Final Statements (Step 7)

Overview

Step 7 of gks_scv_statement_proc performs the final assembly of complete VA-Spec Statement records into gks_dict_scv. This step joins all previously built components -- SCV records, propositions, conditions, citations, and assertion methods -- into the output structure consumed by VCV procedures and the JSON export pipeline.

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CTEs

The step uses several CTEs to prepare intermediate data before the final SELECT.

scv_condition_name

Derives a single human-readable condition name string from gks_scv_condition_sets for use in the classification description extension:

• Single condition -- uses the condition's name field directly
• ConditionSet with 2+ conditions -- produces "N conditions" (e.g., "3 conditions")
• No condition -- falls back to "unspecified condition"

scv_citation / scv_citations

Aggregates citation records with source-specific URL resolution:

Source	URL Format
PubMed	https://pubmed.ncbi.nlm.nih.gov/{id}
PMC	https://www.ncbi.nlm.nih.gov/pmc/articles/{id}
DOI	https://doi.org/{id}
BookShelf	https://www.ncbi.nlm.nih.gov/books/{id}

Citations are collected into an array for the reportedIn field of the final statement.

scv_method

Builds the assertion method record for the specifiedBy field. Includes the method type, method name, and a linked citation document when the assertion method references a publication.

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Output Record Structure

Field	Source	Description
id	SCV	Statement identifier in the format clinvar.submission:{accession}.{version}
type	Static	Always Statement
proposition	Step 5	Full proposition with variant, condition, and qualifiers
classification	SCV	Classification struct with name, primaryCoding, and description extension
strength	SCV	Evidence strength with coded value (somatic assertions only)
direction	SCV	supports or disputes
description	SCV	Classification comment text
contributions	SCV	Three Contribution entries: submitted, created, and evaluated
specifiedBy	CTE	Assertion method with linked citation document
reportedIn	CTE	Array of citation documents
extensions	SCV	Array of SCV-level extensions (see below)
hasEvidenceLines	Step 6	Somatic evidence lines with target proposition and outcome

Extensions

The extensions array on each statement includes:

• clinvarScvId -- the SCV accession identifier
• clinvarScvVersion -- the SCV version number
• clinvarScvReviewStatus -- the review status assigned by ClinVar
• submittedScvClassification -- the original submitted classification label
• submittedScvLocalKey -- the submitter's local key for the assertion
• submissionLevel -- the submission level code and label

Classification Description Extension

The classification.extensions array contains a formatted description string assembled from multiple fields:

for <condition_name>
Classification is based on the <submission_level_label> submission
<evaluated_date> by <submitter_name>

This provides a human-readable summary of the classification context, including the condition, submission level, evaluation date, and submitting organization.

Somatic Evidence Lines

For somatic clinical impact assertions, the hasEvidenceLines field contains evidence line records that wrap the target proposition from Step 6. Each evidence line includes the target proposition (with its somatic-specific predicate and therapy/condition references) and the outcome classification.

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Output

gks_dict_scv -- one row per SCV with the complete VA-Spec Statement record. Pipeline table

Consumed by gks_vcv_proc, gks_vcv_statement_proc, and gks_json_proc for VCV aggregation and JSON export.

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Dependencies

• Upstream Steps: Step 1 (temp_gks_scv), Step 5 (temp_gks_scv_proposition), Step 6 (temp_gks_scv_target_proposition)
• Upstream Procedures: gks_scv_condition_proc (provides gks_scv_condition_sets)
• Downstream Consumers: gks_vcv_proc, gks_vcv_statement_proc, gks_json_proc