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Update examples to VRS 2.0 #151

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Update examples to VRS 2.0 #151

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8c115da
update tpm3-ntrk1 example
jarbesfeld Jul 8, 2024
dbe8349
Ruff format fix for bcr-abl1
jarbesfeld Jul 8, 2024
2b77021
Replace gene_descriptor with gene
jarbesfeld Jul 8, 2024
5656a6d
Replace gene in ABL1 functional example
jarbesfeld Jul 8, 2024
3521a4d
update example bcr_abl1
ahwagner Jul 13, 2024
5fb4383
extend bcr::abl1 example
ahwagner Jul 13, 2024
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208 changes: 114 additions & 94 deletions src/fusor/examples/bcr_abl1.json
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Original file line number Diff line number Diff line change
@@ -1,111 +1,131 @@
{
"type": "CategoricalFusion",
"structural_elements": [
{
"type": "TranscriptSegmentElement",
"transcript": "refseq:NM_004327.3",
"gene_descriptor": {
"type": "GeneDescriptor",
"id": "normalize.gene:BCR",
"gene_id": "hgnc:1014",
"label": "BCR"
"structure": {
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the Structure field should be a VRS Adjacency (for transcript junction descriptions) or a VRS DerivativeMolecule (under development; use for full fusion transcript representations). The former are much more common, as illustrated in this BCR::ABL1 example.

"type": "Adjacency",
"adjoinedSequences": [{
"type": "SequenceLocation",
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The adjoinedSequence SequenceLocation objects for the adjacency are based on genomic coordinates corresponding to the fusion junction; for categorical fusions and many reported assayed fusions, these are typically at (or close to) transcript boundaries as aligned to a chromosome.

"sequenceReference": {
"id": "GRCh38:chr22",
"type": "SequenceReference",
"refgetAccession": "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ",
"residueAlphabet": "na"
},
"element_genomic_end": {
"id": "fusor.location_descriptor:NC_000022.11",
"type": "LocationDescriptor",
"label": "NC_000022.11",
"location": {
"type": "SequenceLocation",
"sequence_id": "refseq:NC_000022.11",
"interval": {
"type": "SequenceInterval",
"start": {
"type": "Number",
"value": 23253980
},
"end": {
"type": "Number",
"value": 23253981
"end": 23290413,
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Note that here we use end (appropriately) but the 5' partner expressed in genomic coordinates should use start if the transcribed sequence is on the negative strand. Using end represents a boundary that includes sequence to the left (here, the sequence left of the aligned genomic coordinates at position 23290413, corresponding to the BCR exon 14).

image

"extensions": [
{
"name": "NM_004327.4:e._14",
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This extension to the genomic coordinate shows the representation of the transcript segment boundary in terms of the VICC exon representation.

"description": "VICC exon representation of the aligned transcript boundary.",
"value": {
"exon_end": 14,
"exon_end_offset": 0,
"sequenceReference":{
"type": "SequenceReference",
"id": "NM_004327.4",
"refgetAccession": "SQ.kpytJsXw3BwLC3oBSjHQS1kwxs4WO3I3",
"residueAlphabet": "na"
}
}
}
},
"exon_end": 2,
"exon_end_offset": 182
},
{
"type": "LinkerSequenceElement",
"linker_sequence": {
"id": "sequence:ACTAAAGCG",
"type": "SequenceDescriptor",
"sequence": "ACTAAAGCG",
"residue_type": "SO:0000348"
}
},
{
"type": "TranscriptSegmentElement",
"transcript": "refseq:NM_005157.5",
"exon_start": 2,
"exon_start_offset": -173,
"gene_descriptor": {
"id": "normalize.gene:ABL1",
"type": "GeneDescriptor",
"label": "ABL1",
"gene_id": "hgnc:76"
},
"element_genomic_start": {
"id": "fusor.location_descriptor:NC_000009.12",
"type": "LocationDescriptor",
"label": "NC_000009.12",
"location": {
"type": "SequenceLocation",
"sequence_id": "refseq:NC_000009.12",
"interval": {
"type": "SequenceInterval",
"start": {
"type": "Number",
"value": 130854064
},
{
"name": "NM_004327.4:c._2782",
"description": "Transcript SequenceLocation of the aligned transcript boundary.",
"value": {
"type": "SequenceLocation",
"sequenceReference": {
"id": "NM_004327.4",
"type": "SequenceReference",
"refgetAccession": "SQ.kpytJsXw3BwLC3oBSjHQS1kwxs4WO3I3",
"residueAlphabet": "na"
},
"end": {
"type": "Number",
"value": 130854065
}
"end": 3234
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Here, we again use end, as we always expect to see in the transcript sequence representation for the 5' partner. For transcripts aligning to the negative strand of a chromsome, this would remain end, even though the chromosome representation (on line 13) would use start.

