Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update examples to VRS 2.0 #151

Draft
wants to merge 6 commits into
base: main
Choose a base branch
from
Draft

Update examples to VRS 2.0 #151

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
88 changes: 28 additions & 60 deletions src/fusor/examples/bcr_abl1.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,30 +4,19 @@
{
"type": "TranscriptSegmentElement",
"transcript": "refseq:NM_004327.3",
"gene_descriptor": {
"type": "GeneDescriptor",
"gene": {
"type": "Gene",
"id": "normalize.gene:BCR",
"gene_id": "hgnc:1014",
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This field does not exist. I think we need to use mappings here

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, this should be a Coding object as used in mappings.

"label": "BCR"
},
"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
}
}
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ",
"residueAlphabet": null,
"end": 23253981
}
},
"exon_end": 2,
Expand All @@ -36,44 +25,32 @@
{
"type": "LinkerSequenceElement",
"linker_sequence": {
"id": "sequence:ACTAAAGCG",
"type": "SequenceDescriptor",
"sequence": "ACTAAAGCG",
"residue_type": "SO:0000348"
"type": "LiteralSequenceExpression",
"sequence": "CCCGTC",
"residue_type": "SO:0000348"
}
},
{
"type": "TranscriptSegmentElement",
"transcript": "refseq:NM_005157.5",
"exon_start": 2,
"exon_start_offset": -173,
"gene_descriptor": {
"gene": {
"id": "normalize.gene:ABL1",
"type": "GeneDescriptor",
"type": "Gene",
"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
},
"end": {
"type": "Number",
"value": 130854065
}
}
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI",
"residueAlphabet": null,
"start": 130854065
}
}
}
}
],
"r_frame_preserved": true,
"critical_functional_domains": [
Expand All @@ -82,29 +59,20 @@
"status": "preserved",
"associated_gene": {
"id": "normalize.gene:hgnc%3A76",
"type": "GeneDescriptor",
"type": "Gene",
"label": "ABL1",
"gene_id": "hgnc:76"
},
"_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",
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can we retain this identifier as a mapping, or something of that nature?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
}
}
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ",
"residueAlphabet": null,
"start": 127,
"end": 202
}
}
}
Expand Down
52 changes: 15 additions & 37 deletions src/fusor/examples/tpm3_ntrk1.json
View file
Open in desktop
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
}
}
}
Expand Down
Loading