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jsstevenson / moa_featurecontextconstraint_example.json
Last active December 1, 2025 18:49
{
"id": "moa.assertion:74",
"type": "Statement",
"description": "Secondary mutations in BCR-ABL may suggest resistance to imatinib in CML.",
"specifiedBy": {
"id": "moa.method:2021",
"type": "Method",
"name": "MOAlmanac (2021)",
"reportedIn": {
"type": "Document",
@jsstevenson
jsstevenson / gist:39d5de8428bc3bc450987530945ee2b8
Created November 21, 2025 21:09
In [21]: input_data = {
...: "location": {
...: "end": 87894077,
...: "start": 87894076,
...: "sequenceReference": {
...: "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB",
...: "type": "SequenceReference"
...: },
...: },
...: "state": {
@jsstevenson
jsstevenson / 2025-10-03-stack trace
Created October 3, 2025 18:24
self = <botocore.awsrequest.AWSHTTPConnectionPool object at 0x11195bf50>, conn = <botocore.awsrequest.AWSHTTPConnection object at 0x1119d4b90>
method = 'POST', url = '/Execute'
body = b'{"sql": "DROP DATABASE IF EXISTS `varcat`;", "secretArn": "arn:aws:secretsmanager:us-east-1:123456789012:secret:dummy", "resourceArn": "arn:aws:rds:us-east-1:123456789012:cluster:dummy"}'
headers = {'Content-Type': b'application/json', 'User-Agent': b'Boto3/1.40.42 md/Botocore#1.40.42 ua/2.1 os/macos#24.6.0 md/arch...vocation-id': b'e1996f6f-cd92-4adf-9410-7fcac12dce9e', 'amz-sdk-request': b'attempt=5; max=5', 'Content-Length': '186'}
retries = Retry(total=False, connect=None, read=None, redirect=0, status=None), timeout = Timeout(connect=60, read=60, total=None)
chunked = False, response_conn = <botocore.awsrequest.AWSHTTPConnection object at 0x1119d4b90>, preload_content = False
decode_content = False, enforce_content_length = True
def _make_request(
self,
@jsstevenson
jsstevenson / metakb_assertion_ingest_fails.txt
Last active August 30, 2025 01:54
civic.eid:3811 can be loaded.
civic.eid:229 can be loaded.
civic.eid:4291 can be loaded.
civic.eid:4290 can be loaded.
civic.eid:4285 can be loaded.
civic.eid:4265 can be loaded.
civic.eid:885 can be loaded.
civic.eid:2994 can be loaded.
civic.aid:5 can be loaded.
civic.eid:2621 can be loaded.
@jsstevenson
jsstevenson / metakb_strenght_nodes.json
Created August 28, 2025 20:47
MetaKB Strength nodes
[
{
"n": {
"identity": 1625,
"labels": [
"Strength"
],
"properties": {
"mappings": "[{\"id\":null,\"extensions\":null,\"coding\":{\"id\":null,\"extensions\":null,\"name\":\"preclinical evidence\",\"system\":\"https://go.osu.edu/evidence-codes\",\"systemVersion\":null,\"code\":\"e000009\",\"iris\":null},\"relation\":\"exactMatch\"}]",
"primary_coding": "{\"id\":null,\"extensions\":null,\"name\":null,\"system\":\"https://civic.readthedocs.io/en/latest/model/evidence/level.html\",\"systemVersion\":null,\"code\":\"D\",\"iris\":null}",
@jsstevenson
jsstevenson / uv-notes.md
Last active April 18, 2025 16:05

uv notes

uv is a Python tool for managing dependencies, builds, and runtimes. Inspired by major players in other languages like cargo and npm. It should further simplify the hassle of dealing with Python runtimes and environments and I would strongly recommend switching over to it.

installation

  1. Cleanup

Get rid of pyenv

@jsstevenson
jsstevenson / dgidb_unique_genes_2024-12-01.md
Last active March 3, 2025 14:47

get DictReader for interactions TSV:

import csv
with open("~/Downloads/interactions.tsv") as f:
    next(f)  # skip header rows
    next(f)
    lines = list(csv.DictReader(f, delimiter="\t"))
@jsstevenson
jsstevenson / maturin_generated_ci.yaml
Created November 29, 2024 20:47
# This file is autogenerated by maturin v1.7.6
# To update, run
#
# maturin generate-ci github -o tmp.yaml
#
name: CI
on:
push:
branches:
@jsstevenson
jsstevenson / bcl2_interaction_scores.txt
Last active November 25, 2024 15:27
SELECT g.name, d.name, i.score, i.gene_specificity, i.drug_specificity, i.evidence_score FROM interactions i LEFT JOIN genes g on g.id = i.gene_id LEFT JOIN drugs d on d.id = i.drug_id WHERE g.name = 'BCL2' ORDER BY i.score
name | name | score | gene_specificity | drug_specificity | evidence_score
------+------------------------------------------------------------+----------------------+---------------------+----------------------+----------------
BCL2 | BORTEZOMIB | 0.007488459062167905 | 0.17546867625942625 | 0.042676899500264064 | 1
BCL2 | CARBOPLATIN | 0.00757760738433657 | 0.17546867625942625 | 0.04318495782764816 | 1
BCL2 | DOCETAXEL ANHYDROUS | 0.007668903858846649 | 0.17546867625942625 | 0.04370525852436681 | 1
BCL2 | VINCRISTINE | 0.007858259509682369 | 0.17546867625942625 | 0.044784400710153646 | 1
BCL2 | DOXORUBICIN HYDROCHLORIDE | 0.008601608382219891 | 0.17546867625942625
@jsstevenson
jsstevenson / exmo_review.md
Last active August 19, 2024 15:39

misc notes

  • Dependencies on intake form seem incomplete -- OBI, Uberon?

  • treatment of 'history' is weird. BFO history (process) is imported but unreferenced. "smoking history" is defined as a "quality" but not as a subclass of "medical history".

Criteria

1. Ontology scope