{"id":"https://openalex.org/W2023809341","doi":"https://doi.org/10.1186/1758-2946-2-s1-p39","title":"Expanding and understanding metabolite space","display_name":"Expanding and understanding metabolite space","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2023809341","doi":"https://doi.org/10.1186/1758-2946-2-s1-p39","mag":"2023809341"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-2-s1-p39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p39","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P39","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P39","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046564913","display_name":"Julio E. Peironcely","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164629","display_name":"Pension Fund for Care and Well-Being","ror":"https://ror.org/05a8epj20","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210164629"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Julio E Peironcely","raw_affiliation_strings":["TNO, Quality of Life, Utrechtseweg 48, Zeist, The Netherlands","TNO, Quality of Life, Zeist, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TNO, Quality of Life, Utrechtseweg 48, Zeist, The Netherlands","institution_ids":["https://openalex.org/I4210164629"]},{"raw_affiliation_string":"TNO, Quality of Life, Zeist, The Netherlands","institution_ids":["https://openalex.org/I4210164629"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026643759","display_name":"Andreas Bender","orcid":"https://orcid.org/0000-0002-6683-7546"},"institutions":[{"id":"https://openalex.org/I4210101928","display_name":"Netherlands Metabolomics Centre","ror":"https://ror.org/00zh5wn98","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210101928"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Andreas Bender","raw_affiliation_strings":["Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]},{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043068354","display_name":"Miguel Rojas\u2010Chert\u00f3","orcid":"https://orcid.org/0000-0002-4659-1446"},"institutions":[{"id":"https://openalex.org/I4210101928","display_name":"Netherlands Metabolomics Centre","ror":"https://ror.org/00zh5wn98","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210101928"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"M Rojas-Chert\u00f3","raw_affiliation_strings":["Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]},{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011648806","display_name":"Theo Reijmers","orcid":null},"institutions":[{"id":"https://openalex.org/I4210101928","display_name":"Netherlands Metabolomics Centre","ror":"https://ror.org/00zh5wn98","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210101928"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"T Reijmers","raw_affiliation_strings":["Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]},{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044095101","display_name":"L Coulier","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164629","display_name":"Pension Fund for Care and Well-Being","ror":"https://ror.org/05a8epj20","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210164629"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"L Coulier","raw_affiliation_strings":["TNO, Quality of Life, Utrechtseweg 48, Zeist, The Netherlands","TNO, Quality of Life, Zeist, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TNO, Quality of Life, Utrechtseweg 48, Zeist, The Netherlands","institution_ids":["https://openalex.org/I4210164629"]},{"raw_affiliation_string":"TNO, Quality of Life, Zeist, The Netherlands","institution_ids":["https://openalex.org/I4210164629"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076255429","display_name":"Thomas Hankemeier","orcid":"https://orcid.org/0000-0001-7871-2073"},"institutions":[{"id":"https://openalex.org/I4210101928","display_name":"Netherlands Metabolomics Centre","ror":"https://ror.org/00zh5wn98","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210101928"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"T Hankemeier","raw_affiliation_strings":["Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Einsteinweg 55, 2333 CC, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]},{"raw_affiliation_string":"Netherlands Metabolomics Centre, University of