Difference between revisions of "OMP ID format"
From OMPwiki
(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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| − | + | modified from original googledoc: | |
https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9 | https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9 | ||
| − | + | ==Prefixes== | |
| − | + | <protect><!--box uid=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c--> | |
| − | + | <!-- | |
| + | ****************************************************************************************** | ||
| + | * | ||
| + | * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** | ||
| + | * | ||
| + | ****************************************************************************************** --> | ||
| + | {| id="Z5397844d6822c" class=" tableEdit " | ||
| − | Pan-gene | + | |- |
| + | !align=left |Pan-genome | ||
| + | || | ||
| + | OMP_PG: vs OMP_PGM vs ? | ||
| + | || | ||
| + | Jim and Michelle suggested OMP_TX (for taxon) or OMP_SP (for species) | ||
| + | |- | ||
| + | !align=left |Pan-gene | ||
| + | || | ||
| + | OMP_GN: vs OMP_PGN vs ? | ||
| + | || | ||
| − | Strain/Substrain | + | |- |
| + | !align=left |Strain/Substrain | ||
| + | || | ||
| + | OMP_ST: vs OMP_STR vs ? | ||
| + | || | ||
| − | Allele | + | |- |
| + | !align=left |Allele | ||
| + | || | ||
| + | OMP_AL: vs OMP_ALL vs ? | ||
| + | || | ||
| − | Annotation | + | |- |
| + | !align=left |Phenotype Annotation | ||
| + | || | ||
| + | OMP_AN: vs. OMP_ANN vs ? | ||
| + | || | ||
| − | + | |- class="tableEdit_footer" | |
| − | + | |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c&page=4329&pagename={{FULLPAGENAMEE}}&type=1&template= edit table]</span> || || | |
| − | + | |} | |
| − | + | <!--box uid=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c--></protect> | |
| − | |||
| − | + | ==Term ID numbers== | |
| + | Decided to not use leading zeros | ||
| − | Pangenome | + | ==Pangenome== |
*Includes only the genomes of strains. | *Includes only the genomes of strains. | ||
*Includes 3 different categories: | *Includes 3 different categories: | ||
| − | 1. core genome: genes present in all strains | + | **1. core genome: genes present in all strains |
| − | 2. Dispensable genome: genes present in two or more strains | + | **2. Dispensable genome: genes present in two or more strains |
| − | 3. Unique genes: specific to single strains | + | **3. Unique genes: specific to single strains |
| − | Strains and | + | ==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:00004 ! K-12 vs. OMP_ST:00004 ! Strain:K-12 | + | |
OMP_ST:00062 ! MG1655 vs. OMP_ST:00062 ! Strain:MG1655 | OMP_ST:00062 ! MG1655 vs. OMP_ST:00062 ! Strain:MG1655 | ||
| − | Should we make the distinction between a strain and its derivatives? | + | |
| + | * Should we make the distinction between a strain and its derivatives? | ||
| + | |||
OMP_ST:00004 ! K-12 | OMP_ST:00004 ! K-12 | ||
| + | |||
OMP_ST:00062 ! K-12_MG1655 vs. OMP_ST:00062 ! MG1655 | OMP_ST:00062 ! K-12_MG1655 vs. OMP_ST:00062 ! MG1655 | ||
Latest revision as of 17:30, 10 June 2014
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
