{"id":"https://openalex.org/W2168465568","doi":"https://doi.org/10.1093/bib/bbp043","title":"Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology","display_name":"Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology","publication_year":2009,"publication_date":"2009-12-02","ids":{"openalex":"https://openalex.org/W2168465568","doi":"https://doi.org/10.1093/bib/bbp043","mag":"2168465568","pmid":"https://pubmed.ncbi.nlm.nih.gov/19955237"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp043","pdf_url":"https://academic.oup.com/bib/article-pdf/11/1/40/481847/bbp043.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/11/1/40/481847/bbp043.pdf","any_repository_has_fulltext":true},"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":true,"raw_author_name":"P. D. Karp","raw_affiliation_strings":["Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com","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":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. M. Paley","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007704760","display_name":"Markus Krummenacker","orcid":"https://orcid.org/0000-0002-2546-3007"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Krummenacker","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053894822","display_name":"Mario Latendresse","orcid":"https://orcid.org/0000-0002-6292-0158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Latendresse","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056132219","display_name":"J. M. Dale","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. M. Dale","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082885520","display_name":"T. J. Lee","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. J. Lee","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035402401","display_name":"P. Kaipa","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P. Kaipa","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004358323","display_name":"Fred Gilham","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"F. Gilham","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064954416","display_name":"Aaron Spaulding","orcid":"https://orcid.org/0000-0001-9727-6756"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Spaulding","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006905727","display_name":"Liviu Popescu","orcid":"https://orcid.org/0000-0003-3010-4743"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L. Popescu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049324718","display_name":"Tomer Altman","orcid":"https://orcid.org/0000-0002-6521-5454"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. Altman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069669892","display_name":"Ian T. Paulsen","orcid":"https://orcid.org/0000-0001-9015-9418"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I. Paulsen","raw_affiliation_strings":["Department of Molecular Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Sciences","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011903148","display_name":"Ingrid M. Keseler","orcid":"https://orcid.org/0000-0003-1738-6117"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I. M. Keseler","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5044919501","display_name":"Ron Caspi","orcid":"https://orcid.org/0000-0002-6113-3590"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Caspi","raw_affiliation_strings":["MetaCyc database"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MetaCyc database","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5082071104"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":14.3241,"has_fulltext":false,"cited_by_count":705,"citation_normalized_percentile":{"value":0.99386736,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"40","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8391000032424927,"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":0.8391000032424927,"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":0.05770000070333481,"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":0.026499999687075615,"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":0.7028020024299622},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6312005519866943},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.5483241677284241},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5267614126205444},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5116298794746399},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.4872986078262329},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.435491681098938},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.43294399976730347},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.43209007382392883},{"id":"https://openalex.org/keywords/reachability","display_name":"Reachability","score":0.42976170778274536},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4218604564666748},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.41315966844558716},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3916938304901123},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3149471879005432},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.256099134683609},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20320415496826172},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16789546608924866},