OMP ID format
From OMPwiki
modified from original googledoc:
Prefixes
| Pan-genome |
OMP_PG: vs OMP_PGM vs ? |
Jim and Michelle suggested OMP_TX (for taxon) or OMP_SP (for species) |
|---|---|---|
| Pan-gene |
OMP_GN: vs OMP_PGN vs ? |
|
| Strain/Substrain |
OMP_ST: vs OMP_STR vs ? |
|
| Allele |
OMP_AL: vs OMP_ALL vs ? |
|
| Phenotype Annotation |
OMP_AN: vs. OMP_ANN vs ? |
|
| edit table |
Term ID numbers
Decided to not use leading zeros
Pangenome
- Includes only the genomes of strains.
- Includes 3 different categories:
- 1. core genome: genes present in all strains
- 2. Dispensable genome: genes present in two or more strains
- 3. Unique genes: specific to single strains
Strains and sub-strains
- In ecoli wiki the prefix for all strains and their derivatives is “strain:” Should we just omit this prefix in OMP?
- Examples:
OMP_ST:00004 ! K-12 vs. OMP_ST:00004 ! Strain:K-12
OMP_ST:00062 ! MG1655 vs. OMP_ST:00062 ! Strain:MG1655
- Should we make the distinction between a strain and its derivatives?
OMP_ST:00004 ! K-12
OMP_ST:00062 ! K-12_MG1655 vs. OMP_ST:00062 ! MG1655
- E.coli_K-12_MG1655
- We will have our own unique ID’s and cross ref with NCBI
