{"id":"https://openalex.org/W4296367463","doi":"https://doi.org/10.1186/s13321-022-00621-8","title":"What makes a reaction network \u201cchemical\u201d?","display_name":"What makes a reaction network \u201cchemical\u201d?","publication_year":2022,"publication_date":"2022-09-19","ids":{"openalex":"https://openalex.org/W4296367463","doi":"https://doi.org/10.1186/s13321-022-00621-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/36123755"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00621-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00621-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00621-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00621-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100672044","display_name":"Stefan C. M\u00fcller","orcid":"https://orcid.org/0000-0002-3541-7856"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Stefan M\u00fcller","raw_affiliation_strings":["Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Christoph Flamm","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de","Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria. studla@bioinf.uni-leipzig.de","Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, Bogot\u00e1, 111321, Colombia. studla@bioinf.uni-leipzig.de","German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases University Leipzig, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de","Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 04103, Leipzig, Germany. studla@bioinf.uni-leipzig.de","Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA. studla@bioinf.uni-leipzig.de","Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, Bogot\u00e1, 111321, Colombia. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases University Leipzig, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 04103, Leipzig, Germany. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA. studla@bioinf.uni-leipzig.de","institution_ids":[]},{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100672044"],"corresponding_institution_ids":["https://openalex.org/I129774422"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1662,"currency":"EUR","value_usd":1792},"fwci":1.8199,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.85680905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"63","last_page":"63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9980000257492065,"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":0.9980000257492065,"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":0.9939000010490417,"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":0.9918000102043152,"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":0.6789922714233398},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4683612585067749}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6789922714233398},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4683612585067749}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-022-00621-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00621-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00621-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:36123755","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36123755","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:feb05e8e4b36482b90ce2749435d99b9","is_oa":true,"landing_page_url":"https://doaj.org/article/feb05e8e4b36482b90ce2749435d99b9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-24 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9484159","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9484159","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-022-00621-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00621-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00621-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3740268834","display_name":null,"funder_award_id":"01IS18026B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8163667563","display_name":null,"funder_award_id":"P33218","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G8871635756","display_name":null,"funder_award_id":"STA 850/58-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320325298","display_name":"Universit\u00e4t Leipzig","ror":"https://ror.org/03s7gtk40"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4296367463.pdf","grobid_xml":"https://content.openalex.org/works/W4296367463.grobid-xml"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W1761701990","https://openalex.org/W1850807863","https://openalex.org/W1880814952","https://openalex.org/W1965692670","https://openalex.org/W1974519483","https://openalex.org/W1976672440","https://openalex.org/W1980965251","https://openalex.org/W1981151876","https://openalex.org/W1983202741","https://openalex.org/W1983823113","https://openalex.org/W1986514804","https://openalex.org/W1988398836","https://openalex.org/W1988741929","https://openalex.org/W1993397775","https://openalex.org/W1994134392","https://openalex.org/W2000773028","https://openalex.org/W2000804241","https://openalex.org/W2008591003","https://openalex.org/W2010861052","https://openalex.org/W2013356895","https://openalex.org/W2015831273","https://openalex.org/W2016341968","https://openalex.org/W2018045523","https://openalex.org/W2019334471","https://openalex.org/W2019582172","https://openalex.org/W2019926612","https://openalex.org/W2020371939","https://openalex.org/W2021930726","https://openalex.org/W2022333401","https://openalex.org/W2024494620","https://openalex.org/W2025569385","https://openalex.org/W2028732503","https://openalex.org/W2029403511","https://openalex.org/W2030207203","https://openalex.org/W2030925767","https://openalex.org/W2033925647","https://openalex.org/W2035814503","https://openalex.org/W2036281295","https://openalex.org/W2036546758","https://openalex.org/W2037614307","https://openalex.org/W2040392433","https://openalex.org/W2044760528","https://openalex.org/W2050017155","https://openalex.org/W2055378322","https://openalex.org/W2061425021","https://openalex.org/W2065433068","https://openalex.org/W2067087023","https://openalex.org/W2078355959","https://openalex.org/W2078429105","https://openalex.org/W2083786039","https://openalex.org/W2083860925","https://openalex.org/W2084516445","https://openalex.org/W2091695815","https://openalex.org/W2099254026","https://openalex.org/W2099701485","https://openalex.org/W2105679831","https://openalex.org/W2107808084","https://openalex.org/W2108959333","https://openalex.org/W2108980529","https://openalex.org/W2109627667","https://openalex.org/W2111979511","https://openalex.org/W2112090702","https://openalex.org/W2115184421","https://openalex.org/W2134233117","https://openalex.org/W2136060005","https://openalex.org/W2137266088","https://openalex.org/W2140103782","https://openalex.org/W2144885342","https://openalex.org/W2145600675","https://openalex.org/W2148677603","https://openalex.org/W2169015768","https://openalex.org/W2170472690","https://openalex.org/W2397550423","https://openalex.org/W2607478799","https://openalex.org/W2747253451","https://openalex.org/W2754872025","https://openalex.org/W2772491215","https://openalex.org/W2785376826","https://openalex.org/W2806627097","https://openalex.org/W2951773666","https://openalex.org/W2952741235","https://openalex.org/W2954949100","https://openalex.org/W2963717743","https://openalex.org/W2964021005","https://openalex.org/W2966968005","https://openalex.org/W3000466327","https://openalex.org/W3022376712","https://openalex.org/W3100284331","https://openalex.org/W3101830518","https://openalex.org/W3103655890","https://openalex.org/W3103786587","https://openalex.org/W3104206318","https://openalex.org/W3118621910","https://openalex.org/W3133921777","https://openalex.org/W3161841750","https://openalex.org/W3176172668","https://openalex.org/W4206681098","https://openalex.org/W4229491797","https://openalex.org/W4235568626"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"\"Chemical\"":[0],"RNs":[1,47],"are":[2],"directed":[3],"hypergraphs":[4],"with":[5],"a":[6,16,27,39],"stoichiometric":[7],"matrix":[8],"[Formula:":[9,51],"see":[10,52],"text]":[11,53],"whose":[12,21],"left":[13],"kernel":[14,23],"contains":[15],"strictly":[17],"positive":[18],"vector":[19],"and":[20,80],"right":[22],"does":[24],"not":[25],"contain":[26],"futile":[28],"cycle":[29],"involving":[30],"an":[31],"irreversible":[32],"reaction.":[33],"This":[34],"simple":[35],"characterization":[36],"also":[37],"provides":[38],"concise":[40],"specification":[41],"of":[42,59,77],"random":[43],"models":[44],"for":[45,69],"chemical":[46,82],"that":[48],"additionally":[49],"constrain":[50],"by":[54],"rank,":[55],"sparsity,":[56],"or":[57],"distribution":[58],"the":[60],"non-zero":[61],"entries.":[62],"Furthermore,":[63],"it":[64],"suggests":[65],"several":[66],"interesting":[67],"avenues":[68],"future":[70],"research,":[71],"in":[72],"particular,":[73],"concerning":[74],"alternative":[75],"representations":[76],"reaction":[78],"networks":[79],"infinite":[81],"universes.":[83]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
