test: update civic onco assertion test fixture

[korikuzma]

I'm working on supporting Oncgenicity CIViC Assertions. Using CIViCpy, this is the exact representation we would use.

Updates:

• Add description
• Add alleleOriginQualifier + geneContextQualifier to propositions
• Update proposition variant: Fix variant aliases, add addtl mapping, add extensions
• Add specifiedBy + extensions to Evidence Line

@ahwagner I had a couple questions/comments about things that feel a little redundant/off to me, and wanted to see if there's a different way we should be representing these:

1. In CIViCpy, we temporarily store a citation extension in each Evidence Line to preserve EID references (GksExporter: Revert temporary extension citations griffithlab/civicpy#219 will eventually revert this). As a result, the same extension is duplicated across Evidence Lines.

Example:

va-spec/tests/fixtures/civic-assertion-oncogenicity.yaml

Lines 352 to 361 in ab2a15c

	extensions: # These are the same across all evidence lines
	- name: citations
	value:
	- https://civicdb.org/links/evidence/74
	- https://civicdb.org/links/evidence/12800
	- https://civicdb.org/links/evidence/78
	- https://civicdb.org/links/evidence/12711
	- https://civicdb.org/links/evidence/12805
	- https://civicdb.org/links/evidence/11723
	- https://civicdb.org/links/evidence/12709

Given that this is a temporary workaround, is it acceptable to keep the EID references duplicated across Evidence Lines, or would you prefer that they be represented elsewhere? If the latter, do you have a suggestion?

2. Using same example above, I do not attempt to determine which specific EID a given code was derived from, nor do I filter EIDs by evidence type. This means an oncogenic assertion may include EIDs associated with non-oncogenic evidence.

In above example, only 12800, 12709, and 11723 EIDs have oncogenic evidence type.

Given this, is it acceptable to submit all associated EIDs, even though some may not correspond directly to the oncogenic assertion evidence?

3. Because oncogenic assertions can be supported by a mix of CIViC evidence types, we do not currently represent Evidence Items in EvidenceLine.hasEvidenceItems. Given that limitation, should I submit only the EIDs described above in 1, or should I also include the PMIDs associated with those EIDs for downstream ClinVar use?

4. Statement.specifiedBy and EvidenceLine.specifiedBy are the identical except for methodType, where statement uses guideline and evidence line uses a value such as functional_domain_location.

Statement:

va-spec/tests/fixtures/civic-assertion-oncogenicity.yaml

Lines 158 to 171 in 43c83fc

	specifiedBy:
	name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022
	reportedIn:
	id: pmid:35101336
	name: Horak et al., 2022, Genet Med.
	title: "Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)"
	doi: 10.1016/j.gim.2022.01.001
	pmid: "35101336"
	urls:
	- https://doi.org/10.1016/j.gim.2022.01.001
	- https://pubmed.ncbi.nlm.nih.gov/35101336/
	type: Document
	methodType: guideline
	type: Method

EvidenceLine:

va-spec/tests/fixtures/civic-assertion-oncogenicity.yaml

Lines 206 to 223 in 43c83fc

	specifiedBy:
	type: Method
	methodType: functional_domain_location
	name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022
	reportedIn:
	doi: 10.1016/j.gim.2022.01.001
	id: pmid:35101336
	name: Horak et al., 2022, Genet Med.
	pmid: "35101336"
	title:
	"Standards for the classification of pathogenicity of somatic variants in
	cancer (oncogenicity): Joint recommendations of Clinical Genome
	Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant
	Interpretation for Cancer Consortium (VICC)"
	type: Document
	urls:
	- https://doi.org/10.1016/j.gim.2022.01.001
	- https://pubmed.ncbi.nlm.nih.gov/35101336/

5. This is how we currently reprsent MANE select transcripts in CIViCpy. For ClinVar This, we'll want to think about how to handle this. Currently, Allele.expressions ordered=False. So would we just look for an extension that says MANE or priority (since non-hgvs could be provied)?
   

   va-spec/tests/fixtures/civic-assertion-oncogenicity.yaml

   Lines 138 to 142 in ca47c43

   	- syntax: hgvs.c
   	value: ENST00000355710.8:c.2753T>C
   	extensions:
   	- name: is_mane_select
   	value: true

6. test: update civic onco assertion test fixture #404 (comment) - confirm system is okay. @ahwagner gave revised changes feat!: store allele origin as mapping, not extension griffithlab/civicpy#236 (comment).

7. Statement.proposition and EvidenceLine.targetProposition are identical (

   va-spec/tests/fixtures/civic-assertion-oncogenicity.yaml

   Line 364 in ab2a15c

   targetProposition: # identical to VariantOncogenicityStatement.proposition

   )
   NOTE: Deleted EvidenceLine.targetProposition, will assume Statement.proposition

8. Clarity on Method Type exists in evidence line for ACMG 2015 profile #407 -- does this mean methodType should not exist in Evidence Lines? This could also impact oncogenicity evdience lines

[ahwagner]

Started reviewing, made it only through assertion, but wanted to provide feedback early

[ahwagner]

Instead of an extension, this is an ideal candidate for an exact match mapping.

[korikuzma]

Not sure what you would want for the system?

    mappings:
      - coding:
          code: SOMATIC
          system: https://civicdb.org
        relation: exactMatch

[ahwagner]

Great work!