{"id":"https://openalex.org/W4416865968","doi":"https://doi.org/10.1093/database/baag027","title":"Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions","display_name":"Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions","publication_year":2025,"publication_date":"2025-12-01","ids":{"openalex":"https://openalex.org/W4416865968","doi":"https://doi.org/10.1093/database/baag027","pmid":"https://pubmed.ncbi.nlm.nih.gov/41377518"},"language":"en","primary_location":{"id":"doi:10.1093/database/baag027","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baag027","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baag027","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Kaelyn Long","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I4210135674","display_name":"Institute of Population and Public Health","ror":"https://ror.org/04dh0w640","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210135674"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Kaelyn Long","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","City University of New York School of Public Health and Health Policy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I174216632"]},{"raw_affiliation_string":"Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I4210135674"]},{"raw_affiliation_string":"City University of New York School of Public Health and Health Policy","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098535482","display_name":"Kai Gravel-Pucillo","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I4210135674","display_name":"Institute of Population and Public Health","ror":"https://ror.org/04dh0w640","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210135674"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Kai Gravel-Pucillo","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","City University of New York School of Public Health and Health Policy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I174216632"]},{"raw_affiliation_string":"Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I4210135674"]},{"raw_affiliation_string":"City University of New York School of Public Health and Health Policy","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052283192","display_name":"Levi Waldron","orcid":"https://orcid.org/0000-0003-2725-0694"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I4210135674","display_name":"Institute of Population and Public Health","ror":"https://ror.org/04dh0w640","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210135674"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Levi Waldron","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","City University of New York School of Public Health and Health Policy"],"raw_orcid":"https://orcid.org/0000-0003-2725-0694","affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I174216632"]},{"raw_affiliation_string":"Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I4210135674"]},{"raw_affiliation_string":"City University of New York School of Public Health and Health Policy","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005450827","display_name":"Sean Davis","orcid":"https://orcid.org/0000-0002-8991-6458"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean Davis","raw_affiliation_strings":["Departments of Biomedical Informatics and Medicine, University of Colorado Anschutz School of Medicine, Denver, CO","University of Colorado Anschutz School of Medicine"],"raw_orcid":"https://orcid.org/0000-0002-8991-6458","affiliations":[{"raw_affiliation_string":"Departments of Biomedical Informatics and Medicine, University of Colorado Anschutz School of Medicine, Denver, CO","institution_ids":["https://openalex.org/I51713134"]},{"raw_affiliation_string":"University of Colorado Anschutz School of Medicine","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019675326","display_name":"Sehyun Oh","orcid":"https://orcid.org/0000-0002-9490-3061"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I4210135674","display_name":"Institute of Population and Public Health","ror":"https://ror.org/04dh0w640","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210135674"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Sehyun Oh","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","City University of New York School of Public Health and Health Policy"],"raw_orcid":"https://orcid.org/0000-0002-9490-3061","affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I174216632"]},{"raw_affiliation_string":"Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY","institution_ids":["https://openalex.org/I4210135674"]},{"raw_affiliation_string":"City University of New York School of Public Health and Health Policy","institution_ids":["https://openalex.org/I174216632"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5019675326"],"corresponding_institution_ids":["https://openalex.org/I174216632","https://openalex.org/I4210135674"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28792864,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2026","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8307999968528748,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8307999968528748,"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/T11937","display_name":"Research Data Management Practices","score":0.06369999796152115,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.020099999383091927,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.9114999771118164},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.7265999913215637},{"id":"https://openalex.org/keywords/harmonization","display_name":"Harmonization","score":0.6122000217437744},{"id":"https://openalex.org/keywords/geospatial-metadata","display_name":"Geospatial metadata","score":0.5848000049591064},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4869999885559082},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.4375999867916107},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.39980000257492065},{"id":"https://openalex.org/keywords/digital-curation","display_name":"Digital curation","score":0.38190001249313354}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.9114999771118164},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7265999913215637},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6324999928474426},{"id":"https://openalex.org/C2779962950","wikidata":"https://www.wikidata.org/wiki/Q5659376","display_name":"Harmonization","level":2,"score":0.6122000217437744},{"id":"https://openalex.org/C193150823","wikidata":"https://www.wikidata.org/wiki/Q1477538","display_name":"Geospatial