{"id":"https://openalex.org/W3194785116","doi":"https://doi.org/10.1093/bioinformatics/btab583","title":"metID: an R package for automatable compound annotation for LC\u2212MS-based data","display_name":"metID: an R package for automatable compound annotation for LC\u2212MS-based data","publication_year":2021,"publication_date":"2021-08-25","ids":{"openalex":"https://openalex.org/W3194785116","doi":"https://doi.org/10.1093/bioinformatics/btab583","mag":"3194785116","pmid":"https://pubmed.ncbi.nlm.nih.gov/34432001"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/568/42039752/btab583.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/568/42039752/btab583.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057437035","display_name":"Xiaotao Shen","orcid":"https://orcid.org/0000-0002-9608-9964"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaotao Shen","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":"https://orcid.org/0000-0002-9608-9964","affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033836561","display_name":"Si Wu","orcid":"https://orcid.org/0000-0001-8050-7167"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Si Wu","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100426907","display_name":"Liang Liang","orcid":"https://orcid.org/0000-0001-5718-0717"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Liang","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083476935","display_name":"Songjie Chen","orcid":"https://orcid.org/0000-0002-9568-5705"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Songjie Chen","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062579994","display_name":"K\u00e9vin Contrepois","orcid":"https://orcid.org/0000-0001-9678-5161"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K\u00e9vin Contrepois","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012172517","display_name":"Zheng\u2010Jiang Zhu","orcid":"https://orcid.org/0000-0002-3272-3567"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112946","display_name":"Shanghai Institute of Organic Chemistry","ror":"https://ror.org/01y3hvq34","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zheng-Jiang Zhu","raw_affiliation_strings":["Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024120181","display_name":"M Snyder","orcid":"https://orcid.org/0000-0003-0784-7987"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael Snyder","raw_affiliation_strings":["Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5012172517","https://openalex.org/A5024120181"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112946","https://openalex.org/I97018004"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":{"value":3478,"currency":"USD","value_usd":3478},"fwci":2.0886,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.88209322,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":100},"biblio":{"volume":"38","issue":"2","first_page":"568","last_page":"569"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9587000012397766,"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":0.9587000012397766,"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/T14393","display_name":"Health, Environment, Cognitive Aging","score":0.022099999710917473,"subfield":{"id":"https://openalex.org/subfields/2307","display_name":"Health, Toxicology and Mutagenesis"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.002899999963119626,"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":0.9155142903327942},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7544868588447571},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5766925811767578},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5758106708526611},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49598798155784607},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4945361316204071},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4389409124851227},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.35465437173843384},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1704501211643219},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13468238711357117}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.9155142903327942},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7544868588447571},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5766925811767578},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5758106708526611},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49598798155784607},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4945361316204071},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4389409124851227},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.35465437173843384},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1704501211643219},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13468238711357117}],"mesh":[{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","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":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":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","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":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/568/42039752/btab583.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34432001","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34432001","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8722759","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722759","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/568/42039752/btab583.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3194785116.pdf","grobid_xml":"https://content.openalex.org/works/W3194785116.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1543068333","https://openalex.org/W1611854178","https://openalex.org/W2295182096","https://openalex.org/W2888303476","https://openalex.org/W2951891306","https://openalex.org/W3029490310","https://openalex.org/W3092328575","https://openalex.org/W6784322881"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"SUMMARY:":[0],"Accurate":[1],"and":[2,16,40,43,47,65,74,93,98],"efficient":[3],"compound":[4,67,86],"annotation":[5,87],"is":[6,70],"a":[7,71,99],"long-standing":[8],"challenge":[9],"for":[10,63],"LC-MS-based":[11],"data":[12,114],"(e.g.":[13],"untargeted":[14],"metabolomics":[15],"exposomics).":[17],"Substantial":[18],"efforts":[19],"have":[20],"been":[21],"devoted":[22],"to":[23,89],"overcoming":[24],"this":[25],"obstacle,":[26],"whereas":[27],"current":[28],"tools":[29],"are":[30,44,102,115],"limited":[31],"by":[32],"the":[33,85],"sources":[34],"of":[35],"spectral":[36],"information":[37,58],"used":[38],"(in-house":[39],"public":[41],"databases)":[42],"not":[45],"automated":[46],"streamlined.":[48],"Therefore,":[49],"we":[50],"developed":[51],"metID,":[52],"an":[53],"R":[54],"package":[55],"that":[56,77],"combines":[57],"from":[59],"all":[60,82],"major":[61],"databases":[62],"comprehensive":[64],"streamlined":[66],"annotation.":[68],"metID":[69],"flexible,":[72],"simple":[73],"powerful":[75],"tool":[76],"can":[78],"be":[79,90],"installed":[80],"on":[81],"platforms,":[83],"allowing":[84],"process":[88],"fully":[91],"automatic":[92],"reproducible.":[94],"A":[95],"detailed":[96],"tutorial":[97],"case":[100],"study":[101],"provided":[103],"in":[104],"Supplementary":[105,113],"Materials.":[106],"AVAILABILITY":[107],"AND":[108],"IMPLEMENTATION:":[109],"https://jaspershen.github.io/metID.":[110],"SUPPLEMENTARY":[111],"INFORMATION:":[112],"available":[116],"at":[117],"Bioinformatics":[118],"online.":[119]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}