Difference between revisions of "OMP ID format"
(Created page with "copied over from the googledoc https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9 OMP ID Format Prefix Pan-genome: ...") |
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Prefix | Prefix | ||
Pan-genome: OMP_PG: vs. OMP_PGM vs. ? | Pan-genome: OMP_PG: vs. OMP_PGM vs. ? | ||
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Annotation: OMP_AN: vs. OMP_ANN vs. ? | Annotation: OMP_AN: vs. OMP_ANN vs. ? | ||
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| + | !|Pan-genome!!Pan-gene!!Strain/Substrain!!Allele!!Phenotype Annotation | ||
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Revision as of 17:18, 10 June 2014
copied over from the googledoc
Prefix Pan-genome: OMP_PG: vs. OMP_PGM vs. ?
Pan-gene: OMP_GN: vs. OMP_PGN vs. ?
Strain/Substrain: OMP_ST: vs. OMP_STR vs. ?
Allele: OMP_AL: vs. OMP_ALL vs. ?
Annotation: OMP_AN: vs. OMP_ANN vs. ?
| Pan-genome | Pan-gene | Strain/Substrain | Allele | Phenotype Annotation |
|---|---|---|---|---|
| edit table |
Jon:
Michelle/JH: for Pan-genome TX for taxon or SP for species
Number
with or without leading zeros? How many zeros?
example OMP_GN:000785 vs. OMP_GN:785
No 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? 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