metadata","level":5,"score":0.5848000049591064},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4893999993801117},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4869999885559082},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4514999985694885},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.445499986410141},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.4375999867916107},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.39980000257492065},{"id":"https://openalex.org/C2775953033","wikidata":"https://www.wikidata.org/wiki/Q5276060","display_name":"Digital curation","level":2,"score":0.38190001249313354},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.3815000057220459},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.38119998574256897},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.35040000081062317},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.3183000087738037},{"id":"https://openalex.org/C158746014","wikidata":"https://www.wikidata.org/wiki/Q17085509","display_name":"Data management plan","level":3,"score":0.3095000088214874},{"id":"https://openalex.org/C30872290","wikidata":"https://www.wikidata.org/wiki/Q1172389","display_name":"Data element","level":3,"score":0.27160000801086426},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.27140000462532043},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.2669999897480011},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.258899986743927}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/database/baag027","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baag027","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"doi:10.1101/2025.11.26.689816","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.11.26.689816","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/12/01/2025.11.26.689816.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41377518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41377518","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":"bioRxiv : the preprint server for biology","raw_type":null},{"id":"pmid:42172141","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42172141","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12687785","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12687785/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13196698","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13196698/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baag027","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baag027","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5130173051","display_name":null,"funder_award_id":"U24CA289073","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7778963292","display_name":null,"funder_award_id":"3U24CA180996-10S1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1482134990","https://openalex.org/W1544923801","https://openalex.org/W2129687578","https://openalex.org/W2149441684","https://openalex.org/W2568035278","https://openalex.org/W2924366642","https://openalex.org/W2939999412","https://openalex.org/W2943485757","https://openalex.org/W2950750198","https://openalex.org/W2952200190","https://openalex.org/W2970771711","https://openalex.org/W3024722698","https://openalex.org/W3093838933","https://openalex.org/W3129379232","https://openalex.org/W3139601120","https://openalex.org/W3205594709","https://openalex.org/W3210129127","https://openalex.org/W4283394500","https://openalex.org/W4298139967","https://openalex.org/W4307510906","https://openalex.org/W4386397671","https://openalex.org/W4386438154","https://openalex.org/W4386443935","https://openalex.org/W4387729351","https://openalex.org/W4392083189","https://openalex.org/W4406599488","https://openalex.org/W4410105840"],"related_works":[],"abstract_inverted_index":{"Public":[0],"omics":[1,38,66,187],"repositories":[2],"contain":[3],"vast":[4],"amounts":[5],"of":[6,36,54,108,178],"valuable":[7],"data,":[8],"but":[9],"their":[10],"metadata":[11,31,116,143,182],"suffers":[12],"from":[13,63],"extreme":[14],"heterogeneity,":[15],"unstandardized":[16],"terminologies,":[17,122],"and":[18,26,52,60,80,104,127,138,157,174],"quality":[19,117],"issues":[20],"that":[21],"severely":[22],"limit":[23],"data":[24,39],"reusability":[25],"cross-study":[27,158],"integration.":[28],"While":[29],"prospective":[30],"standards":[32],"exist,":[33],"the":[34,106,135,150,176],"majority":[35],"published":[37],"remain":[40],"in":[41,71,180],"non-standardized":[42],"formats":[43],"requiring":[44],"retrospective":[45,181],"harmonization.":[46,144],"We":[47,133],"performed":[48],"comprehensive":[49],"manual":[50],"curation":[51,112,172],"harmonization":[53],"metadata,":[55,147],"such":[56],"as":[57],"participant":[58],"characteristics":[59],"study":[61],"conditions,":[62],"212":[64],"027":[65],"samples":[67],"across":[68,131],"468":[69],"studies":[70],"two":[72],"repositories:":[73],"curatedMetagenomicData":[74],"(93":[75],"studies,":[76,83],"22":[77],"588":[78],"samples)":[79],"cBioPortal":[81],"(375":[82],"189":[84],"438":[85],"samples).":[86],"Through":[87],"systematic":[88],"ontology":[89],"mapping,":[90],"we":[91],"consolidated":[92],"redundant,":[93],"dispersed":[94],"information":[95,130],"into":[96],"far":[97],"fewer":[98],"harmonized":[99,146],"columns,":[100],"reduced":[101],"unique":[102],"values,":[103,124],"increased":[105],"completeness":[107],"major":[109],"attributes.":[110,132],"This":[111],"process":[113],"revealed":[114],"common":[115],"issues,":[118],"including":[119],"typos,":[120],"inconsistent":[121],"misplaced":[123],"conflicting":[125],"annotations,":[126],"inappropriately":[128],"merged":[129],"document":[134],"challenges,":[136],"decisions,":[137],"solutions":[139],"during":[140],"this":[141],"large-scale":[142],"The":[145],"accessible":[148],"through":[149],"OmicsMLRepoR":[151],"Bioconductor":[152],"package,":[153],"enables":[154],"repository-wide":[155],"queries":[156],"analyses":[159],"previously":[160],"challenging":[161],"with":[162],"heterogeneous":[163],"metadata.":[164],"Our":[165],"experience":[166],"provides":[167],"practical":[168],"guidance":[169],"for":[170,184],"similar":[171],"efforts":[173],"demonstrates":[175],"value":[177],"investing":[179],"improvement":[183],"existing":[185],"public":[186],"resources.":[188]},"counts_by_year":[],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-12-01T00:00:00"}
