{"file_path": "/workspace/skills/life-science-apis/SKILL.md"}

1	---
2	name: life-science-apis
3	description: How to query public life-science databases from the sandbox with plain HTTP (UniProt, Ensembl, InterPro, PDB, AlphaFold, gnomAD, ClinVar, GTEx, cBioPortal, PubChem, BindingDB, openFDA, OpenAlex, Open Targets, DepMap). Use when a task needs an identifier lookup, sequence, structure, variant, expression, compound, trial or literature record. Every query must be logged.
4	---
5	
6	# Life-science APIs from the sandbox
7	
8	Use `helpers/lsapi.py` (`from lsapi import get_json, get_text`) or plain `requests`. Rules:
9	
10	1. **Log every query.** `lsapi` appends `{ts, url, status, bytes}` to `/mnt/session/outputs/_queries.jsonl`; if you use
11	   `reque
… [more]

{"file_path": "/workspace/skills/life-science-apis/apis/gtex.md"}

awk: cannot open "/workspace/skills/life-science-apis/apis/gtex.md" (No such file or directory)

ls /workspace/skills/life-science-apis/apis/ ; ls /workspace/skills/life-science-apis/helpers/

ls: cannot access '/workspace/skills/life-science-apis/apis/': No such file or directory
ls: cannot access '/workspace/skills/life-science-apis/helpers/': No such file or directory

find /workspace/skills -type f | head -100

/workspace/skills/science-figures/SKILL.md
/workspace/skills/life-science-apis/lsapi.py
/workspace/skills/life-science-apis/gtex.md
/workspace/skills/life-science-apis/SKILL.md
/workspace/skills/life-science-apis/interpro.md
/workspace/skills/life-science-apis/bindingdb.md
/workspace/skills/life-science-apis/openalex.md
/workspace/skills/life-science-apis/openfda.md
/workspace/skills/life-science-apis/gnomad.md
/workspace/skills/life-science-apis/depmap.md
/workspace/skills/life-science-apis/opentargets.md
/workspace/skills/life-science-apis/pubchem.md
/workspace/skills/life-science-apis/cbioportal.md
/workspace/skills/life-science-apis/uniprot.md
/workspace/skills/life-science-apis/alphafol
… [more]

{"file_path": "/workspace/skills/life-science-apis/gtex.md"}

1	# GTEx Portal API v2 — https://gtexportal.org/api/v2
2	- Gene expression by tissue: `GET /expression/medianGeneExpression?gencodeId=ENSG00000141510.18&datasetId=gtex_v8`.
3	- Gene lookup: `GET /reference/gene?geneId=TP53`. eQTLs: `GET /association/singleTissueEqtl?gencodeId=…&tissueSiteDetailId=Liver`.
4	- Gotchas: needs versioned GENCODE ids; tissue ids are like `Brain_Cortex`.

{"file_path": "/workspace/skills/life-science-apis/lsapi.py"}

1	"""Tiny polite HTTP helper with provenance logging. from lsapi import get_json, get_text"""
2	import json, os, time
3	from pathlib import Path
4	import requests
5	
6	LOG = Path(os.environ.get("WB_QUERY_LOG", "/mnt/session/outputs/_queries.jsonl"))
7	_last: dict[str, float] = {}
8	UA = {"User-Agent": "ScientistWorkbench/0.1 (research sandbox; contact via job report)"}
9	
10	
11	def _pace(host: str, min_gap: float = 1.0) -> None:
12	    t = _last.get(host, 0.0)
13	    wait = min_gap - (time.time() - t)
14	    if wait > 0:
15	        time.sleep(wait)
16	    _last[host] = time.time()
17	
18	
19	def _log(url: str, status: int, nbytes: int) -> None:
20	    try:
21	        LOG.parent.mkdir(parent
… [more]

{"file_path": "/workspace/skills/science-figures/SKILL.md"}

1	---
2	name: science-figures
3	description: Conventions for publication-quality scientific figures produced in the sandbox (matplotlib/seaborn). Use whenever a task produces a plot, tree, heatmap, structure view or multi-panel figure; covers layout, annotation, colour, labelling, file output and the figure record in summary.md.
4	---
5	
6	# Science figures
7	
8	**One message per figure.** Decide what the reader must see in three seconds and design for that; move everything else
9	to a table. Multi-panel figures get panel letters (A, B, …) and a one-sentence title per panel.
10	
11	**Layout**
12	- `fig, ax = plt.subplots(figsize=(w, h), constrained_layout=True)`; 7.2 in wide for single/doubl
… [more]

mkdir -p /mnt/session/outputs/scripts
cd /mnt/session/outputs
python3 -c "
import sys
sys.path.insert(0, '/workspace/skills/life-science-apis')
from lsapi import get_json
import json

r = get_json('https://gtexportal.org/api/v2/reference/gene', params={'geneId':'ERBB2'})
print(json.dumps(r, indent=2)[:3000])
"

{
  "data": [
    {
      "chromosome": "chr17",
      "dataSource": "HAVANA",
      "description": "erb-b2 receptor tyrosine kinase 2 [Source:HGNC Symbol;Acc:HGNC:3430]",
      "end": 39730426,
      "entrezGeneId": 2064,
      "gencodeId": "ENSG00000141736.13",
      "gencodeVersion": "v26",
      "geneStatus": "",
      "geneSymbol": "ERBB2",
      "geneSymbolUpper": "ERBB2",
      "geneType": "protein coding",
      "genomeBuild": "GRCh38/hg38",
      "start": 39687914,
      "strand": "+",
      "tss": 39687914
    }
  ],
  "paging_info": {
    "numberOfPages": 1,
    "page": 0,
    "maxItemsPerPage": 250,
    "totalNumberOfItems": 1
  }
}