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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "GEOmetadb" in publications use:'
type: software
license: Artistic-2.0
title: 'GEOmetadb: A compilation of metadata from NCBI GEO'
version: 1.75.0
doi: 10.1093/bioinformatics/btn520
identifiers:
- type: doi
  value: 10.32614/CRAN.package.GEOmetadb
abstract: 'The NCBI Gene Expression Omnibus (GEO) represents the largest public repository
  of microarray data. However, finding data of interest can be challenging using current
  tools. GEOmetadb is an attempt to make access to the metadata associated with samples,
  platforms, and datasets much more feasible. This is accomplished by parsing all
  the NCBI GEO metadata into a SQLite database that can be stored and queried locally.
  GEOmetadb is simply a thin wrapper around the SQLite database along with associated
  documentation. Finally, the SQLite database is updated regularly as new data is
  added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb
  paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798'
authors:
- family-names: Zhu
  given-names: Jack
  email: zhujack@mail.nih.gov
- family-names: Davis
  given-names: Sean
preferred-citation:
  type: article
  title: 'GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.'
  authors:
  - family-names: Zhu
    given-names: Yuelin
  - family-names: Davis
    given-names: Sean
  - family-names: Stephens
    given-names: Robert
  - family-names: Meltzer
    given-names: Paul S.
  - family-names: Chen
    given-names: Yidong
  journal: Bioinformatics (Oxford, England)
  year: '2008'
  month: '12'
  volume: '24'
  issue: '23'
  abstract: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository
    of microarray data. However, finding data in GEO can be challenging. We have developed
    GEOmetadb in an attempt to make querying the GEO metadata both easier and more
    powerful. All GEO metadata records as well as the relationships between them are
    parsed and stored in a local MySQL database. A powerful, flexible web search interface
    with several convenient utilities provides query capabilities not available via
    NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite
    export of the entire GEOmetadb database is also available, rendering the entire
    GEO database accessible with full power of SQL-based queries from within R.
  issn: 1367-4811
  doi: 10.1093/bioinformatics/btn520
  url: http://www.ncbi.nlm.nih.gov/pubmed/18842599
  start: '2798'
  end: '2800'
repository: https://bioc.r-universe.dev
commit: 28688e04f4e57b52f6478c510fc3f5d253b1cf3a
date-released: '2026-03-24'
contact:
- family-names: Zhu
  given-names: Jack
  email: zhujack@mail.nih.gov