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transformation notes.txt
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This file contains info on transforming the following
1. VARIANT
2. DISEASE
3. CRITERION ASSESSMENTS
4. EVIDENCE ITEMS FROM PUBMED INFO
5. CONTRIBUTION / AGENT
(each section below has the above heading as a title)
1. VARIANT
==========
The variant must contain the "preferred transcript" information if possible using the following rules
a. if the clinvarVariantTitle exists presume that it is the preferred transcript (use it to look up the transcript allele bits).
b. if no clinvar id exists then the canonicalTranscriptTitle might exist which is a manufactured description using the Ensembl VEP service lookup of the canonical transcript (ultimate plan)
c. otherwise use the b38 accession and hgvs notation.
Always provide the transcript aligned alleles and "mark" the preferred transcript.
Make sure that if transcripts exist they have a reference to the gene id and symbol for the transcript
Always pass the 37 and 38 genomic alleles.
if available pass the clinvar and dbsnp ids associated with the canonical allele
Given (VCI provided)
"variant": {
"schema_version": "4",
"@type": ["variant","item"],
"uuid": "3aae8164-ec43-4305-8125-fa39c9e85d70",
"@id": "/variants/3aae8164-ec43-4305-8125-fa39c9e85d70/",
"clinvarVariantTitle": "NM_004700.3(KCNQ4):c.825G>C (p.Trp275Cys)",
"clinvarVariantId": "505302",
"clinVarRCVs": [],
"clinVarSCVs": [],
"source": "ClinVar",
look for this.... canonicalTranscriptTitle -> built from the VEP ensembl service call (see Jimmy)
"variationType": "single nucleotide variant",
"variation_type": "single nucleotide variant",
"otherDescription": "",
"carId": "CA21112664",
"hgvsNames": {
"others": [
"NG_008139.1:g.40452G>C",
"NM_004700.3:c.825G>C",
"NP_004691.2:p.Trp275Cys"
],
"GRCh38": "NC_000001.11:g.40819463G>C",
"GRCh37": "NC_000001.10:g.41285135G>C"
},
"molecularConsequenceList": [
{
"hgvsName": "NM_004700.3:c.825G>C",
"term": "missense variant",
"soId": "SO:0001583"
}
],
"molecular_consequence": "missense variant",
"variant_identifier": "505302",
"dbSNPIds": ["956666801"],
"date_created": "2018-08-15T13:23:35.195400+00:00"
},
*****************************************
CG allele registry lookkup result used to create Variant below
{
"@context": "http://reg.genome.network/schema/allele.jsonld",
"@id": "http://reg.genome.network/allele/CA21112664",
"externalRecords": {
"ClinVarAlleles": [
{
"@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=496205[alleleid]",
"alleleId": 496205,
"preferredName": "NM_004700.3(KCNQ4):c.825G>C (p.Trp275Cys)"
}
],
"ClinVarVariations": [
{
"@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/505302",
"RCV": [
"RCV000599794"
],
"variationId": 505302
}
],
"MyVariantInfo_hg19": [
{
"@id": "http://myvariant.info/v1/variant/chr1:g.41285135G>C?assembly=hg19",
"id": "chr1:g.41285135G>C"
}
],
"MyVariantInfo_hg38": [
{
"@id": "http://myvariant.info/v1/variant/chr1:g.40819463G>C?assembly=hg38",
"id": "chr1:g.40819463G>C"
}
],
"dbSNP": [
{
"@id": "http://www.ncbi.nlm.nih.gov/snp/956666801",
"rs": 956666801
}
]
},
"genomicAlleles": [
{
"chromosome": "1",
"coordinates": [
{
"allele": "C",
"end": 40819463,
"referenceAllele": "G",
"start": 40819462
}
],
"hgvs": [
"NC_000001.11:g.40819463G>C",
"CM000663.2:g.40819463G>C"
],
"referenceGenome": "GRCh38",
"referenceSequence": "http://reg.genome.network/refseq/RS000049"
},
{
"chromosome": "1",
"coordinates": [
{
"allele": "C",
"end": 41057722,
"referenceAllele": "G",
"start": 41057721
}
],
"hgvs": [
"NC_000001.9:g.41057722G>C"
],
"referenceGenome": "NCBI36",
"referenceSequence": "http://reg.genome.network/refseq/RS000001"
},
{
"chromosome": "1",
"coordinates": [
{
"allele": "C",
"end": 41285135,
"referenceAllele": "G",
"start": 41285134
