{"id":"https://openalex.org/W1516184414","doi":"https://doi.org/10.1186/1752-0509-1-5","title":"METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks","display_name":"METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks","publication_year":2007,"publication_date":"2007-01-09","ids":{"openalex":"https://openalex.org/W1516184414","doi":"https://doi.org/10.1186/1752-0509-1-5","mag":"1516184414","pmid":"https://pubmed.ncbi.nlm.nih.gov/17408512"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-1-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040090614","display_name":"Christoph Gille","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I192389796","display_name":"Humboldt State University","ror":"https://ror.org/02qt0xs84","country_code":"US","type":"education","lineage":["https://openalex.org/I192389796"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Christoph Gille","raw_affiliation_strings":["Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany. christoph.gille@charite.de","Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany. christoph.gille@charite.de","institution_ids":["https://openalex.org/I7877124","https://openalex.org/I39343248","https://openalex.org/I192389796"]},{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111693736","display_name":"Sabrina Hoffmann","orcid":null},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sabrina Hoffmann","raw_affiliation_strings":["Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, 10117, Berlin, Monbijoustra\u00dfe 2, Germany","Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, 10117, Berlin, Monbijoustra\u00dfe 2, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124"]},{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078409502","display_name":"Hermann\u2212Georg Holzh\u00fctter","orcid":"https://orcid.org/0000-0002-5054-6023"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hermann-Georg Holzh\u00fctter","raw_affiliation_strings":["Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, 10117, Berlin, Monbijoustra\u00dfe 2, Germany","Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, 10117, Berlin, Monbijoustra\u00dfe 2, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124"]},{"raw_affiliation_string":"Institute of Biochemistry Charit\u00e9, Medical Faculty of the Humboldt University, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040090614"],"corresponding_institution_ids":["https://openalex.org/I192389796","https://openalex.org/I39343248","https://openalex.org/I7877124"],"apc_list":null,"apc_paid":null,"fwci":0.4037,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.6093022,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"1","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9822999835014343,"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":0.9822999835014343,"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":0.003700000001117587,"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/T12688","display_name":"Microbial metabolism and enzyme function","score":0.003000000026077032,"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/sbml","display_name":"SBML","score":0.7978570461273193},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7252373695373535},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.6856280565261841},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6178648471832275},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5941838622093201},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4911491572856903},{"id":"https://openalex.org/keywords/compartment","display_name":"Compartment (ship)","score":0.4668726623058319},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.37146836519241333},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3256290555000305},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.260431706905365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20270892977714539},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.12855303287506104},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11511921882629395},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.10024100542068481}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7978570461273193},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7252373695373535},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.6856280565261841},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6178648471832275},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5941838622093201},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4911491572856903},{"id":"https://openalex.org/C203635412","wikidata":"https://www.wikidata.org/wiki/Q17007432","display_name":"Compartment (ship)","level":2,"score":0.4668726623058319},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.37146836519241333},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3256290555000305},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.260431706905365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20270892977714539},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12855303287506104},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11511921882629395},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.10024100542068481},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C111368507","wikidata":"https://www.wikidata.org/wiki/Q43518","display_name":"Oceanography","level":1,"score":0.0},{"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/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"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":"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":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-1-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:17408512","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17408512","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:f44e8818c40749a282ad6e5658486bed","is_oa":false,"landing_page_url":"https://doaj.org/article/f44e8818c40749a282ad6e5658486bed","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Systems