Registry Molecular Signatures Database

The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can

Prefix: msigdb
Alternative Prefixes: msig
Keywords: expression gene family gene group gene set genome/gene health/disease interaction/pathway ontology pathway reaction
License: CC-BY-4.0
Links: Homepage OBO OWL OBO JSON
Publications: https://bioregistry.io/pubmed:16199517

Identifier Standards

Pattern for Local Unique Identifiers: Local unique identifiers in Molecular Signatures Database should match this regular expression:
^M\d+$
Example Local Unique Identifier: M1 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Molecular Signatures Database should match this regular expression:
^msigdb:M\d+$
Example CURIE: msigdb:M1

Contacts

Contact: Jill P. Mesirov 0000-0002-9755-2818
Group Contact: Mailing List
Contributor: creator Charles Tapley Hoyt 0000-0003-4423-4370 cthoyt

Mappings to External Registries

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 2 mappings to external registries with 2 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix	Curate
Biolink	`biolink`	`MSigDB`
Integbio	`integbio`	`nbdc02550`

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 M1 is used to demonstrate the providers available for Molecular Signatures Database. 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
Molecular Signatures Database	`msigdb`	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/M1
Bioregistry	`bioregistry`	https://bioregistry.io/msigdb:M1

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
MMSigDB from Biopragmatics	`biopragmatics`	https://biopragmatics.github.io/providers/msigdb/M1

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("msig")
'msigdb'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("msigdb")
{'msig'}

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("msigdb")
'Molecular Signatures Database'

Get the license:

>>> import bioregistry as br
>>> br.get_license("msigdb")
'CC-BY-4.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("msigdb")
'https://www.gsea-msigdb.org'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("msigdb")
'https://w3id.org/biopragmatics/resources/msigdb/msigdb.obo.gz'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("msigdb")
'https://w3id.org/biopragmatics/resources/msigdb/msigdb.owl.gz'

Get the JSON download link:

>>> import bioregistry as br
>>> br.get_json_download("msigdb")
'https://w3id.org/biopragmatics/resources/msigdb/msigdb.json.gz'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("msigdb")
'Jill P. Mesirov'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("msigdb")
'jmesirov@ucsd.edu'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("msigdb")
'0000-0002-9755-2818'