{"id":"https://openalex.org/W2025996793","doi":"https://doi.org/10.1093/nar/gki042","title":"Metagrowth: a new resource for the building of metabolic hypotheses in microbiology","display_name":"Metagrowth: a new resource for the building of metabolic hypotheses in microbiology","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2025996793","doi":"https://doi.org/10.1093/nar/gki042","mag":"2025996793","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608207"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki042","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gki042","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539996","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006518349","display_name":"Hiroyuki Ogata","orcid":"https://orcid.org/0000-0001-6594-377X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4387154720","display_name":"Laboratoire Information G\u00e9nomique et Structurale","ror":"https://ror.org/05v0fms67","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4387154720"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"H. Ogata","raw_affiliation_strings":["Information G\u00e9nomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. Hiroyuki.Ogata@igs.cnrs-mrs.fr","Information G\u00e9nomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France"],"affiliations":[{"raw_affiliation_string":"Information G\u00e9nomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. Hiroyuki.Ogata@igs.cnrs-mrs.fr","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4387154720"]},{"raw_affiliation_string":"Information G\u00e9nomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4387154720"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5006518349"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4387154720"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":3.8588,"has_fulltext":false,"cited_by_count":196,"citation_normalized_percentile":{"value":0.94083109,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"33","issue":"Database issue","first_page":"D321","last_page":"D324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9850999712944031,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9850999712944031,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9754999876022339,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.9139982461929321},{"id":"https://openalex.org/keywords/rickettsia-prowazekii","display_name":"Rickettsia prowazekii","score":0.734337568283081},{"id":"https://openalex.org/keywords/axenic","display_name":"Axenic","score":0.7068173289299011},{"id":"https://openalex.org/keywords/tropheryma-whipplei","display_name":"Tropheryma whipplei","score":0.6370217204093933},{"id":"https://openalex.org/keywords/rickettsia-conorii","display_name":"Rickettsia conorii","score":0.6111503839492798},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.5708848834037781},{"id":"https://openalex.org/keywords/obligate","display_name":"Obligate","score":0.5523098111152649},{"id":"https://openalex.org/keywords/coxiella-burnetii","display_name":"Coxiella burnetii","score":0.493464857339859},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.374392569065094},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2568744122982025},{"id":"https://openalex.org/keywords/rickettsia","display_name":"Rickettsia","score":0.2500843405723572},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22832700610160828},{"id":"https://openalex.org/keywords/rickettsiosis","display_name":"Rickettsiosis","score":0.12327146530151367},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08834466338157654}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9139982461929321},{"id":"https://openalex.org/C2780329011","wikidata":"https://www.wikidata.org/wiki/Q952862","display_name":"Rickettsia prowazekii","level":4,"score":0.734337568283081},{"id":"https://openalex.org/C2778265057","wikidata":"https://www.wikidata.org/wiki/Q537299","display_name":"Axenic","level":3,"score":0.7068173289299011},{"id":"https://openalex.org/C2780647328","wikidata":"https://www.wikidata.org/wiki/Q2703876","display_name":"Tropheryma whipplei","level":4,"score":0.6370217204093933},{"id":"https://openalex.org/C2777212292","wikidata":"https://www.wikidata.org/wiki/Q2708461","display_name":"Rickettsia conorii","level":5,"score":0.6111503839492798},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.5708848834037781},{"id":"https://openalex.org/C24990904","wikidata":"https://www.wikidata.org/wiki/Q7075144","display_name":"Obligate","level":2,"score":0.5523098111152649},{"id":"https://openalex.org/C2776607032","wikidata":"https://www.wikidata.org/wiki/Q133971","display_name":"Coxiella burnetii","level":2,"score":0.493464857339859},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.374392569065094},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2568744122982025},{"id":"https://openalex.org/C2780414542","wikidata":"https://www.wikidata.org/wiki/Q627992","display_name":"Rickettsia","level":3,"score":0.2500843405723572},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22832700610160828},{"id":"https://openalex.org/C2778434417","wikidata":"https://www.wikidata.org/wiki/Q646664","display_name":"Rickettsiosis","level":4,"score":0.12327146530151367},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08834466338157654},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C2777440137","wikidata":"https://www.wikidata.org/wiki/Q653078","display_name":"Whipple's disease","level":3,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003470","descriptor_name":"Culture Media","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":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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki042","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gki042","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608207","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.109.1400","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.109.1400","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/reprint/33/suppl_1/D321.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:163501","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC539996","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:539996","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539996","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:539996","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539996","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W31270631","https://openalex.org/W1569904835","https://openalex.org/W1598617551","https://openalex.org/W1911163705","https://openalex.org/W1911635991","https://openalex.org/W1963584517","https://openalex.org/W1999536502","https://openalex.org/W2025663053","https://openalex.org/W2036274081","https://openalex.org/W2037704659","https://openalex.org/W2047228180","https://openalex.org/W2053419354","https://openalex.org/W2053673511","https://openalex.org/W2062015456","https://openalex.org/W2100641815","https://openalex.org/W2103708054","https://openalex.org/W2109336572","https://openalex.org/W2111973517","https://openalex.org/W2113221321","https://openalex.org/W2126161931","https://openalex.org/W2128276963","https://openalex.org/W2142237411","https://openalex.org/W2158784643","https://openalex.org/W2164217177","https://openalex.org/W2169810918","https://openalex.org/W2336422260","https://openalex.org/W4231551535"],"related_works":["https://openalex.org/W4213248661","https://openalex.org/W2126161931","https://openalex.org/W2290715207","https://openalex.org/W2153232310","https://openalex.org/W2149169181","https://openalex.org/W4254437992","https://openalex.org/W4247650710","https://openalex.org/W4254066994","https://openalex.org/W2268144514","https://openalex.org/W2025996793"],"abstract_inverted_index":{"Metagrowth":[0,92,106],"is":[1,107],"a":[2],"new":[3,97],"type":[4],"of":[5,14,17,32,38,60,91],"knowledge":[6],"base":[7],"developed":[8],"to":[9,29,95],"guide":[10],"the":[11,30,33],"experimental":[12],"studies":[13],"culture":[15,99],"conditions":[16],"obligate":[18,39],"parasitic":[19],"bacteria.":[20,105],"We":[21],"have":[22],"gathered":[23],"biological":[24],"evidences":[25,62],"giving":[26],"possible":[27],"clues":[28],"development":[31],"axenic":[34,98],"(i.e.":[35],"'cell-free')":[36],"growth":[37],"parasites":[40],"from":[41,67],"various":[42],"sources":[43],"including":[44],"published":[45],"literature,":[46],"genomic":[47],"sequence":[48],"information,":[49],"metabolic":[50],"databases":[51],"and":[52,63,85],"transporter":[53],"databases.":[54],"The":[55,88],"database":[56],"entries":[57,71],"are":[58,72],"composed":[59],"those":[61,104],"specific":[64],"hypotheses":[65],"derived":[66],"them.":[68],"Currently,":[69],"200":[70],"available":[73],"for":[74,103],"Rickettsia":[75,77],"prowazekii,":[76],"conorii,":[78],"Tropheryma":[79],"whipplei,":[80],"Treponema":[81],"pallidum,":[82],"Mycobacterium":[83],"tuberculosis":[84],"Coxiella":[86],"burnetii.":[87],"web":[89],"interface":[90],"helps":[93],"users":[94],"design":[96],"media":[100],"eventually":[101],"suitable":[102],"accessible":[108],"at":[109],"http://igs-server.cnrs-mrs.fr/axenic/.":[110]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":12}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
