{"id":"https://openalex.org/W2153131751","doi":"https://doi.org/10.1142/s0219720010004604","title":"QUERYING METABOLISM UNDER DIFFERENT PHYSIOLOGICAL CONSTRAINTS","display_name":"QUERYING METABOLISM UNDER DIFFERENT PHYSIOLOGICAL CONSTRAINTS","publication_year":2010,"publication_date":"2010-04-01","ids":{"openalex":"https://openalex.org/W2153131751","doi":"https://doi.org/10.1142/s0219720010004604","mag":"2153131751","pmid":"https://pubmed.ncbi.nlm.nih.gov/20401946"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720010004604","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004604","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035836413","display_name":"Ali Cakmak","orcid":"https://orcid.org/0000-0002-1382-6130"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"ALI CAKMAK","raw_affiliation_strings":["Department of Electrical Engineering & Computer Science, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016412404","display_name":"G\u00fcltekin \u00d6zsoyo\u011flu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"GULTEKIN OZSOYOGLU","raw_affiliation_strings":["Department of Electrical Engineering & Computer Science, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113951492","display_name":"Richard W. Hanson","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"RICHARD W. HANSON","raw_affiliation_strings":["Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035836413"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5287,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.66390977,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"08","issue":"02","first_page":"247","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9973999857902527,"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":0.9973999857902527,"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":0.9873999953269958,"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":0.9865999817848206,"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":0.7187480926513672},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5543611645698547},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.49840879440307617},{"id":"https://openalex.org/keywords/production","display_name":"Production (economics)","score":0.4166649878025055},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3206941485404968},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23824387788772583},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22116270661354065},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20677581429481506}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7187480926513672},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5543611645698547},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.49840879440307617},{"id":"https://openalex.org/C2778348673","wikidata":"https://www.wikidata.org/wiki/Q739302","display_name":"Production (economics)","level":2,"score":0.4166649878025055},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3206941485404968},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23824387788772583},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22116270661354065},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20677581429481506},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C139719470","wikidata":"https://www.wikidata.org/wiki/Q39680","display_name":"Macroeconomics","level":1,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720010004604","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004604","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20401946","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20401946","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W68894444","https://openalex.org/W1482250407","https://openalex.org/W1524809087","https://openalex.org/W1561767438","https://openalex.org/W1574470162","https://openalex.org/W1594613389","https://openalex.org/W1595961914","https://openalex.org/W1606784130","https://openalex.org/W1757722203","https://openalex.org/W1758395617","https://openalex.org/W1784944639","https://openalex.org/W1964491374","https://openalex.org/W1989284002","https://openalex.org/W1993170943","https://openalex.org/W1994656497","https://openalex.org/W1996791690","https://openalex.org/W2017723268","https://openalex.org/W2019631913","https://openalex.org/W2022858952","https://openalex.org/W2023764523","https://openalex.org/W2029058413","https://openalex.org/W2029415078","https://openalex.org/W2037614307","https://openalex.org/W2046760236","https://openalex.org/W2051110041","https://openalex.org/W2053190303","https://openalex.org/W2055193911","https://openalex.org/W2058221907","https://openalex.org/W2065432632","https://openalex.org/W2073251435","https://openalex.org/W2087939423","https://openalex.org/W2093241068","https://openalex.org/W2096144498","https://openalex.org/W2101135726","https://openalex.org/W2102653059","https://openalex.org/W2103599442","https://openalex.org/W2106411520","https://openalex.org/W2111905282","https://openalex.org/W2114525532","https://openalex.org/W2116324021","https://openalex.org/W2134580783","https://openalex.org/W2137321945","https://openalex.org/W2140040278","https://openalex.org/W2147154405","https://openalex.org/W2147714160","https://openalex.org/W2148996444","https://openalex.org/W2155967165","https://openalex.org/W2156855851","https://openalex.org/W2157239641","https://openalex.org/W2158784643","https://openalex.org/W2163855763","https://openalex.org/W2165674132","https://openalex.org/W2167909188","https://openalex.org/W2170739315","https://openalex.org/W2171959112","https://openalex.org/W2317278163","https://openalex.org/W2319507795","https://openalex.org/W4295816494","https://openalex.org/W4301860484","https://openalex.org/W6629919104"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Metabolism":[0],"is":[1,110],"a":[2,62,83],"representation":[3],"of":[4,16,37,44,79,85,96],"the":[5,10,77,80,115],"biochemical":[6],"principles":[7,43],"that":[8],"govern":[9],"production,":[11],"consumption,":[12],"degradation,":[13],"and":[14,55,67,89,103,106],"biosynthesis":[15],"metabolites":[17],"in":[18,25],"living":[19],"cells.":[20],"Organisms":[21],"respond":[22],"to":[23,75],"changes":[24],"their":[26],"physiological":[27,90],"conditions":[28],"or":[29],"environmental":[30],"perturbations":[31],"(i.e.":[32],"constraints)":[33],"via":[34],"cooperative":[35],"implementation":[36],"such":[38],"principles.":[39,118],"Querying":[40],"inner":[41],"working":[42],"metabolism":[45,63,81],"under":[46],"different":[47],"constraints":[48],"provides":[49],"invaluable":[50],"insights":[51],"for":[52],"both":[53,101],"researchers":[54,74],"educators.":[56],"In":[57],"this":[58],"paper,":[59],"we":[60],"propose":[61],"query":[64,70,94,108],"language":[65],"(MQL)":[66],"discuss":[68],"its":[69,107],"processing.":[71],"MQL":[72,97],"enables":[73],"explore":[76],"behavior":[78],"with":[82,100],"wide-range":[84],"predicates":[86],"including":[87],"dietary":[88],"condition":[91],"specifications.":[92],"The":[93],"results":[95],"are":[98],"enriched":[99],"textual":[102],"visual":[104],"representations,":[105],"processing":[109],"completely":[111],"tailored":[112],"based":[113],"on":[114],"underlying":[116],"metabolic":[117]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}