}
},
{
"name": "gene",
"description": "The gene concept (BCR) associated with this fusion partner.",
"value": {
"code": "hgnc:1014",
"system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
"label": "BCR"
Comment on lines +47 to +49
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This is a GKS Coding object.

}
}
}
]},
{
"type": "SequenceLocation",
"sequenceReference": {
"id": "GRCh38:chr9",
"type": "SequenceReference",
"refgetAccession": "SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI",
"residueAlphabet": "na"
},
"start": 130854064,
"extensions": [
{
"name": "NM_005157.6:e.2_",
"description": "VICC exon representation of the aligned transcript boundary.",
"value": {
"exon_start": 2,
"exon_start_offset": 0,
"sequenceReference":{
"id": "NM_005157.6",
"type": "SequenceReference",
"refgetAccession": "SQ.w8Qg3x-PQ2akJrJQeGEN-_eBUMo1H1CL",
"residueAlphabet": "na"
}
}
},
{
"name": "NM_005157.6:c.80_",
"description": "Transcript SequenceLocation of the aligned transcript boundary.",
"value": {
"type": "SequenceLocation",
"sequenceReference": {
"id": "NM_005157.6",
"type": "SequenceReference",
"refgetAccession": "SQ.w8Qg3x-PQ2akJrJQeGEN-_eBUMo1H1CL",
"residueAlphabet": "na"
},
"end": 273
}
},
{
"name": "gene",
"description": "The gene concept (ABL1) associated with this fusion partner.",
"value": {
"code": "hgnc:76",
"system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
"label": "ABL1"
}
}
]
}],
"linker": {
"type": "LiteralSequenceExpression",
"sequence": "CCCGTC"
}
],
"r_frame_preserved": true,
"critical_functional_domains": [
},
"readingFramePreserved": true,
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using camelCase, similar to usage in GKS specs

"criticalFunctionalDomains": [
{
"type": "FunctionalDomain",
"status": "preserved",
"associated_gene": {
"id": "normalize.gene:hgnc%3A76",
"type": "GeneDescriptor",
"label": "ABL1",
"gene_id": "hgnc:76"
"gene": {
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mostly noting this to help myself as I am working on the updates to fusor - this should be associatedGene

"code": "hgnc:76",
"system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
"label": "ABL1"
},
"_id": "interpro:IPR000980",
"id": "interpro:IPR000980",
"label": "SH2 domain",
"sequence_location": {
"id": "fusor.location_descriptor:NP_005148.2",
"type": "LocationDescriptor",
"location": {
"type": "SequenceLocation",
"sequence_id": "refseq:NP_005148.2",
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can we retain this identifier as a mapping, or something of that nature?

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I think so? I was more following the convention in element_genomic_end and element_genomic_start where I removed the identifier

"interval": {
"type": "SequenceInterval",
"start": {
"type": "Number",
"value": 127
},
"end": {
"type": "Number",
"value": 202
}
}
}
"sequenceLocation": {
"type": "SequenceLocation",
"sequenceReference": {
"id": "GRCh38:chr22",
"type": "SequenceReference",
"refgetAccession": "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ",
"residueAlphabet": "na"
},
"start": 127,
"end": 202
}
}
]
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52 changes: 15 additions & 37 deletions src/fusor/examples/tpm3_ntrk1.json
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Original file line number Diff line number Diff line change
Expand Up @@ -6,62 +6,40 @@
"transcript": "refseq:NM_152263.3",
"exon_end": 8,
"exon_end_offset": 0,
"gene_descriptor": {
"gene": {
"id": "normalize.gene:TPM3",
"type": "GeneDescriptor",
"type": "Gene",
"label": "TPM3",
"gene_id": "hgnc:12012"
},
"element_genomic_end": {
"id": "fusor.location_descriptor:NC_000001.11",
"type": "LocationDescriptor",
"label": "NC_000001.11",
"location": {
"type": "SequenceLocation",
"sequence_id": "refseq:NC_000001.11",
"interval": {
"type": "SequenceInterval",
"start": {
"type": "Number",
"value": 154170399
},
"end": {
"type": "Number",
"value": 154170400
}
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": null,
"start": 154170399
}
}
}
},
{
"type": "TranscriptSegmentElement",
"transcript": "refseq:NM_002529.3",
"exon_start": 10,
"exon_start_offset": 0,
"gene_descriptor": {
"gene": {
"id": "normalize.gene:NTRK1",
"type": "GeneDescriptor",
"type": "Gene",
"label": "NTRK1",
"gene_id": "hgnc:8031"
},
"element_genomic_start": {
"id": "fusor.location_descriptor:NC_000001.11",
"type": "LocationDescriptor",
"label": "NC_000001.11",
"location": {
"type": "SequenceLocation",
"sequence_id": "refseq:NC_000001.11",
"interval": {
"type": "SequenceInterval",
"start": {
"type": "Number",
"value": 156874626
},
"end": {
"type": "Number",
"value": 156874627
}
}
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": null,
"start": 156874626
}
}
}
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