New data and new features on PomBase web site

Wed, 2012-11-07

We are pleased to announce that we have updated both data and web site features for PomBase.

Most importantly, we have added new data types, and upgraded the gene pages to display them.

We have also added more annotations of existing data types, bringing the web site content up to September 11, 2012. The new annotations include the first contributions to come in via the new community curation system, and we thank the researchers who are participating in the initial phase of community curation.

New annotation types:

  • Phenotype annotations now use the Fission Yeast Phenotype Ontology (FYPO), and include allele details, expression levels, and experimental conditions. With FYPO, more detailed phenotypes can be described, and links between terms for related phenotypes support improved phenotype searches.
  • Many GO annotations now include "annotation extensions" that provide additional specificity. For example, extensions may capture the substrate of a catalytic activity, the cell cycle phase during which a function or process occurs, or any of several other types of supporting information for the annotation. Annotation extensions are described in more detail below.

You can see these new data types on many gene pages, such as cdc2 or pka1.

New web site features:

  • Annotation display - Gene page GO and phenotype displays have been revamped to show new annotation types described above.
  • Ontology term pages - Each ontology term ID now links to pages with information about the term and lists of genes annotated to it.
  • Ontology graph links - GO and phenotype annotation sections now include links to graphical ontology displays in the genome browser.
  • Sequence highlighting - Sequence download now offers an option to show colour highlighting of regions such as UTRs, introns and exons.
  • Versions - Each gene page now shows the current data version in the format PomBase:x.y, where x is the Ensembl Genomes (EG) version, and y is the Chado version. The sequence, and sequence feature locations, remain stable within any EG version, whereas annotations change with each Chado update.
  • Protein family information is now included in the Protein Features gene page section.
  • The Protein Feature section includes a link to the Pfam entry for a protein.
  • Transcript source data (e.g. for UTR coordinates) is now displayed in the Transcript Features section.
  • A Documentation page contains links to relevant portions of the Ensembl Genomes documentation. (More documentation will be added over the coming months.)

What are annotation extensions?

Annotation extensions are a form of supporting data that can be added GO annotations (or other ontology annotations) to capture additional details not provided by the ontology term itself.

The information in GO annotation extensions encompasses several effector-target relationships, such as

  • localisation dependencies
  • substrates of functions, e.g. targets of a protein kinase -- see the has_substrate extensions on Cdc2's "protein serine/threonine kinase" (GO:0004674) annotations
  • activators and inhibitors
  • regulation targets of signalling pathways or transcription factors

Additional extensions describe spatial and temporal aspects of processes. For example, several S. pombe annotations now include extensions that indicate in which phase of the cell cycle a gene product is found in a cellular component or involved in a process -- see the pka1 annotations to "nucleus" (GO:0005634) and "cytoplasm" (GO:0005737).

You may also find the GO wiki page on annotation extensions informative, although it is primarily aimed at curators.

Annotation extensions can also be used with phenotype annotations. The most common usage of phenotype annotation extensions is to capture which gene, protein, etc. was used in an assay. For example, the sam5 (G441E) mutation of pka1 causes nuclear accumulation of Ste11. This is represented by annotation to the ontology term "nuclear protein accumulation" (FYPO:0000255), with the extension "assayed_using(PomBase:SPBC32C12.02)". Extensions can also indicate expressivity or penetrance for a phenotype.