OMIM Annotation Standards - Revision history

Cjm: Replacing page with 'Moved to [http://www.obofoundry.org/wiki/index.php/PATO:OMIM_Annotation_Standards OMIM_Annotation_Standards]'

2010-01-15T19:43:28Z

Replacing page with 'Moved to [http://www.obofoundry.org/wiki/index.php/PATO:OMIM_Annotation_Standards OMIM_Annotation_Standards]'

Nicolew: /* Basic Rules */

2007-11-05T22:53:34Z

Basic Rules

Nicolew: /* Basic Rules */

2007-11-05T22:45:58Z

Basic Rules

Nicolew: New page: This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax. ==Basic Rules=...

2007-11-05T20:50:37Z

New page: This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax. ==Basic Rules=...

New page

This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax.

==Basic Rules==
# Use the ncbo 'config'. This will include automatic updates to the latest ontologies from SF.
# No use of MP, though it can be used to look for good cross-products
# Use the same style for gene ids. ie. OMIM:601653.0005 (database:identifier dot allele designation)
# no postcomposition using GO:Biological_Process with a continuant
# limit the post-comp relation to part_of. we can discuss this- but this is what we do at zfin, so at least the zebrafish data is biased in this way already
# If its known that a process is affected (usually when there is more than one time point), annotate to the process in addition to the anatomy.
# Annotate to both general omim id, as well as the alleles.
#* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles. when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
# When a PATO term is missing, always annotate to the next most specific term. If a branch is missing, annotate to the general term "quality".
# use standard notation like OMIM:1234567.0001/OMIM:1234567.0001 to indicate known homozygosity
# use OMIM:1234567.0001/+ to indicate known heterozygosity
# use OMIM:1234567.0001/OMIM:1234567.0002 to indicate any known trans-het
# indicate dominance/recessiveness in the Genetic Context box.
# if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
# mark annotations as 'abnormal', except in the case of 'remarkable normality'. (see below)

==Remarkable Normality==
There is a special case wherein a particular phenotype character is expected, and is observed NOT to occur, or what we call 'remarkable normality'.
But this truly is a reflection of one 'normal' phenotype ''in comparison'' to the 'mutant' phenotype.
# in the first pass, be sure to list the phenotype as it is listed in the other mutants, but add the qualifier of 'normal'.
==Comparative Statements==

← Older revision		Revision as of 19:43, 15 January 2010
Line 1:		Line 1:
−	~~This page is~~ to ~~describe the rules that the NCBO curators are employing for translating the OMIM gene~~/~~disease description pages into phenotype statements using EQ syntax.~~	+	Moved to [http://www.obofoundry.org/wiki/index.php/PATO:OMIM_Annotation_Standards OMIM_Annotation_Standards]
−
−	~~==Basic Rules==~~
−	~~# Use the ncbo 'config'. This will include automatic updates to the latest ontologies from SF.~~
−	~~# No use of MP, though it can be used to look for good cross-products~~
−	~~# Use the same style for gene ids. ie. OMIM:601653.0005 (database:identifier dot allele designation)~~
−	~~# no postcomposition using GO:Biological_Process with a continuant~~
−	~~# limit the post-comp relation to part_of. we can discuss this- but this is what we do at zfin, so at least the zebrafish data is biased in this way already~~
−	~~# If its known that a process is affected (usually when there is more than one time point), annotate to the process in addition to the anatomy.~~
−	~~# Annotate to both general omim id, as well as the alleles.~~
−	#* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles. when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
−	#*Sometimes there is phenotype data in the body of the OMIM record (eg. general OMIM ID) that does not refer to an allelic variant. However, many times in the body of the OMIM record it does in fact use the allelic variant ID (and refers to the allelic variants section). In this case, we don't need to record it for the general ID AND the allelic variant, just the allelic variant. Think of the general OMIM ID (as we are using it) as being all non-indicated alleles, rather than a general phenotype description of all alleles.
−	~~# When a PATO term is missing, always annotate to the next most specific term. If a branch is missing, annotate to the general term "quality".~~
−	~~# use standard notation like OMIM:1234567.0001~~/~~OMIM:1234567~~.~~0001 to indicate known homozygosity~~
−	~~# use OMIM:1234567~~.~~0001~~/~~+ to indicate known heterozygosity~~
−	~~# use OMIM:1234567.0001~~/~~OMIM:1234567~~.~~0002 to indicate any known trans-het~~
−	~~# indicate dominance~~/~~recessiveness in the Genetic Context box.~~
−	~~# if OMIM~~:~~1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?~~
−	~~# mark annotations as 'abnormal', except in the case of 'remarkable normality'. (see below)~~
−	~~# dates that annotations are created will be set automatically in the background by phenote.~~
−	~~# be sure to indicate incomplete_penetrance in the cases where multiple family members are described with the same genotype but different phenotypes.~~
−
−	~~==Remarkable Normality==~~
−	~~There is a special case wherein a particular phenotype character is expected, and is observed NOT to occur, or what we call 'remarkable normality'.~~
−	~~But this truly is a reflection of one 'normal' phenotype ''in comparison'' to the 'mutant' phenotype.~~
−	~~# in the first pass, be sure to list the phenotype as it is listed in the other mutants, but add the qualifier of 'normal'.~~
−	~~==Comparative Statements==~~

@@ Line 18: / Line 18: @@
 # if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
 # mark annotations as 'abnormal', except in the case of 'remarkable normality'.  (see below)
-# dates that annotations are created will be set automatically.
+# dates that annotations are created will be set automatically in the background by phenote.
 ==Remarkable Normality==

@@ Line 10: / Line 10: @@
 # Annotate to both general omim id, as well as the alleles.
 #* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles.  when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
 # When a PATO term is missing, always annotate to the next most specific term.  If a branch is missing, annotate to the general term "quality".
 # use standard notation like OMIM:1234567.0001/OMIM:1234567.0001 to indicate known homozygosity
@@ Line 17: / Line 18: @@
 # if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
 # mark annotations as 'abnormal', except in the case of 'remarkable normality'.  (see below)
 ==Remarkable Normality==