PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.
- Prefix
pombase- Alternative Prefixes
- PomBase
- Keywords
- life science
- Links
- Homepage
- Contact
- Missing Contact
- Pattern for Local Unique Identifiers
-
Local identifiers in PomBase should match this regular expression:
^S\w+(\.)?\w+(\.)?$ - Example Local Unique Identifier
- SPCC13B11.01 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from PomBase should match this regular expression:
^pombase:S\w+(\.)?\w+(\.)?$ - Example CURIE
- pombase:SPCC13B11.01
- Publications
-
- 2019 PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information
- 2016 Model organism databases: essential resources that need the support of both funders and users
- 2014 PomBase 2015: updates to the fission yeast database
- 2014 A method for increasing expressivity of Gene Ontology annotations using a compositional approach
- 2014 Canto: an online tool for community literature curation
- 2013 FYPO: the fission yeast phenotype ontology
- 2012 Gene Ontology annotations and resources
- 2011 The Gene Ontology: enhancements for 2011
- 2011 PomBase: a comprehensive online resource for fission yeast
Ontology
A summary of the relations in the Bioregistry schema can be found here.
- In Collection
- Global Biodata Coalition - Global Core Biodata Resources
Metaregistry PomBase
The metaregistry provides mappings between the Bioregistry and other registries. There are 12 mappings to external registries for this resource with 6 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
PomBase
|
|
Biolink
|
biolink |
PomBase
|
|
FAIRSharing
|
fairsharing |
FAIRsharing.8jsya3
|
|
GO
|
go |
PomBase
|
|
Integbio
|
integbio |
nbdc00332
|
|
Identifiers.org
|
miriam |
pombase
|
|
N2T
|
n2t |
pombase
|
|
NCBI
|
ncbi |
PomBase
|
|
Prefix Commons
|
prefixcommons |
pombase
|
|
re3data
|
re3data |
r3d100011478
|
|
UniProt
|
uniprot |
DB-0031
|
|
Wikidata
|
wikidata |
P6245
|
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 SPCC13B11.01 is used to demonstrate the providers
available for PomBase. A guide for curating additional providers can be found
here.
| Name | Metaprefix | URI |
|---|---|---|
| PomBase | pombase |
https://www.pombase.org/gene/SPCC13B11.01 |
| Bioregistry | bioregistry |
https://bioregistry.io/pombase:SPCC13B11.01 |
| Identifiers.org | miriam |
https://identifiers.org/pombase:SPCC13B11.01 |
| Name-to-Thing | n2t |
https://n2t.net/pombase:SPCC13B11.01 |
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/pombase:SPCC13B11.01 |