Chado for Prokaryotes
From GMOD
This page was started as a stub for producing a set of best practices for using Chado for prokaryotes.
Contents
Problems in adapting Chado for prokaryotes
The major challenges in adapting chado for prokaryotes are:
- Representation of features as Sequence Ontology types
- Circular genomes
Representation of features
Chado features are instances of ontology nodes. Genome features should be instances of types in the Sequence Ontology (SO). However
- SO uses a eukaryotic definition of gene that is not well suited to bacterial genomes
- Feature relationships in SO are based on eukaryotic models
- Feature types not in SO
The ideal solution is to work with SO to modify the ontology to work with both prokaryotes and eukaryotes. This is an ongoing activity that prokaryotic groups can participate in, and where SO has requested help from experts in bacterial genetics and genomics. In the meantime, MODs need to decide how to deploy Chado.
One solution has been to ignore "gene" as a feature type.
