OMP ID format: Difference between revisions

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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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copied over from the googledoc
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


OMP ID Format
==Prefixes==
Prefix
<protect><!--box uid=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c-->
Pan-genome: OMP_PG: vs. OMP_PGM vs. ?
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*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. **
*
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{|  id="Z5397844d6822c"  class=" tableEdit " 


Pan-gene: OMP_GN: vs. OMP_PGN vs. ?
|-
!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: OMP_ST: vs. OMP_STR vs. ?
|-
!align=left  |Strain/Substrain
||
OMP_ST: vs OMP_STR vs ?
||


Allele: OMP_AL: vs. OMP_ALL vs. ?
|-
!align=left  |Allele
||
OMP_AL: vs OMP_ALL vs ?
||


Annotation: OMP_AN: vs. OMP_ANN vs. ?
|-
!align=left  |Phenotype Annotation
||
OMP_AN: vs. OMP_ANN vs ?
||




Jon:  
|- class="tableEdit_footer"
Michelle/JH: for Pan-genome TX for taxon or SP for species
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c&page=4329&pagename={{FULLPAGENAMEE}}&type=1&template= edit table]</span> || ||
Number
|}
with or without leading zeros? How many zeros?
<!--box uid=d41d8cd98f00b204e9800998ecf8427e.4329.Z5397844d6822c--></protect>
example OMP_GN:000785 vs. OMP_GN:785


No leading zeros
==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 Sub-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:


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: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 22:30, 10 June 2014

modified from original googledoc:

https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9

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
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