ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.
- Prefix
arrayexpress- Keywords
- cdna/est expression genome/gene microarray nucleotide protein repository rna
- License
- http://www.ebi.ac.uk/Information/termsofuse.html
- Links
- Homepage
- Publications
- 2019 ArrayExpress update - from bulk to single-cell expression data
- 2014 ArrayExpress update--simplifying data submissions
- https://bioregistry.io/pubmed:21071405
- https://bioregistry.io/pubmed:19015125
- https://bioregistry.io/pubmed:17132828
- https://bioregistry.io/pubmed:16939801
- https://bioregistry.io/pubmed:15608260
- https://bioregistry.io/pubmed:14744115
- 2003 ArrayExpress--a public repository for microarray gene expression data at the EBI
- References
- GitHub PR https://github.com/biopragmatics/bioregistry/pull/1141
Identifier Standards
- Pattern for Local Unique Identifiers
-
Local unique identifiers in ArrayExpress should match this
regular expression:
^[AEP]-\w{4}-\d+$ - Example Local Unique Identifier
- E-MEXP-1712 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from ArrayExpress should match
this regular expression:
^arrayexpress:[AEP]-\w{4}-\d+$ - Example CURIE
- arrayexpress:E-MEXP-1712
Contacts
- Contact
-
Alvis Brazma
0000-0001-5988-7409
- Identifier Space Owner
-
European Bioinformatics Institute
- Contributor
-
contributor
Sumir H. Pandit
0000-0002-1216-4761
sumirp
Ontology
A summary of the relations in the Semantic Farm schema can be found here.
- In Collection (1)
- Synapse.org external links
Mappings to External Registries
Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 8 mappings to external registries with 4 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
ARRAYEXPRESS
|
|
Cellosaurus
|
cellosaurus |
ArrayExpress
|
|
Integbio
|
integbio |
nbdc00009
|
|
Identifiers.org
|
miriam |
arrayexpress
|
|
N2T
|
n2t |
arrayexpress
|
|
Prefix Commons
|
prefixcommons |
arrayexpress
|
|
re3data
|
re3data |
r3d100010222
|
|
Wikidata (E)
|
wikidata.entity |
Q106638376
|
Providers
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 E-MEXP-1712 is used to demonstrate the providers
available for ArrayExpress. Some providers may use a different example, which is displayed in the table below.
A guide for curating additional providers can be found
here.
| Provider Name | Provider Code | URI |
|---|---|---|
| ArrayExpress | arrayexpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1712 |
| Bioregistry | bioregistry |
https://bioregistry.io/arrayexpress:E-MEXP-1712 |
| Identifiers.org | miriam |
https://identifiers.org/arrayexpress:E-MEXP-1712 |
| Name-to-Thing | n2t |
https://n2t.net/arrayexpress:E-MEXP-1712 |
Extra Providers
Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Provider Name | Provider Code | URL |
|---|---|---|
| Bio2RDF | bio2rdf |
http://bio2rdf.org/arrayexpress:E-MEXP-1712 |
| ArrayExpress through OmicsDI | omicsdi |
https://www.omicsdi.org/dataset/arrayexpress-repository/E-MEXP-1712 |