Leiden, LACDR, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210101928"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1078464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9993000030517578,"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":0.9976000189781189,"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":0.6256581544876099},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4762309193611145},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4658986032009125},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.4531335234642029},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20435011386871338}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6256581544876099},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4762309193611145},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4658986032009125},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.4531335234642029},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20435011386871338},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-2-s1-p39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p39","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P39","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:93659b3ed63e4d2b8bb9645d6510caa2","is_oa":false,"landing_page_url":"https://doaj.org/article/93659b3ed63e4d2b8bb9645d6510caa2","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":"Journal of Cheminformatics, Vol 2, Iss Suppl 1, p P39 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2867173","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2867173","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-2-s1-p39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p39","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P39","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2023809341.pdf","grobid_xml":"https://content.openalex.org/works/W2023809341.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1991286793","https://openalex.org/W2060531713","https://openalex.org/W2165681080"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2521903434","https://openalex.org/W1753739957","https://openalex.org/W2085913165","https://openalex.org/W2011282322","https://openalex.org/W2024044986","https://openalex.org/W2005550771","https://openalex.org/W323632276","https://openalex.org/W2418404479"],"abstract_inverted_index":{"In":[0,84],"metabolomics":[1],"the":[2,27,37,71,88,95,134,160,210,218,223,254,264,272,279],"identity":[3],"and":[4,47,78,120,235,275,284],"role":[5],"of":[6,26,29,41,136,213,281],"low":[7],"mass":[8],"molecules":[9,55,170,193],"called":[10,64],"metabolites":[11,42,108,197],"that":[12,59,113,131,171,257],"are":[13,19,194,205,258],"produced":[14],"in":[15,44,48,116,155,178,181,222],"cell":[16],"metabolic":[17],"processes":[18],"investigated.":[20],"These":[21,54],"make":[22],"them":[23],"valuable":[24],"indicators":[25],"phenotype":[28],"a":[30,103,282],"biological":[31],"system.":[32],"The":[33,239],"'Metabolite":[34,89,153],"Space'":[35,154],"is":[36,102,144,243],"total":[38],"chemical":[39,237],"universe":[40,212],"present":[43,177,221],"all":[45,49,263],"compartments":[46],"states":[50],"from":[51,94,195,253],"any":[52],"organism.":[53],"exhibit":[56],"common":[57],"features":[58,173],"form":[60],"what":[61],"can":[62],"be":[63,129],"'metabolite":[65,148],"likeness'.":[66],"Here,":[67],"we":[68,91,158,267],"focus":[69],"on":[70],"human":[72,107,118],"metabolite":[73,225,241,273],"space,":[74,139,274],"including":[75],"both":[76],"endogenous":[77],"exogenous":[79],"(such":[80],"as":[81,250],"drug)":[82],"metabolites.":[83,214,260],"order":[85,150],"to":[86,128,146,151,167,175,208,245,269,277,285],"analyze":[87],"Space',":[90],"collected":[92],"data":[93],"Human":[96],"Metabolome":[97],"Database":[98],"(HMDB)":[99],"[1]":[100],"which":[101],"comprehensive":[104],"database":[105],"for":[106],"containing":[109],"over":[110],"7000":[111],"compounds":[112,127],"were":[114],"identified":[115,130],"several":[117],"biofluids":[119],"tissues.":[121],"As":[122],"there":[123],"still":[124,184],"remain":[125],"many":[126],"lay":[132],"outside":[133],"boundaries":[135],"this":[137,141],"known":[138,211],"exploring":[140],"unknown":[142],"region":[143],"crucial":[145],"evaluate":[147],"likeness'.\r\n\r\nIn":[149],"expand":[152,209],"our":[156],"approach":[157],"employed":[159],"Retrosynthetic":[161],"Combinatorial":[162],"Analysis":[163],"Procedure":[164],"(RECAP)":[165],"[2]":[166],"generate":[168],"new":[169,192,219,240],"possess":[172],"similar":[174],"those":[176,251],"metabolites,":[179],"however":[180],"other":[182,236,246],"(but":[183],"likely)":[185],"rearrangements.":[186],"We":[187,215],"studied":[188,217],"how":[189],"discernible":[190],"these":[191],"real":[196],"and,":[198],"hence,":[199],"whether":[200],"synthetic":[201],"organic":[202],"chemistry":[203,220],"reactions":[204],"indeed":[206],"able":[207],"further":[216],"expanded":[224],"space":[226,242],"by":[227],"looking":[228],"at":[229],"Murcko":[230],"assemblies":[231],"[3],":[232],"ring":[233],"systems":[234],"properties.":[238,289],"compared":[244],"small":[247],"molecules,":[248],"such":[249],"obtained":[252],"ZINC":[255],"database,":[256],"not":[259],"By":[261],"combining":[262],"above":[265],"analyses":[266],"expect":[268],"characterize":[270],"better":[271],"furthermore,":[276],"predict":[278],"metabolite-likeness":[280],"molecule":[283],"understand":[286],"its":[287],"immanent":[288]},"counts_by_year":[],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}