The GMOD wiki will be in read-only mode on Tuesday, March 11th, while we perform server upgrades. It will be back in action by Wednesday, March 12th.
Chado New Users
This page, and it's associated discussion page follow the learning curve for new Chado users learning the system at CSHL.
Getting an empty Chado PostgreSQL on our machines
- Zheng - on PC with Fedora. See Zheng's installation notes
- Mike - on Intel Mac running Fedora partition
- Jim -
- on PPC Mac the hard way See Jim's installation notes
- on CentOS server in Texas
If the easy way fails, the old documentation outside the wiki can be pretty confusing.
Loading the Ontologies
This works via make ontologies. How to do updates?
Getting the Sequence Module Working
Migration from other databases
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:
- Sample yeast data from GFF3 bulk loader. The problem with this is that it doesn't reflect a real use case for Chado, since SGD does not use the Chado Schema
- FlyBase SQL dump. Zheng got this and loaded it. One problem.
- It's huge
Understanding how things are represented in Chado
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:
- A [feature]
- Note that the field seqlen could be problematic - added a note.
- If the gene is mapped to the sequence, there should be a featureloc
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?
Polycistronic transcription units
As of this writing, the description of handling dicistronic genes is not very clear. Based on the GFF3 spec:
- Parenting a CDS/polypeptide directly on a gene is deprecated because the gene (sensu eukaryota) includes nontranscribed regions
- A solution is to give the mRNA feature multiple parents. Thus lacZ, lacY and lacA would all be parents of lacZYA, which in turn would be parent via a derives_from relationship to the LacZ, LacY and LacA polypeptides.
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?