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G473593538","display_name":null,"funder_award_id":"Molecular","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5077415591","display_name":null,"funder_award_id":"GM077678","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6777668075","display_name":null,"funder_award_id":"GM080746","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G69280378","display_name":null,"funder_award_id":"GM075742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7602723344","display_name":null,"funder_award_id":"GM07767","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320310010","display_name":"University of Georgia","ror":"https://ror.org/00te3t702"},{"id":"https://openalex.org/F4320310536","display_name":"University of Virginia","ror":"https://ror.org/0153tk833"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4241630616.pdf","grobid_xml":"https://content.openalex.org/works/W4241630616.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1603241183","https://openalex.org/W1960974681","https://openalex.org/W1986708244","https://openalex.org/W1996047071","https://openalex.org/W2058501095","https://openalex.org/W2162115836","https://openalex.org/W2530896378","https://openalex.org/W2531153203","https://openalex.org/W2559588208","https://openalex.org/W2577168473","https://openalex.org/W2594503598","https://openalex.org/W2607313420","https://openalex.org/W2743919575","https://openalex.org/W2749464300","https://openalex.org/W2763472614","https://openalex.org/W2766195206","https://openalex.org/W2785345478","https://openalex.org/W2794727335","https://openalex.org/W2802279707","https://openalex.org/W2803251554","https://openalex.org/W2859249641","https://openalex.org/W2888038490","https://openalex.org/W2898951869","https://openalex.org/W2943987703","https://openalex.org/W2950614386","https://openalex.org/W2952699241","https://openalex.org/W4237725837","https://openalex.org/W6747891776","https://openalex.org/W6813711271"],"related_works":["https://openalex.org/W273500195","https://openalex.org/W2043019925","https://openalex.org/W4236056781","https://openalex.org/W4293768956","https://openalex.org/W2808533663","https://openalex.org/W2148010638","https://openalex.org/W2010185761","https://openalex.org/W1993050440","https://openalex.org/W3186737914","https://openalex.org/W2767154380"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Biological":[2],"systems":[3],"function":[4],"through":[5,57,113],"dynamic":[6],"interactions":[7],"among":[8],"genes":[9],"and":[10,15,42,48,59,76,139,170,206,209],"their":[11],"products,":[12],"regulatory":[13],"circuits":[14],"metabolic":[16,70,124],"networks.":[17],"Our":[18],"development":[19,68,128],"of":[20,40,51,69,85,129,177,190],"the":[21,28,67,83,91,98,114,155,184,191],"Pathway":[22,101,146],"Tools":[23,102,147],"software":[24,103,214],"was":[25],"motivated":[26],"by":[27],"need":[29],"to":[30,46,65,77,81],"construct":[31],"biological":[32],"knowledge":[33],"resources":[34],"that":[35,43],"combine":[36],"these":[37],"many":[38],"types":[39],"data,":[41],"enable":[44],"users":[45],"find":[47],"comprehend":[49],"data":[50,87,168,234],"interest":[52],"as":[53,55],"quickly":[54],"possible":[56],"query":[58],"visualization":[60],"tools.":[61],"Further,":[62],"we":[63,95],"sought":[64],"support":[66,110],"flux":[71],"models":[72,130],"from":[73],"pathway":[74,79,161],"databases,":[75],"use":[78],"information":[80,232],"leverage":[82],"interpretation":[84],"high-throughput":[86],"sets.":[88],"Results":[89],"In":[90],"past":[92],"4":[93],"years":[94],"have":[96,181],"enhanced":[97],"already":[99],"extensive":[100],"in":[104,239],"several":[105,149],"respects.":[106],"It":[107],"can":[108],"now":[109],"metabolic-model":[111],"execution":[112],"Web,":[115],"it":[116,126],"provides":[117],"a":[118,136,163,220],"more":[119],"accurate":[120],"gap":[121],"filler":[122],"for":[123,131,166,173,198,217,224],"models;":[125],"supports":[127,148],"organism":[132,199],"communities":[133],"distributed":[134],"across":[135],"spatial":[137],"grid;":[138],"model":[140],"results":[141],"may":[142],"be":[143],"visualized":[144],"graphically.":[145],"new":[150,194],"omics-data":[151],"analysis":[152,169],"tools":[153,197],"including":[154],"Omics":[156],"Dashboard,":[157],"multi-pathway":[158],"diagrams":[159],"called":[160],"collages,":[162],"pathway-covering":[164],"algorithm":[165,172],"metabolomics":[167],"an":[171],"generating":[174],"mechanistic":[175],"explanations":[176],"multi-omics":[178],"data.":[179],"We":[180],"also":[182],"improved":[183,201],"core":[185],"pathway/genome":[186],"databases":[187],"management":[188],"capabilities":[189],"software,":[192],"providing":[193],"multi-organism":[195],"search":[196],"communities,":[200],"graphics":[202],"rendering,":[203],"faster":[204],"performance":[205],"re-designed":[207],"gene":[208],"metabolite":[210],"pages.":[211],"Availability":[212],"The":[213],"is":[215,222],"free":[216],"academic":[218],"use;":[219],"fee":[221],"required":[223],"commercial":[225],"use.":[226],"See":[227],"http://pathwaytools.com.":[228],"Contact":[229],"pkarp@ai.sri.com":[230],"Supplementary":[231,233],"are":[235],"available":[236],"at":[237],"Briefings":[238],"Bioinformatics":[240],"online.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":41},{"year":2023,"cited_by_count":51},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":35},{"year":2020,"cited_by_count":10}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
