This page, and it’s associated discussion page follow the learning curve for new Chado users learning the system at CSHL.
If the easy way fails, the old documentation outside the wiki can be pretty confusing.
This works via make ontologies. How to do updates?
We think GFF3 can be thought of as a view into Chado using the Sequence module and the CV module, or we can think of GFF3 as a denormalized view of Chado.
To understand Chado Best Practices, where the documentation is sometimes incomplete, we’ve tried to get some samples of Chado data in use. Things we’ve looked at so far, and comments on them:
Chado Best Practices describes some of the representations. Unfortunately it’s somewhat incomplete at present.
Chado uses a eukaryotic-centric gene definition which is based on monocistronic mRNAs. In this view, the gene includes information in the genomic DNA outside of the part that codes for the mRNA. To represent a gene, there needs to be:
Completing the representation of the gene seems to require additional features of types ‘mRNA’ and ‘exon’ (and ‘polypeptide’ if it’s protein coding). What happens if software tries to write a feature record as a gene without creating these? Presumably the gene feature has to be entered first in order to have an object_id for feature_relationship.
mRNA features are entered with part_of relationships to genes. This is straightforward in cases where the mRNA is derived from a high-quality full length cDNA (but what’s the feature_relationship type?). Does an mRNA have to have a featureloc? What if the CDS is known but the precise ends of the UTRs are not?
As of this writing, the description of handling dicistronic genes is not very clear. Based on the GFF3 spec:
tRNAs, rRNAs, snRNAs etc have similar relationships to genes. Note that even in eukaryotes, rRNAs and tRNAs are often polycistronic transcripts!
Polypeptides derive_from mRNAs
Note that proteins ≠ polypeptides. Hemoglobin is a heterotetramer of two α and two β subunits. Is there a feature type that represents this?