Merge pull request #565 from ga4gh/variation_annotation

@jeromekelleher: I agree about times -- we should go for consistency.

I can't tell whether your comment is intended to hold on this merge or not.

I created #568 to choose a consistent time format. If we can get a quick decision on that, the path becomes easy.

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
 @@@@@@@@@@@@@@

doc/source/schemas/alleleAnnotationmethods.rst

@@ -365,14 +365,14 @@ Gets an `VariantAnnotationSet` 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 <metadata_date_time>`
-  :type created: string
-  :field updated:
+  :type createDateTime: string
+  :field updateDateTime:
     The time at which this record was last updated.
       Format: :ref:`ISO 8601 <metadata_date_time>`
-  :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 <metadata_date_time>`
-  :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 <metadata_date_time>`
-  :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<OntologyTerm>
-  :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 <metadata_date_time>` 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.

doc/source/schemas/readmethods.rst

@@ -200,14 +200,14 @@ 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 <metadata_date_time>`
-  :type created: string
-  :field updated:
+  :type createDateTime: string
+  :field updateDateTime:
     The time at which this record was last updated.
       Format: :ref:`ISO 8601 <metadata_date_time>`
-  :type updated: string
+  :type updateDateTime: string
   :field runTime:
     The time at which this experiment was performed.
       Granularity here is variable (e.g. date only).
@@ -278,14 +278,14 @@ 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 <metadata_date_time>`
-  :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 <metadata_date_time>`
-  :type updated: string
+  :type updateDateTime: string
   :field type:
     The type of analysis.
   :type type: null|string

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 <metadata_date_time>`
-  :type created: string
-  :field updated:
+  :type createDateTime: string
+  :field updateDateTime:
     The time at which this record was last updated.
       Format: :ref:`ISO 8601 <metadata_date_time>`
-  :type updated: string
+  :type updateDateTime: string
   :field runTime:
     The time at which this experiment was performed.
       Granularity here is variable (e.g. date only).
@@ -221,14 +221,14 @@ See {TODO: LINK TO READS OVERVIEW} for more information.
   :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 <metadata_date_time>`
-  :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 <metadata_date_time>`
-  :type updated: string
+  :type updateDateTime: string
   :field type:
     The type of analysis.
   :type type: null|string