}
],
"hgvs": [
"NC_000001.10:g.41285135G>C",
"CM000663.1:g.41285135G>C"
],
"referenceGenome": "GRCh37",
"referenceSequence": "http://reg.genome.network/refseq/RS000025"
},
{
"coordinates": [
{
"allele": "C",
"end": 40452,
"referenceAllele": "G",
"start": 40451
}
],
"hgvs": [
"NG_008139.1:g.40452G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS000885"
}
],
"transcriptAlleles": [
{
"coordinates": [
{
"allele": "C",
"end": 907,
"referenceAllele": "G",
"start": 906
}
],
"hgvs": [
"ENST00000347132.9:c.825G>C"
],
"proteinEffect": {
"hgvs": "ENSP00000262916.6:p.Trp275Cys",
"hgvsWellDefined": "ENSP00000262916.6:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS262332"
},
{
"coordinates": [
{
"allele": "C",
"end": 511,
"referenceAllele": "G",
"start": 510
}
],
"hgvs": [
"ENST00000443478.3:n.511G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS297357"
},
{
"coordinates": [
{
"allele": "C",
"end": 144,
"referenceAllele": "G",
"start": 143
}
],
"hgvs": [
"ENST00000506017.1:n.144G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS337656"
},
{
"coordinates": [
{
"allele": "C",
"end": 825,
"referenceAllele": "G",
"start": 824
}
],
"hgvs": [
"ENST00000509682.6:n.825G>C"
],
"proteinEffect": {
"hgvs": "ENSP00000423756.2:p.Trp275Cys",
"hgvsWellDefined": "ENSP00000423756.2:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS340393"
},
{
"coordinates": [
{
"allele": "C",
"end": 907,
"referenceAllele": "G",
"start": 906
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"NM_004700.3:c.825G>C"
],
"proteinEffect": {
"hgvs": "NP_004691.2:p.Trp275Cys",
"hgvsWellDefined": "NP_004691.2:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS029850"
},
{
"coordinates": [
{
"allele": "C",
"end": 907,
"referenceAllele": "G",
"start": 906
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"NM_172163.2:c.825G>C"
],
"proteinEffect": {
"hgvs": "NP_751895.1:p.Trp275Cys",
"hgvsWellDefined": "NP_751895.1:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS042665"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XM_011542417.1:c.825G>C"
],
"proteinEffect": {
"hgvs": "XP_011540719.1:p.Trp275Cys",
"hgvsWellDefined": "XP_011540719.1:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS109348"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XM_011542418.1:c.825G>C"
],
"proteinEffect": {
"hgvs": "XP_011540720.1:p.Trp275Cys",
"hgvsWellDefined": "XP_011540720.1:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS109349"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XM_011542419.1:c.825G>C"
],
"proteinEffect": {
"hgvs": "XP_011540721.1:p.Trp275Cys",
"hgvsWellDefined": "XP_011540721.1:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS109350"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XM_011542420.1:c.825G>C"
],
"proteinEffect": {
"hgvs": "XP_011540722.1:p.Trp275Cys",
"hgvsWellDefined": "XP_011540722.1:p.Trp275Cys"
},
"referenceSequence": "http://reg.genome.network/refseq/RS109351"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XR_946798.1:n.831G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS140380"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XR_946799.1:n.831G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS140381"
},
{
"coordinates": [
{
"allele": "C",
"end": 831,
"referenceAllele": "G",
"start": 830
}
],
"gene": "http://reg.genome.network/gene/GN006298",
"geneNCBI_id": 9132,
"geneSymbol": "KCNQ4",
"hgvs": [
"XR_946800.1:n.831G>C"
],
"referenceSequence": "http://reg.genome.network/refseq/RS140382"
}
],
"type": "nucleotide"
}
*****************************************
OUTPUT of VCI transform of Variant
"allele": {
"canonicalAlleleType": "nucleotide",
"complexity": "simple",
"id": "CAR:CA21112664",
"relatedContextualAllele": [
{
"alleleName": [
{
"name": "NC_000001.11:g.40819463G>C",
"nameType": "hgvs"
