S. pombe gene characterisation progress since 2006; see the Gene Characterisation page for more details

Did You Know ... ?

PomBase has recently launched a community curation project that enables researchers to contribute publication-based annotations directly to database curators. By involving bench scientists directly in the curation process, PomBase improves the timeliness and depth of its annotations, and raises awareness of the value curation adds to scientific databases and literature. Like all annotations in PomBase, community contributions are shared among databases such as GO, BioGRID, UniProtKB, etc. If you have a publication that you would like to curate for PomBase, you can go to the curation tool, Canto, and search for its PubMed ID, or contact the PomBase curators via the helpdesk.

About PomBase

PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets

News

Thursday, 11th Dec, 2014

PomBase has implemented network visualisations for fission yeast in esyN, using data curated by BioGRID and PomBase. esyN is a web-based tool for building, sharing, and viewing network data developed by Dan Bean and Giorgio Favrin in the Cambridge Systems Biology Centre, University of Cambridge, UK.

On gene pages, we have links to gene-specific interaction networks in esyN in the table headers of the Interactions sections:

  • The Genetic Interactions section links to all interactions centred on the gene and curated in BioGRID
  • The Physical interactions section has links to two datasets:
    • All physical interactions curated in BioGRID for the gene
    • ...
Thursday, 11th Dec, 2014

To make the Gene Ontology (GO) annotations easier to read on PomBase gene pages, we have introduced a new, streamlined display that presents just the essentials. The summary shows the term name (hyperlinked to the ontology term page), the count of genes annotated to the term, and any annotation extensions. All of the previously visible annotation details are still available -- simply click the "Summary" button to switch to the "Full" view. Or click the "+" and "-" icons to expand or collapse the annotation to a single term.
 
In addition, the top of the Biological Process table now lists any GO slim terms applicable to the gene.

Thursday, 13th Nov, 2014

We have updated the data available on the PomBase web site to include manual curation through October 27, 2014, including 225 community-curated publications. The gene page Phenotype section now includes data from the high-throughput microscopy analysis of viable deletion mutants reported in:

Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE. A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression. Dev Cell. 2014 Oct 27;31(2):227-39. doi: 10.1016/j.devcel.2014.09.005 PMID:25373780. Links to the...