{"id":"https://openalex.org/W2914132662","doi":"https://doi.org/10.1093/database/bay145","title":"Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis","display_name":"Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis","publication_year":2018,"publication_date":"2018-12-29","ids":{"openalex":"https://openalex.org/W2914132662","doi":"https://doi.org/10.1093/database/bay145","mag":"2914132662","pmid":"https://pubmed.ncbi.nlm.nih.gov/30649296"},"language":"en","primary_location":{"id":"doi:10.1093/database/bay145","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay145","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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/bay145","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068592358","display_name":"Guocai Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guocai Chen","raw_affiliation_strings":["School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101617456","display_name":"Juan Camilo Ram\u00edrez","orcid":"https://orcid.org/0000-0003-0045-4144"},"institutions":[{"id":"https://openalex.org/I4210101155","display_name":"Universidad Antonio Nari\u00f1o","ror":"https://ror.org/014hpw227","country_code":"CO","type":"education","lineage":["https://openalex.org/I4210101155"]}],"countries":["CO"],"is_corresponding":false,"raw_author_name":"Juan Camilo Ram\u00edrez","raw_affiliation_strings":["Universidad Antonio Nari\u00f1o, Bogot\u00e1, Colombia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidad Antonio Nari\u00f1o, Bogot\u00e1, Colombia","institution_ids":["https://openalex.org/I4210101155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075755687","display_name":"Nan Deng","orcid":"https://orcid.org/0000-0002-9228-4519"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nan Deng","raw_affiliation_strings":["Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100686073","display_name":"Xing Qiu","orcid":"https://orcid.org/0000-0002-2330-3544"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xing Qiu","raw_affiliation_strings":["Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031127583","display_name":"Canglin Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Canglin Wu","raw_affiliation_strings":["TechWave International. Inc., Houston, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TechWave International. Inc., Houston, Texas, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091809743","display_name":"W. Jim Zheng","orcid":"https://orcid.org/0000-0001-7411-6047"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"W Jim Zheng","raw_affiliation_strings":["School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045155778","display_name":"Hulin Wu","orcid":"https://orcid.org/0000-0002-5809-5407"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hulin Wu","raw_affiliation_strings":["Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA","institution_ids":["https://openalex.org/I919571938"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5045155778","https://openalex.org/A5091809743"],"corresponding_institution_ids":["https://openalex.org/I919571938"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.117,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.7832025,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"2019","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":0.9976000189781189,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9959999918937683,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/metadata","display_name":"Metadata","score":0.8984178900718689},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8192309141159058},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.6037563681602478},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6026644110679626},{"id":"https://openalex.org/keywords/restructuring","display_name":"Restructuring","score":0.5631482601165771},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4792768657207489},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.47314393520355225},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3669295310974121},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32955417037010193}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8984178900718689},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8192309141159058},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.6037563681602478},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6026644110679626},{"id":"https://openalex.org/C45237549","wikidata":"https://www.wikidata.org/wiki/Q1376796","display_name":"Restructuring","level":2,"score":0.5631482601165771},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4792768657207489},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.47314393520355225},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3669295310974121},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32955417037010193},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/bay145","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay145","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":"pmid:30649296","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30649296","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:europepmc.org:5324780","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6333964","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6333964","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6333964","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/bay145","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay145","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/G130880267","display_name":null,"funder_award_id":"7R01AI087135","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2865024217","display_name":null,"funder_award_id":"HHSN272201700019C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3120388081","display_name":null,"funder_award_id":"RP170668","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1550258693","https://openalex.org/W1692319794","https://openalex.org/W1984582532","https://openalex.org/W1986129954","https://openalex.org/W2018462761","https://openalex.org/W2020541351","https://openalex.org/W2048677619","https://openalex.org/W2064266162","https://openalex.org/W2082180192","https://openalex.org/W2094678200","https://openalex.org/W2100239923","https://openalex.org/W2101696428","https://openalex.org/W2118258530","https://openalex.org/W2122402213","https://openalex.org/W2124045889","https://openalex.org/W2133559194","https://openalex.org/W2134319420","https://openalex.org/W2159092541","https://openalex.org/W2160697532","https://openalex.org/W2168546553","https://openalex.org/W2513574994","https://openalex.org/W2519672349","https://openalex.org/W2572898255","https://openalex.org/W2624746686","https://openalex.org/W2734646376","https://openalex.org/W2781236732","https://openalex.org/W2888598589","https://openalex.org/W2889976358","https://openalex.org/W2951403620","https://openalex.org/W6632766574","https://openalex.org/W6637329107","https://openalex.org/W6726286638","https://openalex.org/W6726830853","https://openalex.org/W6754457164"],"related_works":["https://openalex.org/W2376397586","https://openalex.org/W2377702023","https://openalex.org/W76424774","https://openalex.org/W2376263261","https://openalex.org/W1974318783","https://openalex.org/W2029119203","https://openalex.org/W1506264906","https://openalex.org/W3127177933","https://openalex.org/W2376259828","https://openalex.org/W2905940832"],"abstract_inverted_index":{"Motivation:":[0],"Gene":[1],"Expression":[2],"Omnibus":[3],"(GEO)":[4],"and":[5,39,47,51,77],"other":[6,88],"publicly":[7,132],"available":[8,90,133],"data":[9,134],"store":[10],"their":[11],"metadata":[12,36],"in":[13,74,91,107,135],"the":[14,35,68,75,78,108,115,126,136],"format":[15],"of":[16,37,70,117,128,131,138],"unstructured":[17],"English":[18],"text,":[19],"which":[20],"is":[21],"very":[22],"difficult":[23],"for":[24],"automated":[25],"reuse.":[26],"Results:":[27],"We":[28],"employed":[29],"text":[30],"mining":[31],"techniques":[32],"to":[33,124],"analyze":[34],"GEO":[38,42,49,118],"developed":[40],"Restructured":[41],"database":[43],"(ReGEO).":[44],"ReGEO":[45,82],"reorganizes":[46],"categorizes":[48],"series":[50,85],"makes":[52,84],"them":[53],"searchable":[54,86],"by":[55,87],"two":[56],"new":[57],"attributes":[58,66,89],"extracted":[59],"automatically":[60],"from":[61],"each":[62],"series'":[63],"metadata.":[64],"These":[65],"are":[67],"number":[69],"time":[71],"points":[72],"tested":[73],"experiment":[76,97],"disease":[79],"being":[80],"investigated.":[81],"also":[83],"GEO,":[92],"such":[93],"as":[94,102,104],"platform":[95],"organism,":[96],"type,":[98],"associated":[99],"PubMed":[100],"ID":[101],"well":[103],"general":[105],"keywords":[106],"study's":[109],"description.":[110],"Our":[111],"approach":[112,123],"greatly":[113],"expands":[114],"usability":[116],"data,":[119],"demonstrating":[120],"a":[121],"credible":[122],"improve":[125],"utility":[127],"vast":[129],"amount":[130],"era":[137],"Big":[139],"Data":[140],"research.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
