PomBase
Homepage http://www.pombase.org
Countries that developed this resource United Kingdom
Created in 2010
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: PomBase; PomBase; DOI: https://doi.org/10.25504/FAIRsharing.8jsya3; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Apr 11 2021 10:13 p.m.
Record updated: Nov. 21, 2018, 10:57 a.m. by The FAIRsharing Team.
| FAQ | http://www.pombase.org/faq |
| contact form | http://www.pombase.org/feedback |
| help | http://www.pombase.org/submit-data/help- ... |
| Mailing List | Pombelist mailing list |
| online documentation | http://www.pombase.org/documentation |
| wikipedia | https://en.wikipedia.org/wiki/PomBase |
Additional Information
| Contact | PomBase Helpdesk |
| BLAST | http://genomebrowser.pombase.org/Multi/blastview |
| Canto - Community annotation tool | http://curation.pombase.org/pombe/ |
Conditions of Use
Applies to: Data useData Versioning
| versioning by genome sequence update | https://www.pombase.org/status/sequencing-updates |
| daily updates | https://www.pombase.org |
| Monthly Chado database dumps (PostgresQL) are available to download | http://curation.pombase.org/dumps/releases/ |
| Historical data versions September 2012 - January 2017 | https://www.pombase.org/about/version-history |
Data Access
| web interface | https://www.pombase.org |
| Monthly Chado database dumps (PostgresQL) are available to download | http://curation.pombase.org/dumps/releases/ |
PomBase 2015: updates to the fission yeast database.
McDowall MD,Harris MA,Lock A,Rutherford K,Staines DM,Bahler J,Kersey PJ,Oliver SG,Wood V
Nucleic Acids Res 2014
Canto: an online tool for community literature curation.
Rutherford KM,Harris MA,Lock A,Oliver SG,Wood V
Bioinformatics 2014
A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP,Harris MA,Alam-Faruque Y,Blake JA,Carbon S,Dietze H,Dimmer EC,Foulger RE,Hill DP,Khodiyar VK,Lock A,Lomax J,Lovering RC,Mutowo-Meullenet P,Sawford T,Van Auken K,Wood V,Mungall CJ
BMC Bioinformatics 2014
The Gene Ontology: enhancements for 2011.
Nucleic Acids Res 2011
Gene Ontology annotations and resources.
Blake JA,Dolan M,Drabkin H,Hill DP,Li N,Sitnikov D,Bridges S,Burgess S,Buza T,McCarthy F,Peddinti D,Pillai L,Carbon S,Dietze H,Ireland A,Lewis SE,Mungall CJ,Gaudet P,Chrisholm RL,Fey P,Kibbe WA,Basu S,Siegele DA,McIntosh BK,Renfro DP,Zweifel AE,Hu JC,Brown NH,Tweedie S,Alam-Faruque Y,Apweiler R,Auchinchloss A,Axelsen K,Bely B,Blatter M-,Bonilla C,Bouguerleret L,Boutet E,Breuza L,Bridge A,Chan WM,Chavali G,Coudert E,Dimmer E,Estreicher A,Famiglietti L,Feuermann M,Gos A,Gruaz-Gumowski N,Hieta R,Hinz C,Hulo C,Huntley R,James J,Jungo F,Keller G,Laiho K,Legge D,Lemercier P,Lieberherr D,Magrane M,Martin MJ,Masson P,Mutowo-Muellenet P,O'Donovan C,Pedruzzi I,Pichler K,Poggioli D,Porras Millan P,Poux S,Rivoire C,Roechert B,Sawford T,Schneider M,Stutz A,Sundaram S,Tognolli M,Xenarios I,Foulgar R,Lomax J,Roncaglia P,Khodiyar VK,Lovering RC,Talmud PJ,Chibucos M,Giglio MG,Chang H-,Hunter S,McAnulla C,Mitchell A,Sangrador A,Stephan R,Harris MA,Oliver SG,Rutherford K,Wood V,Bahler J,Lock A,Kersey PJ,McDowall DM,Staines DM,Dwinell M,Shimoyama M,Laulederkind S,Hayman T,Wang S-,Petri V,Lowry T,D'Eustachio P,Matthews L,Balakrishnan R,Binkley G,Cherry JM,Costanzo MC,Dwight SS,Engel SR,Fisk DG,Hitz BC,Hong EL,Karra K,Miyasato SR,Nash RS,Park J,Skrzypek MS,Weng S,Wong ED,Berardini TZ,Huala E,Mi H,Thomas PD,Chan J,Kishore R,Sternberg P,Van Auken K,Howe D,Westerfield M
Nucleic Acids Res 2012
FYPO: the fission yeast phenotype ontology.
Harris MA,Lock A,Bahler J,Oliver SG,Wood V
Bioinformatics 2013
PomBase: a comprehensive online resource for fission yeast.
Wood V., Harris MA., McDowall MD., Rutherford K., Vaughan BW., Staines DM., Aslett M., Lock A., Bähler J., Kersey PJ., Oliver SG.,
Nucleic Acids Res. 2012
Model organism databases: essential resources that need the support of both funders and users.
Oliver SG,Lock A,Harris MA,Nurse P,Wood V
BMC Biol 2016
Reporting Guidelines
No guidelines defined
Terminology Artifacts
Models and Formats
- Gene Transfer Format
- FASTA Sequence Format
- CHADO XML
- ENA Sequence Flat File Format
- Genome Annotation File version 1
- OBO Format Syntax and Semantics
- Gene Ontology (GO) Gene Association File Format 2.0
- Gene Ontology (GO) Gene Association File Format 2.1
- Gene Ontology (GO) Gene Association File Format 2.2
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
This record is not implemented by any policy.
Record Maintainer
This record is maintained by PomBase
Funds
The Wellcome Trust, UK (Charitable foundation)
European Commission under FP7 Grant Agreement (Government body)
Maintains
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK (University)
University College London, UK (University)
Grant Number(s)
WT090548MA (The Wellcome Trust, UK)
