| Label | Color | Hex | Description |
|---|---|---|---|
| priority:high |  |
#ee0701 |
High priority |
| priority:medium |  |
#ff5f1f |
Medium priority |
| priority:low |  |
#fbca04 |
Low priority |
| enhancement |  |
#00FF7F |
New feature or request |
| requirement |  |
#DC143C |
Required |
| bug |  |
#FF0000 |
Something isn't working |
| documentation |  |
#DEB887 |
Changes to documentation only |
| technical debt |  |
#6495ED |
A feature/requirement implemented in a sub-optimal way & must be re-written. Contrast to "cleanup" |
Kori Kuzma korikuzma
korikuzma
/ unable_to_normalize_cancer_hotspots_v2
Created
December 24, 2021 13:51
Terms variation-normalizer is unable to normalize in cancer hotspots v2
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| TP53 spliceX187_splicesplice | |
| TP53 spliceX307_splicesplice | |
| MYD88 L265P | |
| TP53 spliceX126_splicesplice | |
| B2M M1R | |
| MET spliceX1010_splicesplice | |
| CDK4 R24L | |
| TP53 spliceX261_splicesplice | |
| TP53 spliceX331_splicesplice | |
| HIST1H3B K28M |
korikuzma
/ github_labels.md
Created
April 13, 2023 16:58
korikuzma
/ hackathon_responses.ipynb
Last active
June 16, 2023 13:19
Biocommons Hackathon 2023 Ranked Choice Results
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korikuzma
/ gist:4385ef29ef76b956c73bdf84f922f5ad
Last active
June 26, 2024 17:47
Example of oncogenicitySubmission where citation gives error when including both db/id and url records (excluded other fields for brevity). In this example, it can be processed by ClinVar but errors out.
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| { | |
| "assertionCriteria": { | |
| "db": "PubMed", | |
| "id": "36063163" | |
| }, | |
| "oncogenicitySubmission": [ | |
| { | |
| "citation": [ | |
| { | |
| "db": "PubMed", |
korikuzma
/ gist:d90bf9f48936efda0ad6e72f3639581e
Last active
June 26, 2024 17:39
Example of oncogenicitySubmission where citation gives error when including only url (excluded other fields for brevity). In this example, it can be processed by ClinVar but errors out.
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| { | |
| "assertionCriteria": { | |
| "db": "PubMed", | |
| "id": "36063163" | |
| }, | |
| "oncogenicitySubmission": [ | |
| { | |
| "oncogenicityClassification": { | |
| "citation": [ | |
| { |
korikuzma
/ gist:50fdb30967882d33dfce8caa03ec26d1
Created
June 26, 2024 17:40
Example of oncogenicitySubmission where citation fails validation when including db/id/url all in one record (excluded other fields for brevity)
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| { | |
| "assertionCriteria": { | |
| "db": "PubMed", | |
| "id": "36063163" | |
| }, | |
| "oncogenicitySubmission": [ | |
| { | |
| "oncogenicityClassification": { | |
| "citation": [ | |
| { |
korikuzma
/ civic-categorical-variant-example.json
Created
September 12, 2024 17:44
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| { | |
| "id": "civic.mpid:33", | |
| "type": "CategoricalVariant", | |
| "description": "EGFR L858R has long been recognized as a functionally significant mutation in cancer, and is one of the most prevalent single mutations in lung cancer. Best described in non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first and second generation TKI's like gefitinib and neratinib. NSCLC patients with this mutation treated with TKI's show increased overall and progression-free survival, as compared to chemotherapy alone. Third generation TKI's are currently in clinical trials that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in treating patients that failed to respond to earlier generation TKI therapies.", | |
| "label": "EGFR L858R", | |
| "constraints": { | |
| "definingContext": { | |
| "id": "ga4gh:VA.S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ", | |
| "type": "Allele", | |
| "label": "L858R", |