},
{
"name": "CM000663.2:g.40819463G>C",
"nameType": "hgvs"
}
],
"contextualAlleleType": "genomic",
"preferred": true,
"referenceCoordinate": {
"end": {
"index": 40819463
},
"refState": "G",
"referenceSequence": {
"label": "NC_000001.11",
"reference": "http://reg.genome.network/refseq/RS000049"
},
"start": {
"index": 40819462
}
},
"relatedCanonicalAllele": "CAR:CA21112664",
"state": "C",
"type": "ContextualAllele"
},
{
"alleleName": [
{
"name": "NC_000001.9:g.41057722G>C",
"nameType": "hgvs"
}
],
"contextualAlleleType": "genomic",
"referenceCoordinate": {
"end": {
"index": 41057722
},
"refState": "G",
"referenceSequence": {
"label": "NC_000001.9",
"reference": "http://reg.genome.network/refseq/RS000001"
},
"start": {
"index": 41057721
}
},
"relatedCanonicalAllele": "CAR:CA21112664",
"state": "C",
"type": "ContextualAllele"
},
{
"alleleName": [
{
"name": "NC_000001.10:g.41285135G>C",
"nameType": "hgvs"
},
{
"name": "CM000663.1:g.41285135G>C",
"nameType": "hgvs"
}
],
"contextualAlleleType": "genomic",
"referenceCoordinate": {
"end": {
"index": 41285135
},
"refState": "G",
"referenceSequence": {
"label": "NC_000001.10",
"reference": "http://reg.genome.network/refseq/RS000025"
},
"start": {
"index": 41285134
}
},
"relatedCanonicalAllele": "CAR:CA21112664",
"state": "C",
"type": "ContextualAllele"
},
{
"alleleName": [
{
"name": "NG_008139.1:g.40452G>C",
"nameType": "hgvs"
}
],
"contextualAlleleType": "genomic",
"referenceCoordinate": {
"end": {
"index": 40452
},
"refState": "G",
"referenceSequence": {
"label": "",
"reference": "http://reg.genome.network/refseq/RS000885"
},
"start": {
"index": 40451
}
},
"relatedCanonicalAllele": "CAR:CA21112664",
"state": "C",
"type": "ContextualAllele"
}
],
"relatedIdentifier": [
{
"label": "NM_004700.3(KCNQ4):c.825G>C (p.Trp275Cys)"
},
{
"id": "dbSNP:956666801"
}
],
"type": "CanonicalAllele"
},
2. DISEASE
==========
Can be a string name with a list of hpo phenos and a definition
usually a mondo id
also include the moi which is a combo of the top-level moi and the 2nd-level adjective (essentially a hierarchy with unknown and other as choices)
see translation table in doc.
3. CRITERION ASSESSMENTS
========================
the "Met" assessments get the "explanation" and all the pmid evidence in the panel
the "Not Met" assessments all get passed, but
- they only get "explanations" if they have only one associated or they are in a mutually exclusive group and no other member of the group is "Met"
- they only get the pmids for the panel if their is no other "Met" assessment anywhere in the panel - then they get the pmids as evidence.
NOTE: we need to "MARK" the criterion assessments with PMID evidence that is not a 1:1 in a panel.
we need to "MARK" the criterion assessments with explanations that are not a 1:1 in a panel.
4. EVIDENCE ITEMS FROM PUBMED INFO
==================================
the text of the literature evidence acts as a generic evidence information item, the set of literature evidence items get bundled under an evidence line that supports the associated criterion assessment
The pmids themselves are sources for the evidence text associated to the pmid.
5. CONTRIBUTION / AGENT
=======================
If an affiliation exists for the approver then only the affiliation will be included in the contribution at the interpretation level (no indivudal user info)
If no affiliation exists for the interp then the approver (user) will be the contribution for the interpretation and listed
The role of the contribution at the interpretation level will be "Approver". (not interpreter). no contributions for now on criterion assessments.
Two contributions need to exist at the top level interp
1 - Approver, approved date, affiliation, if not then user
2 - Publisher, published date, affiliation, if not then user