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11978697776794434},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.11133882403373718},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.09422320127487183}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7028020024299622},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6312005519866943},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.5483241677284241},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5267614126205444},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5116298794746399},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.4872986078262329},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.435491681098938},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.43294399976730347},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.43209007382392883},{"id":"https://openalex.org/C136643341","wikidata":"https://www.wikidata.org/wiki/Q1361526","display_name":"Reachability","level":2,"score":0.42976170778274536},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4218604564666748},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.41315966844558716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3916938304901123},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3149471879005432},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.256099134683609},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20320415496826172},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16789546608924866},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11978697776794434},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.11133882403373718},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.09422320127487183},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbp043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp043","pdf_url":"https://academic.oup.com/bib/article-pdf/11/1/40/481847/bbp043.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":"pmid:19955237","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19955237","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmid:31813964","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31813964","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2032678","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2810111","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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8453236","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8453236","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbp043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp043","pdf_url":"https://academic.oup.com/bib/article-pdf/11/1/40/481847/bbp043.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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2168465568.pdf","grobid_xml":"https://content.openalex.org/works/W2168465568.grobid-xml"},"referenced_works_count":114,"referenced_works":["https://openalex.org/W399385914","https://openalex.org/W1490553060","https://openalex.org/W1502649855","https://openalex.org/W1509396824","https://openalex.org/W1537280715","https://openalex.org/W1565170002","https://openalex.org/W1566014475","https://openalex.org/W1574470162","https://openalex.org/W1603241183","https://openalex.org/W1695430372","https://openalex.org/W1835571316","https://openalex.org/W1966408199","https://openalex.org/W1966614672","https://openalex.org/W1969709265","https://openalex.org/W1970594207","https://openalex.org/W1971185254","https://openalex.org/W1975147762","https://openalex.org/W1984345785","https://openalex.org/W1984852783","https://openalex.org/W1990098464","https://openalex.org/W1991056282","https://openalex.org/W1996047071","https://openalex.org/W1999895438","https://openalex.org/W2003947856","https://openalex.org/W2004340874","https://openalex.org/W2007868900","https://openalex.org/W2013171416","https://openalex.org/W2017065632","https://openalex.org/W2019240775","https://openalex.org/W2021239799","https://openalex.org/W2029007900","https://openalex.org/W2036496916","https://openalex.org/W2042067428","https://openalex.org/W2053419354","https://openalex.org/W2058501095","https://openalex.org/W2073837631","https://openalex.org/W2078775934","https://openalex.org/W2083280521","https://openalex.org/W2085993965","https://openalex.org/W2089691764","https://openalex.org/W2094491295","https://openalex.org/W2094739913","https://openalex.org/W2096144498","https://openalex.org/W2096245011","https://openalex.org/W2096608686","https://openalex.org/W2098676247","https://openalex.org/W2099526830","https://openalex.org/W2100209768","https://openalex.org/W2100525485","https://openalex.org/W2101292724","https://openalex.org/W2101641168","https://openalex.org/W2103017472","https://openalex.org/W2106193566","https://openalex.org/W2106197985","https://openalex.org/W2106323366","https://openalex.org/W2107522712","https://openalex.org/W2111825982","https://openalex.org/W2113024448","https://openalex.org/W2117364474","https://openalex.org/W2118572979","https://openalex.org/W2119464316","https://openalex.org/W2119958068","https://openalex.org/W2121191916","https://openalex.org/W2124450302","https://openalex.org/W2126669894","https://openalex.org/W2127057035","https://openalex.org/W2127640118","https://openalex.org/W2128601422","https://openalex.org/W2132206153","https://openalex.org/W2132