Update examples to VRS 2.0 #151
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| "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
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note that the gene descriptor in the ABL1 functional domain example should be updated to a GKS |
src/fusor/examples/bcr_abl1.json
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| "gene_descriptor": { | ||
| "type": "GeneDescriptor", | ||
| "gene": { | ||
| "type": "Gene", | ||
| "id": "normalize.gene:BCR", | ||
| "gene_id": "hgnc:1014", |
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This field does not exist. I think we need to use mappings here
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Yes, this should be a Coding object as used in mappings.
src/fusor/examples/bcr_abl1.json
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| "gene_descriptor": { | ||
| "type": "GeneDescriptor", | ||
| "gene": { | ||
| "type": "Gene", | ||
| "id": "normalize.gene:BCR", | ||
| "gene_id": "hgnc:1014", |
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Yes, this should be a Coding object as used in mappings.
| "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.
| "structure": { | ||
| "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.
| "end": 23290413, | ||
| "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.
| "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).
| "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.
| "r_frame_preserved": true, | ||
| "critical_functional_domains": [ | ||
| }, | ||
| "readingFramePreserved": true, |
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using camelCase, similar to usage in GKS specs
| "code": "hgnc:1014", | ||
| "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/", | ||
| "label": "BCR" |
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This PR is stale because it has been open 3 day(s) with no activity. Please review this PR. |
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This PR is stale because it has been open 3 day(s) with no activity. Please review this PR. |
| "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
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This PR is stale because it has been open 3 day(s) with no activity. Please review this PR. |
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This PR is stale because it has been open 3 day(s) with no activity. Please review this PR. |
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@jarbesfeld @katiestahl @jsstevenson I think this issue still needs to be addressed. I'm also looking at the nomenclature tests and I think |
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Yeah, there's a few things here. We also need to tackle the big adjacency change that alex was originally proposing. |
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@jsstevenson IIRC we're holding off on adjacency for a bit. I re-opened #172 and made a PR to update the examples |
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This PR is stale because it has been open 3 day(s) with no activity. Please review this PR. |
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