disease-trajectories

name: disease-trajectories description: Mine Disease Trajectories (DT/DisTraj) outputs for comorbidity/trajectory candidates, including parsing DT JSON/TSV, extracting directed pairs, filtering by sex or significance, and mapping signals into dismech comorbidity YAML.

Disease Trajectories Mining

Use this skill when you need to mine DT (Disease Trajectories / DisTraj) artifacts and convert them into dismech comorbidity entries.

Quick start

1. Locate a DT JSON file (often includes a phase_dict or edge list).
2. Extract normalized edges with the script below.
3. Pick candidate pairs and map to comorbidity YAML signals.

Example:

python .claude/skills/disease-trajectories/scripts/dt_extract_edges.py path/to/dt.json --format tsv > /tmp/dt_edges.tsv

Workflow

1) Locate DT artifacts

• Search for candidate files:
  • rg --files -g "*.json" and look for names like phase_dict, trajectories, edges.
• If the DT data is external, download and keep the raw file in a scratch location (do not edit in place).

2) Inspect schema quickly

Use a quick introspection to identify top-level keys:

python - <<'PY'
import json
from pathlib import Path
p = Path("path/to/dt.json")
obj = json.loads(p.read_text())
print(type(obj))
if isinstance(obj, dict):
    print(list(obj.keys())[:20])
PY

If there is a phase_dict mapping, it usually encodes pair keys like ICD_A-ICD_B and may include sex stratification. If there is an edges/pairs list, inspect the field names for A/B, sex, and directionality.

3) Extract normalized edges

Use the bundled script:

python .claude/skills/disease-trajectories/scripts/dt_extract_edges.py path/to/dt.json --format tsv > /tmp/dt_edges.tsv

What the script does:

• Handles phase_dict mappings with pair keys like E12-L28.
• Handles edge lists under edges, links, pairs, data, or trajectories.
• Normalizes fields to a consistent row format with disease_a_id, disease_b_id, directionality metrics, sex, p-value, FDR, and source path.

4) Filter candidate pairs

Use standard tools on the TSV output (examples):

• Filter for a specific ICD pair:
  • rg "^E12\tL28\t" /tmp/dt_edges.tsv
• Filter by directionality:
  • awk -F '\t' 'NR==1 || $11=="A_BEFORE_B"' /tmp/dt_edges.tsv
• Filter by sex:
  • awk -F '\t' 'NR==1 || $3=="male"' /tmp/dt_edges.tsv

5) Map to dismech comorbidity YAML

Create or update a comorbidity file under kb/comorbidities/.

Minimum signal mapping:

• source: DISEASE_TRAJECTORIES
• method: EHR_TEMPORAL_COMORBIDITY
• signal_disorder_a_id: ICD code from DT
• signal_disorder_b_id: ICD code from DT
• directionality: map from DT (A_BEFORE_B / B_BEFORE_A / SAME_TIME / UNKNOWN)
• a_before_b, b_before_a, same_time: preserve DT proportions if provided
• demographics.sex: set if DT is stratified
• mapping_notes: explain any ICD to dismech mapping or grouping

Example snippet:

association_signals:
  - source: DISEASE_TRAJECTORIES
    method: EHR_TEMPORAL_COMORBIDITY
    signal_disorder_a_id: ICD10:E12
    signal_disorder_b_id: ICD10:L28
    demographics:
      sex: MALE
    directionality: A_BEFORE_B
    a_before_b: 1.0
    b_before_a: 0.0
    same_time: 0.0

6) Validate

Run:

just validate-comorbidity kb/comorbidities/<file>.yaml

Scripts

• scripts/dt_extract_edges.py
  • Input: DT JSON
  • Output: TSV/CSV/JSONL with normalized edge fields
  • Use when the DT format is unknown or mixed

Notes and cautions

• Do not assume DT directionality is causal. Preserve A_before_B, B_before_A, and same_time metrics as reported.
• If a DT pair uses grouped ICD codes (e.g., L28), record the grouping in mapping_notes.
• Keep DT signals separate from literature signals; they can coexist under association_signals.