{"id":"https://openalex.org/W2890947828","doi":"https://doi.org/10.1093/bioinformatics/bty719","title":"<i>meta</i>Graphite\u2013a new layer of pathway annotation to get metabolite networks","display_name":"<i>meta</i>Graphite\u2013a new layer of pathway annotation to get metabolite networks","publication_year":2018,"publication_date":"2018-09-03","ids":{"openalex":"https://openalex.org/W2890947828","doi":"https://doi.org/10.1093/bioinformatics/bty719","mag":"2890947828","pmid":"https://pubmed.ncbi.nlm.nih.gov/30184047"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty719","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty719","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5070887609","display_name":"Gabriele Sales","orcid":"https://orcid.org/0000-0003-2078-5661"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Gabriele Sales","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091476817","display_name":"Enrica Calura","orcid":"https://orcid.org/0000-0001-8463-2432"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enrica Calura","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082717632","display_name":"Chiara Romualdi","orcid":"https://orcid.org/0000-0003-4792-9047"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Chiara Romualdi","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"raw_orcid":"https://orcid.org/0000-0003-4792-9047","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070887609"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4848,"has_fulltext":false,"cited_by_count":42,"citation_normalized_percentile":{"value":0.82587733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"35","issue":"7","first_page":"1258","last_page":"1260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.46059998869895935,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.46059998869895935,"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":0.09179999679327011,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.08209999650716782,"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/annotation","display_name":"Annotation","score":0.8134379386901855},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.7013460397720337},{"id":"https://openalex.org/keywords/layer","display_name":"Layer (electronics)","score":0.6718539595603943},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6011239290237427},{"id":"https://openalex.org/keywords/graphite","display_name":"Graphite","score":0.4198923110961914},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39281806349754333},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2556725740432739},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22096484899520874},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2150726020336151},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.1258387565612793},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1098598837852478},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.10510039329528809}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8134379386901855},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.7013460397720337},{"id":"https://openalex.org/C2779227376","wikidata":"https://www.wikidata.org/wiki/Q6505497","display_name":"Layer (electronics)","level":2,"score":0.6718539595603943},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6011239290237427},{"id":"https://openalex.org/C2779698641","wikidata":"https://www.wikidata.org/wiki/Q5309","display_name":"Graphite","level":2,"score":0.4198923110961914},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39281806349754333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2556725740432739},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22096484899520874},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2150726020336151},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.1258387565612793},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1098598837852478},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.10510039329528809},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"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":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty719","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty719","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30184047","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30184047","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:www.research.unipd.it:11577/3279122","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/3279122","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5143347771","display_name":null,"funder_award_id":"IG: 17185","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2044055595","https://openalex.org/W2106248311","https://openalex.org/W2109912704","https://openalex.org/W2110687686","https://openalex.org/W2129702158","https://openalex.org/W2154972152","https://openalex.org/W2157646380","https://openalex.org/W2163410580","https://openalex.org/W2165040702","https://openalex.org/W2295182096","https://openalex.org/W2567219477"],"related_works":["https://openalex.org/W2521903434","https://openalex.org/W1753739957","https://openalex.org/W2361861616","https://openalex.org/W2085913165","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2011282322","https://openalex.org/W2392921965","https://openalex.org/W2024044986"],"abstract_inverted_index":{"MOTIVATION:":[0],"Metabolomics":[1],"is":[2,145],"an":[3],"emerging":[4],"'omics'":[5],"science":[6],"involving":[7],"the":[8,24,33,63,68,103],"characterization":[9],"of":[10,29,35,39,59,65,72,82],"metabolites":[11],"and":[12,27,44,70,95,114],"metabolism":[13],"in":[14,106],"biological":[15],"systems.":[16],"Few":[17],"bioinformatic":[18],"tools":[19],"have":[20,77],"been":[21],"developed":[22],"for":[23],"visualization,":[25],"exploration":[26],"analysis":[28],"metabolomic":[30,73],"data":[31,152],"within":[32,92],"context":[34],"metabolic":[36],"pathways:":[37],"some":[38],"them":[40],"became":[41],"rapidly":[42],"obsolete":[43],"are":[45,50,153],"no":[46],"longer":[47],"supported,":[48],"others":[49],"based":[51],"on":[52,122,147],"a":[53,79],"single":[54],"database.":[55],"A":[56],"systematic":[57],"collection":[58],"existing":[60],"annotations":[61],"has":[62],"potential":[64],"considerably":[66],"boosting":[67],"investigation":[69],"contextualization":[71],"measurements.":[74],"RESULTS:":[75],"We":[76],"released":[78],"major":[80,108],"update":[81],"our":[83],"Bioconductor":[84],"package":[85,101],"graphite":[86,142],"which":[87],"explicitly":[88],"tracks":[89],"small":[90],"molecules":[91],"pathway":[93],"topologies":[94],"their":[96],"interactions":[97],"with":[98],"proteins.":[99],"The":[100,140],"gathers":[102],"information":[104],"stored":[105],"eight":[107],"databases,":[109],"oriented":[110],"both":[111],"at":[112,115,155],"genes":[113],"metabolites,":[116],"across":[117],"14":[118],"different":[119],"species.":[120],"Depending":[121],"user":[123],"preferences,":[124],"all":[125],"pathways":[126],"can":[127],"be":[128],"retrieved":[129],"as":[130],"gene-only,":[131],"gene":[132],"metabolite":[133],"or":[134],"metabolite-only":[135],"networks.":[136],"AVAILABILITY":[137],"AND":[138],"IMPLEMENTATION:":[139],"new":[141],"version":[143],"(1.24)":[144],"available":[146,154],"Bioconductor.":[148],"SUPPLEMENTARY":[149],"INFORMATION:":[150],"Supplementary":[151],"Bioinformatics":[156],"online.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2018-09-27T00:00:00"}
