{"id":"https://openalex.org/W2291698312","doi":"https://doi.org/10.1093/bioinformatics/btv702","title":"Representation and inference of cellular architecture for metabolic reconstruction and modeling","display_name":"Representation and inference of cellular architecture for metabolic reconstruction and modeling","publication_year":2015,"publication_date":"2015-12-01","ids":{"openalex":"https://openalex.org/W2291698312","doi":"https://doi.org/10.1093/bioinformatics/btv702","mag":"2291698312","pmid":"https://pubmed.ncbi.nlm.nih.gov/26628588"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv702","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv702","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/7/1074/49018306/bioinformatics_32_7_1074.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/32/7/1074/49018306/bioinformatics_32_7_1074.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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 Paley","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"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"],"raw_orcid":null,"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/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":"Peter D. Karp","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"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":1,"corresponding_author_ids":["https://openalex.org/A5082071104"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.09104648,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"32","issue":"7","first_page":"1074","last_page":"1079"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9144999980926514,"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":0.9144999980926514,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.022199999541044235,"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":0.008999999612569809,"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/multicellular-organism","display_name":"Multicellular organism","score":0.7999734878540039},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7017573714256287},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.660547137260437},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.5758841037750244},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.5536370277404785},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5509803891181946},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5431316494941711},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.519742488861084},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5143345594406128},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4583832621574402},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3417249321937561},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2844471037387848},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28291767835617065},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17422086000442505},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.14838537573814392}],"concepts":[{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.7999734878540039},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7017573714256287},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.660547137260437},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.5758841037750244},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.5536370277404785},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5509803891181946},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5431316494941711},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.519742488861084},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5143345594406128},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4583832621574402},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3417249321937561},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2844471037387848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28291767835617065},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17422086000442505},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.14838537573814392},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv702","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv702","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/7/1074/49018306/bioinformatics_32_7_1074.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:26628588","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26628588","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:open-archive.highwire.org:bioinfo:32/7/1074","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/7/1074","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4907387","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4907387","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/btv702","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv702","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/7/1074/49018306/bioinformatics_32_7_1074.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":0.4000000059604645,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G132031321","display_name":null,"funder_award_id":"R01GM075742","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G462345482","display_name":null,"funder_award_id":"R01GM075742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G50490301","display_name":null,"funder_award_id":"RC2 GM092729","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5479500660","display_name":null,"funder_award_id":"GM092729","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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/W2291698312.pdf","grobid_xml":"https://content.openalex.org/works/W2291698312.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1502649855","https://openalex.org/W1996047071","https://openalex.org/W2125776280","https://openalex.org/W2126468077","https://openalex.org/W2128601422","https://openalex.org/W2132218677","https://openalex.org/W2134394193","https://openalex.org/W2150908245","https://openalex.org/W2152456759","https://openalex.org/W2162115836","https://openalex.org/W2168465568","https://openalex.org/W2170806980","https://openalex.org/W2171911221","https://openalex.org/W2988775587","https://openalex.org/W4230770774","https://openalex.org/W4236875018","https://openalex.org/W6818307145"],"related_works":["https://openalex.org/W4254238697","https://openalex.org/W2505404359","https://openalex.org/W93506351","https://openalex.org/W1995226864","https://openalex.org/W2768690359","https://openalex.org/W2475096012","https://openalex.org/W2280157287","https://openalex.org/W2163903195","https://openalex.org/W2035423850","https://openalex.org/W4223896405"],"abstract_inverted_index":{"MOTIVATION:":[0],"Metabolic":[1],"modeling":[2],"depends":[3],"on":[4],"accurately":[5,26],"representing":[6,58],"the":[7,42,59,74,91,99,128,160],"cellular":[8,22,28,43,60,75,94,111,136,146,161],"locations":[9],"of":[10,21,41,77,82,93,116,127,164,169],"enzyme-catalyzed":[11],"and":[12,54,118,142,191],"transport":[13],"reactions.":[14],"We":[15,31,72,105,131,153],"sought":[16,33],"to":[17,50,124,138,148],"develop":[18],"a":[19,34,68,78,83,87,107,156,195],"representation":[20,35,126,157],"compartmentation":[23],"that":[24,36,55,158],"would":[25,37,56],"capture":[27],"location":[29],"information.":[30,170],"further":[32],"support":[38],"automated":[39],"inference":[40],"compartments":[44,61],"present":[45,62],"in":[46,63],"newly":[47],"sequenced":[48],"organisms":[49],"speed":[51],"model":[52],"development,":[53],"enable":[57,125],"multiple":[64],"cell":[65,84],"types":[66],"within":[67],"multicellular":[69,88],"organism.":[70],"RESULTS:":[71],"define":[73],"architecture":[76],"unicellular":[79],"organism,":[80,89],"or":[81,150],"type":[85],"from":[86],"as":[90],"collection":[92],"components":[95],"it":[96],"contains":[97],"plus":[98],"topological":[100],"relationships":[101],"among":[102],"those":[103],"components.":[104],"developed":[106,155],"tool":[108],"for":[109,134,144,188,194,197],"inferring":[110],"architectures":[112,137,147],"across":[113],"many":[114],"domains":[115],"life":[117],"extended":[119],"our":[120],"Cell":[121,175],"Component":[122,176],"Ontology":[123,177],"inferred":[129],"architectures.":[130],"provide":[132],"software":[133,143,184],"visualizing":[135],"verify":[139],"their":[140],"correctness":[141],"editing":[145],"modify":[149],"correct":[151],"them.":[152],"also":[154],"records":[159],"compartment":[162],"assignments":[163],"reactions":[165],"with":[166],"minimal":[167],"duplication":[168],"AVAILABILITY":[171],"AND":[172],"IMPLEMENTATION:":[173],"The":[174,181],"is":[178,185,192],"freely":[179,186],"available.":[180],"Pathway":[182],"Tools":[183],"available":[187,193,207],"academic":[189],"research":[190],"fee":[196],"commercial":[198],"use.":[199],"CONTACT:":[200],"pkarp@ai.sri.com":[201],"SUPPLEMENTARY":[202],"INFORMATION:":[203],"Supplementary":[204],"data":[205],"are":[206],"at":[208],"Bioinformatics":[209],"online.":[210]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