926880","https://openalex.org/W2132992030","https://openalex.org/W2133298156","https://openalex.org/W2133452284","https://openalex.org/W2134221731","https://openalex.org/W2134394193","https://openalex.org/W2135030836","https://openalex.org/W2135206190","https://openalex.org/W2135435176","https://openalex.org/W2136514583","https://openalex.org/W2137141752","https://openalex.org/W2139135429","https://openalex.org/W2139400351","https://openalex.org/W2139898508","https://openalex.org/W2140300290","https://openalex.org/W2141626941","https://openalex.org/W2141729174","https://openalex.org/W2144885342","https://openalex.org/W2145477956","https://openalex.org/W2147472054","https://openalex.org/W2147714160","https://openalex.org/W2148602507","https://openalex.org/W2152415665","https://openalex.org/W2153091158","https://openalex.org/W2155201905","https://openalex.org/W2155225302","https://openalex.org/W2155254562","https://openalex.org/W2155471967","https://openalex.org/W2158784643","https://openalex.org/W2159675211","https://openalex.org/W2162853466","https://openalex.org/W2165674132","https://openalex.org/W2169267759","https://openalex.org/W2169385519","https://openalex.org/W2170427655","https://openalex.org/W2410295001","https://openalex.org/W2482371382","https://openalex.org/W2604823638","https://openalex.org/W2626108727","https://openalex.org/W2915985519","https://openalex.org/W2916475656","https://openalex.org/W3103786587","https://openalex.org/W4210430020","https://openalex.org/W4230392683","https://openalex.org/W4248664566"],"related_works":["https://openalex.org/W2374260038","https://openalex.org/W2216418212","https://openalex.org/W2020641517","https://openalex.org/W1990404960","https://openalex.org/W2072874942","https://openalex.org/W2075919068","https://openalex.org/W1974325331","https://openalex.org/W2045478141","https://openalex.org/W2950078152","https://openalex.org/W2118803783"],"abstract_inverted_index":{"MOTIVATION:":[0],"Biological":[1],"systems":[2],"function":[3],"through":[4,56,112],"dynamic":[5],"interactions":[6],"among":[7],"genes":[8],"and":[9,14,41,47,58,75,138,169,205,208],"their":[10],"products,":[11],"regulatory":[12],"circuits":[13],"metabolic":[15,69,123],"networks.":[16],"Our":[17],"development":[18,67,127],"of":[19,39,50,68,84,128,176,189],"the":[20,27,66,82,90,97,113,154,183,190],"Pathway":[21,100,145],"Tools":[22,101,146],"software":[23,102,213],"was":[24],"motivated":[25],"by":[26],"need":[28],"to":[29,45,64,76,80],"construct":[30],"biological":[31],"knowledge":[32],"resources":[33],"that":[34,42],"combine":[35],"these":[36],"many":[37],"types":[38],"data,":[40],"enable":[43],"users":[44],"find":[46],"comprehend":[48],"data":[49,86,167,233],"interest":[51],"as":[52,54],"quickly":[53],"possible":[55],"query":[57],"visualization":[59],"tools.":[60],"Further,":[61],"we":[62,94],"sought":[63],"support":[65,109],"flux":[70],"models":[71,129],"from":[72],"pathway":[73,78,160],"databases,":[74],"use":[77],"information":[79],"leverage":[81],"interpretation":[83],"high-throughput":[85],"sets.":[87],"RESULTS:":[88],"In":[89],"past":[91],"4":[92],"years":[93],"have":[95,180],"enhanced":[96],"already":[98],"extensive":[99],"in":[103,238],"several":[104,148],"respects.":[105],"It":[106],"can":[107],"now":[108],"metabolic-model":[110],"execution":[111],"Web,":[114],"it":[115,125],"provides":[116],"a":[117,135,162,219],"more":[118],"accurate":[119],"gap":[120],"filler":[121],"for":[122,130,165,172,197,216,223],"models;":[124],"supports":[126,147],"organism":[131,198],"communities":[132],"distributed":[133],"across":[134],"spatial":[136],"grid;":[137],"model":[139],"results":[140],"may":[141],"be":[142],"visualized":[143],"graphically.":[144],"new":[149,193],"omics-data":[150],"analysis":[151,168],"tools":[152,196],"including":[153],"Omics":[155],"Dashboard,":[156],"multi-pathway":[157],"diagrams":[158],"called":[159],"collages,":[161],"pathway-covering":[163],"algorithm":[164,171],"metabolomics":[166],"an":[170],"generating":[173],"mechanistic":[174],"explanations":[175],"multi-omics":[177],"data.":[178],"We":[179],"also":[181],"improved":[182,200],"core":[184],"pathway/genome":[185],"databases":[186],"management":[187],"capabilities":[188],"software,":[191],"providing":[192],"multi-organism":[194],"search":[195],"communities,":[199],"graphics":[201],"rendering,":[202],"faster":[203],"performance":[204],"re-designed":[206],"gene":[207],"metabolite":[209],"pages.":[210],"AVAILABILITY:":[211],"The":[212],"is":[214,221],"free":[215],"academic":[217],"use;":[218],"fee":[220],"required":[222],"commercial":[224],"use.":[225],"See":[226],"http://pathwaytools.com.":[227],"CONTACT:":[228],"pkarp@ai.sri.com.":[229],"SUPPLEMENTARY":[230],"INFORMATION:":[231],"Supplementary":[232],"are":[234],"available":[235],"at":[236],"Briefings":[237],"Bioinformatics":[239],"online.":[240]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":44},{"year":2022,"cited_by_count":39},{"year":2021,"cited_by_count":44},{"year":2020,"cited_by_count":53},{"year":2019,"cited_by_count":39},{"year":2018,"cited_by_count":39},{"year":2017,"cited_by_count":65},{"year":2016,"cited_by_count":54},{"year":2015,"cited_by_count":52},{"year":2014,"cited_by_count":49},{"year":2013,"cited_by_count":60},{"year":2012,"cited_by_count":52}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2016-06-24T00:00:00"}
