Registry Gene Expression Omnibus

Logo for Gene Expression Omnibus The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.

Prefix: geo
Keywords: cdna/est expression gene expression genome image/movie repository sequence
License: http://www.nlm.nih.gov/copyright.html
Links: Homepage
Publications: 2012 NCBI GEO: archive for functional genomics data sets--update; https://bioregistry.io/pubmed:21097893; https://bioregistry.io/pubmed:18940857; 2006 NCBI GEO standards and services for microarray data; https://bioregistry.io/pubmed:17099226; https://bioregistry.io/pubmed:16939800; https://bioregistry.io/pubmed:16888359; https://bioregistry.io/pubmed:15608262; 2002 Gene Expression Omnibus: NCBI gene expression and hybridization array data repository; 2000 One-stop shop for microarray data; 2012 MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting

Identifier Standards

Pattern for Local Unique Identifiers: Local identifiers in Gene Expression Omnibus should match this regular expression:
^G(PL|SM|SE|DS)\d+$
Example Local Unique Identifier: GDS1234 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Gene Expression Omnibus should match this regular expression:
^geo:G(PL|SM|SE|DS)\d+$
Example CURIE: geo:GDS1234

Contacts

Contact: Tanya Barrett 0000-0002-9448-8064

Ontology

A summary of the relations in the Bioregistry schema can be found here.

In Collection: Resources mentioned in "Sharing biological data: why, when, and how" Synapse.org external links

Metaregistry Gene Expression Omnibus

The metaregistry provides mappings between the Bioregistry and other registries. There are 8 mappings to external registries for this resource with 4 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
Cellosaurus	`cellosaurus`	`GEO`
EDAM	`edam`	`1147`
GO	`go`	`GEO`
Integbio	`integbio`	`nbdc00080`
Identifiers.org	`miriam`	`geo`
N2T	`n2t`	`geo`
Prefix Commons	`prefixcommons`	`geo`
re3data	`re3data`	`r3d100010283`

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier GDS1234 is used to demonstrate the providers available for Gene Expression Omnibus. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Name	Metaprefix	URI
Gene Expression Omnibus	`geo`	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GDS1234
Bioregistry	`bioregistry`	https://bioregistry.io/geo:GDS1234
Identifiers.org	`miriam`	https://identifiers.org/geo:GDS1234
Name-to-Thing	`n2t`	https://n2t.net/geo:GDS1234

Extra Providers

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Code	Name	URL
`bio2rdf`	Bio2RDF	http://bio2rdf.org/geo:GDS1234

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("geo")
'Gene Expression Omnibus'

Get the license:

>>> import bioregistry as br
>>> br.get_license("geo")
'http://www.nlm.nih.gov/copyright.html'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("geo")
'https://www.ncbi.nlm.nih.gov/geo/'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("geo")
'Tanya Barrett'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("geo")
'barrett@ncbi.nlm.nih.gov'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("geo")
'0000-0002-9448-8064'