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PomBase 2015: updates to the fission yeast database.

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V - Nucleic Acids Res. (2014)

Bottom Line: Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates.Both in-house curators and community researchers provide manually curated data to PomBase.The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus).

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK mcdowall@ebi.ac.uk.

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PomBase gene page views for example annotations: (A) GO (gene ste11 - SPBC32C12.02); (B) FYPO (gene cdc2 - SPBC11B10.09); (C) Gene expression (gene clr3 - SPBC800.03). These examples highlight the display of annotation extensions and their use within the context of different ontologies.
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Figure 2: PomBase gene page views for example annotations: (A) GO (gene ste11 - SPBC32C12.02); (B) FYPO (gene cdc2 - SPBC11B10.09); (C) Gene expression (gene clr3 - SPBC800.03). These examples highlight the display of annotation extensions and their use within the context of different ontologies.

Mentions: To accommodate annotation extensions, PomBase has adapted its Chado and Ensembl relational database schemata and loading procedures and enhanced the gene page ontology annotation displays. On PomBase gene pages, annotation extensions are shown in rows below the ontology term, with the relevant evidence code and annotation source. Identifiers and relation strings are converted to human-friendly text, such as a gene name or ontology term, wherever possible. For example, Figure 2A shows annotations to GO:0045944 from the ste11 (SPBC32C12.02) gene page. Annotations without extensions are displayed first, followed by those with extensions, and the bottom row shows a compound annotation extension (26).


PomBase 2015: updates to the fission yeast database.

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V - Nucleic Acids Res. (2014)

PomBase gene page views for example annotations: (A) GO (gene ste11 - SPBC32C12.02); (B) FYPO (gene cdc2 - SPBC11B10.09); (C) Gene expression (gene clr3 - SPBC800.03). These examples highlight the display of annotation extensions and their use within the context of different ontologies.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383888&req=5

Figure 2: PomBase gene page views for example annotations: (A) GO (gene ste11 - SPBC32C12.02); (B) FYPO (gene cdc2 - SPBC11B10.09); (C) Gene expression (gene clr3 - SPBC800.03). These examples highlight the display of annotation extensions and their use within the context of different ontologies.
Mentions: To accommodate annotation extensions, PomBase has adapted its Chado and Ensembl relational database schemata and loading procedures and enhanced the gene page ontology annotation displays. On PomBase gene pages, annotation extensions are shown in rows below the ontology term, with the relevant evidence code and annotation source. Identifiers and relation strings are converted to human-friendly text, such as a gene name or ontology term, wherever possible. For example, Figure 2A shows annotations to GO:0045944 from the ste11 (SPBC32C12.02) gene page. Annotations without extensions are displayed first, followed by those with extensions, and the bottom row shows a compound annotation extension (26).

Bottom Line: Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates.Both in-house curators and community researchers provide manually curated data to PomBase.The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus).

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK mcdowall@ebi.ac.uk.

Show MeSH