From 5144747642fd9864f00ea48f9bedf35925e17e17 Mon Sep 17 00:00:00 2001 From: Sarah Hunt Date: Fri, 26 Feb 2016 11:25:00 +0000 Subject: [PATCH 1/3] update docs to remove impact --- doc/source/api/alleleAnnotations.rst | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/doc/source/api/alleleAnnotations.rst b/doc/source/api/alleleAnnotations.rst index cdc1ac33..84c232f5 100644 --- a/doc/source/api/alleleAnnotations.rst +++ b/doc/source/api/alleleAnnotations.rst @@ -63,29 +63,6 @@ transcripts. The record includes: * A ``HGVSAnnotation`` record containing variant descriptions at all relevant levels. * ``AlleleLocation`` records describing the changes at cDNA, CDS and protein level. * A set of results from prediction packages analyzing the allele impact. -* A summary impact classification reflecting the highest impact consequence. - -Predicted Molecular Impact Classification -@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - -The predicted molecular impact is a simple prioritization based on the putative -deleteriousness of the variant allele on the transcript, which is popular with -users of annotation tools. This is usually calculated based on naive algorithms -and may not accurately predict true impact at protein level. - -Predicted Molecular Impact classification is summarized using the terms: - -+----------+-----------------------------------------------+-------------------------------------------+ -| Impact | Meaning | Example SO terms | -+==========+===============================================+===========================================+ -| HIGH | Highly likely to disrupt protein function | splice_donor_variant, stop_gained | -+----------+-----------------------------------------------+-------------------------------------------+ -| MODERATE | Moderately likely to disrupt protein function | missense_variant, inframe_insertion | -+----------+-----------------------------------------------+-------------------------------------------+ -| LOW | Not likely to disrupt protein function | synonymous_variant, stop_retained_variant | -+----------+-----------------------------------------------+-------------------------------------------+ -| MODIFIER | No predicted effect | 3_prime_UTR_variant, intron_variant | -+----------+-----------------------------------------------+-------------------------------------------+ Search Options @@@@@@@@@@@@@@ From 31dc2f2862c4c20a4956fe9140c0fa86082db138 Mon Sep 17 00:00:00 2001 From: Andrew Jesaitis Date: Fri, 26 Feb 2016 16:56:47 -0700 Subject: [PATCH 2/3] Updates diagram to be consistent with schema in master * Removes Imapact Enum * Changes created to createDateTime on VariantAnnoation --- doc/source/_static/variant_annotation_schema.gliffy | 2 +- doc/source/_static/variant_annotation_schema.svg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/_static/variant_annotation_schema.gliffy b/doc/source/_static/variant_annotation_schema.gliffy index 94d89009..3941bc94 100644 --- a/doc/source/_static/variant_annotation_schema.gliffy +++ 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impact Impact

HGVSAnnotation hgvsAnnotation

cDNALocation union{null, AlleleLocation}

CDSLocation union{null, AlleleLocation}

proteinLocation union{null, AlleleLocation}

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transcriptEffects array<TranscriptEffect>

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cDNALocation union{null, AlleleLocation}

CDSLocation union{null, AlleleLocation}

proteinLocation union{null, AlleleLocation}

analysisResults array<AnalysisResult> 

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VariantAnnotation

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id string

variantId string

variantAnnotationSetId string

createDateTime union {null, string}

transcriptEffects array<TranscriptEffect>

info map<array<string>>

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experiment. :type description: null|string - :field created: + :field createDateTime: The time at which this record was created. Format: :ref:`ISO 8601 ` - :type created: string - :field updated: + :type createDateTime: string + :field updateDateTime: The time at which this record was last updated. Format: :ref:`ISO 8601 ` - :type updated: string + :type updateDateTime: string :field runTime: The time at which this experiment was performed. Granularity here is variable (e.g. date only). @@ -443,14 +443,14 @@ Gets an `VariantAnnotationSet` by ID. :type name: null|string :field description: :type description: null|string - :field created: + :field createDateTime: The time at which this record was created. Format: :ref:`ISO 8601 ` - :type created: null|string - :field updated: + :type createDateTime: null|string + :field updateDateTime: The time at which this record was last updated. Format: :ref:`ISO 8601 ` - :type updated: string + :type updateDateTime: string :field type: The type of analysis. :type type: null|string @@ -499,16 +499,6 @@ Gets an `VariantAnnotationSet` by ID. non-genomic coordinate system such as a CDS or protein and holds the reference and alternate sequence where appropriate -.. avro:enum:: Impact - - :symbols: HIGH|MODERATE|LOW|MODIFIER - Impact is a simple prioritization for the effect of an allele which is used - in the annotation record. - IMPORTANT: - Prioritization methods are a crude estimates and are not assumed to be - reliable: a 'HIGH' Impact may actually not cause any disruption - in protein function or expression. - .. avro:record:: VariantAnnotationSet :field id: @@ -561,9 +551,6 @@ Gets an `VariantAnnotationSet` by ID. :field effects: Effect of variant on this feature :type effects: array - :field impact: - Highest Impact from the predicted effects - :type impact: Impact :field hgvsAnnotation: Human Genome Variation Society variant descriptions :type hgvsAnnotation: HGVSAnnotation @@ -593,9 +580,9 @@ Gets an `VariantAnnotationSet` by ID. :field variantAnnotationSetId: The ID of the variant annotation set this record belongs to. :type variantAnnotationSetId: string - :field created: + :field createDateTime: The :ref:`ISO 8601 ` time at which this record was created. - :type created: null|string + :type createDateTime: null|string :field transcriptEffects: The transcript effect annotation for the alleles of this variant. Each one represents the effect of a single allele on a single transcript. diff --git a/doc/source/schemas/readmethods.rst b/doc/source/schemas/readmethods.rst index a79de529..b9bca32f 100644 --- a/doc/source/schemas/readmethods.rst +++ b/doc/source/schemas/readmethods.rst @@ -223,14 +223,14 @@ Gets a `org.ga4gh.models.ReadGroup` by ID. :field description: A description of the experiment. :type description: null|string - :field created: + :field createDateTime: The time at which this record was created. Format: :ref:`ISO 8601 ` - :type created: string - :field updated: + :type createDateTime: string + :field updateDateTime: The time at which this record was last updated. Format: :ref:`ISO 8601 ` - :type updated: string + :type updateDateTime: string :field runTime: The time at which this experiment was performed. Granularity here is variable (e.g. date only). @@ -301,14 +301,14 @@ Gets a `org.ga4gh.models.ReadGroup` by ID. :type name: null|string :field description: :type description: null|string - :field created: + :field createDateTime: The time at which this record was created. Format: :ref:`ISO 8601 ` - :type created: null|string - :field updated: + :type createDateTime: null|string + :field updateDateTime: The time at which this record was last updated. Format: :ref:`ISO 8601 ` - :type updated: string + :type updateDateTime: string :field type: The type of analysis. :type type: null|string diff --git a/doc/source/schemas/reads.rst b/doc/source/schemas/reads.rst index 02f4eece..7bcc1f6b 100644 --- a/doc/source/schemas/reads.rst +++ b/doc/source/schemas/reads.rst @@ -143,14 +143,14 @@ See {TODO: LINK TO READS OVERVIEW} for more information. :field description: A description of the experiment. :type description: null|string - :field created: + :field createDateTime: The time at which this record was created. Format: :ref:`ISO 8601 ` - :type created: string - :field updated: + :type createDateTime: string + :field updateDateTime: The time at which this record was last updated. Format: :ref:`ISO 8601 ` - :type updated: string + :type updateDateTime: string :field runTime: The time at which this experiment was performed. 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