WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.
- Prefix
wormbase- Preferred Prefix
WormBase- Alternative Prefixes
- wormbase WB WB_REF wb
- Keywords
- anatomy blast c elegans catalog database faseb list gene gene expression gene function gene mapping gene prediction geneotype genome genomic sequence genomics life science ortholog orthology assignment phenotype roundworm transposon family wormmart
- License
- CC0-1.0
- Links
- Homepage
- Publications
- 2020 WormBase: a modern Model Organism Information Resource
- 2018 WormBase 2017: molting into a new stage
- https://bioregistry.io/pubmed:24194605
- 2011 Toward an interactive article: integrating journals and biological databases
- 2010 The BioGRID Interaction Database: 2011 update
- 2010 Localizing triplet periodicity in DNA and cDNA sequences
- 2010 Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology
- 2009 The Gene Ontology in 2010: extensions and refinements
- 2009 WormBase: a comprehensive resource for nematode research
- 2009 Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation
- 2009 The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
- 2008 nGASP--the nematode genome annotation assessment project
- https://bioregistry.io/pubmed:17991679
- https://bioregistry.io/pubmed:15608221
- 2001 WormBase: network access to the genome and biology of Caenorhabditis elegans
Identifier Standards
- Pattern for Local Unique Identifiers
-
Local identifiers in WormBase should match this regular expression:
^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$ - Example Local Unique Identifier
- WBGene00000001 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from WormBase should match this regular expression:
^WormBase:(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$ - Example CURIE
- WormBase:WBGene00000001
Contacts
- Contact
- Todd W Harris 0000-0003-3406-163X tharris
- Contributors
- contributor Chris Mungall 0000-0002-6601-2165 cmungall
Metaregistry WormBase
The metaregistry provides mappings between the Bioregistry and other registries. There are 15 mappings to external registries for this resource with 12 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
WormBase
|
|
Biolink
|
biolink |
WBVocab
|
|
EDAM
|
edam |
1805
|
|
FAIRSharing
|
fairsharing |
FAIRsharing.zx1td8
|
|
GO
|
go |
WB_REF
|
|
Integbio
|
integbio |
nbdc00740
|
|
Identifiers.org
|
miriam |
wb
|
|
N2T
|
n2t |
wb
|
|
NCBI
|
ncbi |
WormBase
|
|
Pathguide
|
pathguide |
426
|
|
Prefix Commons
|
prefixcommons |
wormbase
|
|
re3data
|
re3data |
r3d100010424
|
|
RRID
|
rrid |
WB-STRAIN:WBStrain
|
|
UniProt
|
uniprot |
DB-0110
|
|
Wikidata
|
wikidata |
P3860
|
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 WBGene00000001 is used to demonstrate the providers
available for WormBase. Some providers may use a different example, which is displayed in the table below.
A guide for curating additional providers can be found
here.
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 |
|---|---|---|
agr |
WormBase through the Alliance of Genome Resources | https://www.alliancegenome.org/gene/WB:WBGene00000001 |
bio2rdf |
Bio2RDF | http://bio2rdf.org/wormbase:WBGene00000001 |
wormbase.c_elegans |
WormBase C. Elegans Gene Portal | http://www.wormbase.org/species/c_elegans/gene/WBGene00000001 |