{"id":"https://openalex.org/W7130705359","doi":"https://doi.org/10.5281/zenodo.18355813","title":"Vaginal Microbial Genome Collection (VMGC) MIDAS-compatible pangenome database","display_name":"Vaginal Microbial Genome Collection (VMGC) MIDAS-compatible pangenome database","publication_year":2026,"publication_date":"2026-01-23","ids":{"openalex":"https://openalex.org/W7130705359","doi":"https://doi.org/10.5281/zenodo.18355813"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.18355813","doi":"https://doi.org/10.5281/zenodo.18355813","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18355813","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"volume":null,"type":"dataset","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.18355813","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087288531","display_name":"Claire A. Dubin","orcid":"https://orcid.org/0000-0003-0319-6013","observed_orcids":["https://orcid.org/0000-0003-0319-6013"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dubin, Claire","raw_affiliation_strings":["University of California, San Francisco"],"raw_orcid":"https://orcid.org/0000-0003-0319-6013","affiliations":[{"raw_affiliation_string":"University of California, San Francisco","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087288531"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10428","display_name":"Reproductive tract infections research","score":0.8925999999046326,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10428","display_name":"Reproductive tract infections research","score":0.8925999999046326,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08240000158548355,"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/T10066","display_name":"Gut microbiota and health","score":0.008700000122189522,"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/vaginal-microbiota","display_name":"vaginal microbiota","score":0.9950000047683716},{"id":"https://openalex.org/keywords/pan-genome","display_name":"pan-genome","score":0.9359999895095825},{"id":"https://openalex.org/keywords/midas","display_name":"MIDAS","score":0.5789999961853027},{"id":"https://openalex.org/keywords/lactobacillus-crispatus","display_name":"Lactobacillus crispatus","score":0.9089999794960022},{"id":"https://openalex.org/keywords/accessory-genes","display_name":"accessory genes","score":0.871999979019165},{"id":"https://openalex.org/keywords/cervical-intraepithelial-neoplasia","display_name":"cervical intraepithelial neoplasia","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5947999954223633},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5842000246047974},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5120000243186951},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4043999910354614},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.3449999988079071},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.31439998745918274},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3127000033855438},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2849000096321106},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2840000092983246},{"id":"https://openalex.org/C2777867728","wikidata":"https://www.wikidata.org/wiki/Q2033849","display_name":"Streptococcus sanguinis","level":4,"score":0.26440000534057617},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2556000053882599}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.18355813","doi":"https://doi.org/10.5281/zenodo.18355813","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18355813","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.18355814","doi":"https://doi.org/10.5281/zenodo.18355814","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18355814","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.18355813","doi":"https://doi.org/10.5281/zenodo.18355813","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18355813","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4414144999","https://openalex.org/W7134245454","https://openalex.org/W4394021627","https://openalex.org/W6930497550","https://openalex.org/W6977280260","https://openalex.org/W7093337807","https://openalex.org/W7117693195","https://openalex.org/W7128005480","https://openalex.org/W7162496481","https://openalex.org/W4319447645"],"abstract_inverted_index":{"This":[0],"is":[1],"a":[2,76,106],"MIDAS-compatible":[3],"pangenome":[4],"database":[5,18,24,36,79],"constructed":[6],"from":[7],"the":[8,17,23,35],"Vaginal":[9],"Microbial":[10],"Genome":[11],"Collection":[12],"(VMGC).":[13],"Installation":[14],"1.":[15],"Download":[16],"wget":[19],"https://zenodo.org/records/18355814/files/VMGC_MIDAS_db.tar.gz":[20],"2.":[21],"Uncompress":[22],"Note:":[25],"Uncompressed":[26],"size":[27],"=":[28],"59GB":[29],"tar":[30],"-zxf":[31],"VMGC_MIDAS_db.tar.gz":[32],"3.":[33],"Specify":[34],"path":[37],"in":[38],"MIDAS":[39,78],"commands":[40],"midas":[41],"[command_name]":[42],"[other":[43],"arguments]":[44],"--midasdb_dir":[45],"/path/to/db/location/VMGC_MIDAS_db":[46],"--midasdb_name":[47],"localdb":[48],"Citation":[49],"Please":[50],"cite":[51],"our":[52],"paper":[53],"if":[54],"you":[55],"use":[56],"this":[57],"database:":[58,108],"Dubin":[59],"CA,":[60],"Zhao":[61],"C,":[62],"Pollard":[63],"KS,":[64],"Oskotsky":[65],"T,":[66],"Golob":[67],"JL,":[68],"Sirota":[69],"M.":[70],"Expanding":[71],"vaginal":[72],"microbiome":[73],"pangenomes":[74],"via":[75],"custom":[77,107],"reveals":[80],"Lactobacillus":[81],"crispatus":[82],"accessory":[83],"genes":[84],"associated":[85],"with":[86],"cervical":[87],"dysplasia.":[88],"bioRxiv.":[89],"Preprint":[90],"posted":[91],"online":[92],"September":[93],"11,":[94],"2025:2025.09.11.675634.":[95],"doi:10.1101/2025.09.11.675634":[96],"Additional":[97],"Resources":[98],"MIDAS:":[99],"https://github.com/pollardlab/MIDAS":[100],"VMGC:":[101],"https://www.nature.com/articles/s41564-024-01751-5":[102],"Pipline":[103],"for":[104],"constructing":[105],"https://github.com/clairedubin/MIDASv3_nextflow":[109]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-02-21T00:00:00"}
