Bradford Condon PhD

Bioinformatics, Web & Mobile Development

Tripal Country: Chado Feature Annotations

Welcome to Tripal Country!

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Tripal feature annotations might be a little unintuitive, especially for non-biologists. This guide is to solidify my own knowledge of what goes where and why: hopefully it will be helpful to some developers as well.

Executive Summary

  • KEGG, IPR, GO annotations go in feature_cvterm. The annotations show up in the “Annotation” field
  • BLAST annotations go in blast_hit_data. The annotations show in up the “Homology” field

The feature table

The feature table is where all sequences live in Chado as dictated by the sequence module. I won’t go into detail as there are other guides available for this module.

The feature_cvterm table

The feature_cvterm table is the simplest way to annotate a feature. You just need a feature_id and a cvterm_id, which will be the KEGG, IPR, or GO cvterm id. Additional info for the annotation goes in feature_cvtermprop.

The blast_hit_data table

Blast annotations loaded in from the analysis_blast module go somewhere different: to the blast_hit_data table. Why?

Tripal sites can use whatever BLAST annotations they would like. This might mean a custom gene set, even the genbank nr database. To use the feature_cvterm annotation table, you’d need a cvterm for each entry in your blast database! The blast_hit_data table means you dont need to do this. That’s my rationale for it, at least- I didn’t write it!

All of the information for the blast result is available in the blast_hit_data table. This includes the name and accession of the hit with its full description and url, the scores, percent identity, e value, and number of hits.