Biology, Vol 1, Iss 1, p 5 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1191421","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1839895","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-1-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1516184414.pdf","grobid_xml":"https://content.openalex.org/works/W1516184414.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1573172796","https://openalex.org/W1578104218","https://openalex.org/W1588504519","https://openalex.org/W1597762351","https://openalex.org/W1996529795","https://openalex.org/W2010597490","https://openalex.org/W2034993111","https://openalex.org/W2070587756","https://openalex.org/W2082344308","https://openalex.org/W2096144498","https://openalex.org/W2099039198","https://openalex.org/W2144000913","https://openalex.org/W2147102794","https://openalex.org/W2147714160","https://openalex.org/W2155225393","https://openalex.org/W2155331065"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2374260038","https://openalex.org/W2097410126","https://openalex.org/W2216418212","https://openalex.org/W2020641517","https://openalex.org/W2075919068","https://openalex.org/W2133150343","https://openalex.org/W2160334008","https://openalex.org/W2047632644"],"abstract_inverted_index":{"BACKGROUND:":[0],"One":[1],"central":[2],"goal":[3],"of":[4,12,26,34,40,84,103,111,115,174,185,211,223,240,251,273,285,306,322,329],"computational":[5,93,262],"systems":[6],"biology":[7],"is":[8,64,198,213,265,296],"the":[9,24,31,35,49,56,101,108,128,152,156,168,271,274,280,304],"mathematical":[10],"modelling":[11],"complex":[13],"metabolic":[14,82,104,307],"reaction":[15,162,197],"networks.":[16,105,308],"The":[17,96,238,309],"first":[18],"and":[19,44,52,68,74,135,176,178,193,232,244,290,318,325,338],"most":[20],"time-consuming":[21],"step":[22],"in":[23,30,77,137,145,202],"development":[25],"such":[27],"models":[28],"consists":[29],"stoichiometric":[32],"reconstruction":[33,102],"network,":[36],"i.":[37],"e.":[38],"compilation":[39],"all":[41],"metabolites,":[42],"reactions":[43,86,113,117,125,212,229,243],"transport":[45,246],"processes":[46,222,247],"relevant":[47,126],"to":[48,55,66,79,91,127,167,182,200,217,270,300],"considered":[50,129,169],"network":[51,83,130,170],"their":[53],"assignment":[54],"various":[57],"cellular":[58,206],"compartments.":[59],"Therefore":[60],"an":[61,257],"information":[62,120,173,187,302],"system":[63],"required":[65],"collect":[67],"manage":[69,301],"data":[70],"from":[71,122,164,343],"different":[72,235],"databases":[73],"scientific":[75],"literature":[76],"order":[78],"generate":[80],"a":[81,138,161,183,196,208,297],"biochemical":[85,112,116,124,242],"that":[87],"can":[88,131,147,253,339],"be":[89,132,148,254,340],"subjected":[90],"further":[92,261],"analyses.":[94],"RESULTS:":[95],"computer":[97],"program":[98,310],"METANNOGEN":[99,171,252,264,295],"facilitates":[100],"It":[106,333],"uses":[107],"well-known":[109],"database":[110],"KEGG":[114,146,165],"as":[118,256],"primary":[119],"source":[121],"which":[123],"selected,":[133],"edited":[134],"stored":[136],"separate,":[139],"user-defined":[140],"database.":[141],"Reactions":[142],"not":[143,160,335],"contained":[144],"entered":[149,226],"manually":[150],"into":[151],"system.":[153],"To":[154],"aid":[155],"decision":[157],"whether":[158],"or":[159,316],"selected":[163],"belongs":[166],"contains":[172],"SWISSPROT":[175],"ENSEMBL":[177],"provides":[179],"Web":[180],"links":[181],"number":[184,210],"important":[186],"sources":[188],"like":[189,227],"METACYC,":[190],"BRENDA,":[191],"NIST,":[192],"REACTOME.":[194],"If":[195],"reported":[199],"occur":[201],"more":[203],"than":[204],"one":[205,218],"compartment,":[207],"corresponding":[209],"generated":[214,292],"each":[215],"referring":[216],"specific":[219,287],"compartment.":[220],"Transport":[221],"metabolites":[224],"are":[225],"chemical":[228],"where":[230],"reactants":[231],"products":[233],"have":[234],"compartment":[236],"attributes.":[237],"list":[239],"compartmentalized":[241],"membrane":[245],"compiled":[248],"by":[249],"means":[250],"exported":[255],"SBML":[258,275],"file":[259],"for":[260,303],"analysis.":[263],"highly":[266],"customizable":[267],"with":[268],"respect":[269],"content":[272],"output":[276],"file,":[277],"additional":[278],"data-fields,":[279],"graphical":[281],"input":[282],"form,":[283],"highlighting":[284],"project":[286],"search":[288],"terms":[289],"dynamically":[291],"Web-links.":[293],"CONCLUSION:":[294],"flexible":[298],"tool":[299],"design":[305],"requires":[311],"Java":[312],"Runtime":[313],"Environment":[314],"1.4":[315],"higher":[317],"about":[319,326],"100":[320],"MB":[321,328],"free":[323,330],"RAM":[324],"200":[327],"HD":[331],"space.":[332],"does":[334],"require":[336],"installation":[337],"directly":[341],"Java-webstarted":[342],"http://3d-alignment.eu/metannogen/.":[344]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
