OMP ID format - Revision history

Siegele: /* Strains and sub-strains */

2014-06-10T22:30:26Z

Strains and sub-strains

← Older revision		Revision as of 22:30, 10 June 2014
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	**Examples:		**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

Siegele: /* Strains and sub-strains */

2014-06-10T22:29:55Z

Strains and sub-strains

← Older revision		Revision as of 22:29, 10 June 2014
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	==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

Siegele at 22:28, 10 June 2014

2014-06-10T22:28:48Z

← Older revision		Revision as of 22:28, 10 June 2014
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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
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			==Term ID numbers==
			Decided to not use leading zeros

	~~Jon:~~		==Pangenome==
	~~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 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?		In ecoli wiki the prefix for all strains and their derivatives is “strain:” Should we just omit this prefix in OMP?

Siegele: Table edited by Siegele via TableEdit

2014-06-10T22:26:34Z

Table edited by Siegele via TableEdit

← Older revision		Revision as of 22:26, 10 June 2014
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	\|\|		\|\|
	OMP_PG: vs OMP_PGM vs ?		OMP_PG: vs OMP_PGM vs ?
			\|\|
			Jim and Michelle suggested OMP_TX (for taxon) or OMP_SP (for species)
	\|-		\|-
	!align=left \|Pan-gene		!align=left \|Pan-gene
	\|\|		\|\|
	OMP_GN: vs OMP_PGN vs ?		OMP_GN: vs OMP_PGN vs ?
			\|\|

	\|-		\|-
	!align=left \|Strain/Substrain		!align=left \|Strain/Substrain
	\|\|		\|\|
	OMP_ST: vs OMP_STR vs ?		OMP_ST: vs OMP_STR vs ?
			\|\|

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

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


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Siegele at 22:21, 10 June 2014

2014-06-10T22:21:19Z

← Older revision		Revision as of 22:21, 10 June 2014
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	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

	~~Prefix~~		==Prefixes==
	~~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. ?~~

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Siegele: Table edited by Siegele via TableEdit

2014-06-10T22:20:30Z

Table edited by Siegele via TableEdit

← Older revision		Revision as of 22:20, 10 June 2014
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	*		*
	****************************************************************************************** -->		****************************************************************************************** -->
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			\|-
			!align=left \|Pan-genome
			\|\|
			OMP_PG: vs OMP_PGM vs ?
			\|-
			!align=left \|Pan-gene
			\|\|
			OMP_GN: vs OMP_PGN vs ?
			\|-
			!align=left \|Strain/Substrain
			\|\|
			OMP_ST: vs OMP_STR vs ?
			\|-
			!align=left \|Allele
			\|\|
			OMP_AL: vs OMP_ALL vs ?
	\|-		\|-
	!\|~~Pan-genome!!Pan-gene!!Strain/Substrain!!Allele!!~~Phenotype Annotation		!align=left \|Phenotype Annotation
			\|\|
			OMP_AN: vs. OMP_ANN vs ?

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Siegele at 22:18, 10 June 2014

2014-06-10T22:18:53Z

@@ Line 3: / Line 3: @@
 https://docs.google.com/document/d/1N3PQM4Prar9aZn5NlJCZJ0rCx7w_G_s2IbIBYXl8CO0/edit#heading=h.whbibz64jbk9
 Prefix
 Pan-genome: 		OMP_PG:	vs.	OMP_PGM	vs.	?
@@ Line 14: / Line 13: @@
 Annotation:		OMP_AN:	vs.	OMP_ANN	vs.	?

Siegele: 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: ..."

2014-06-10T22:16:22Z

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: ..."

New page

copied over from the googledoc

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

OMP ID Format
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. ?

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