When to use

Use this skill when the user provides their own:

• clinical phenotypes / symptoms / diagnoses (free text, bullet lists, clinical note-like text), and/or
• drugs/medications (names, dosages, frequencies).

Examples that should trigger:

• “Symptoms: ataxia, seizures, developmental delay. Meds: levetiracetam 500 mg BID.”
• “I’m taking metformin 500mg daily and have fatigue, polyuria, blurry vision.”

When NOT to use

Do not use this skill when:

• The user asks general questions (e.g., “What is HPO?”, “What is a phenotype?”, “What is GLP-1?”).
• The user provides text that is not personal clinical information (news articles, academic paragraphs, code, etc.).
• The user asks you to interpret someone else’s private clinical record (PHI) without clear permission.

Safety & privacy

• Treat user input as potentially sensitive clinical information.
• Do not upload user text or extracted results anywhere (this skill is local-only).
• Before writing any input to disk, redact obvious identifiers:
  • emails, phone numbers, street addresses
  • MRN-like long numeric identifiers (e.g., 8+ digits)
  • names when clearly presented as “Name: …”
• If the message appears to include highly identifying PHI (e.g., name + DOB + address, or name + MRN), pause and ask for confirmation to proceed, recommending the user remove identifiers first.

Requirements / setup

• Python: python3 available on PATH.
• Network access (only for initial PhenoSnap download if missing).
• HPO OBO file:
  • Default expected path: {baseDir}/resources/hp.obo
  • Override path via environment variable: HPO_OBO_PATH
  • This skill does not auto-download hp.obo. You must supply it.

Recommended (best practice):

• Use a virtual environment (venv/conda) before running this skill, because it may install Python packages via pip.

Inputs & outputs

• Input text file (redacted):
  • {baseDir}/artifacts/phenosnap_inputs/input_<YYYYMMDD_HHMMSS>.txt
• Output JSON file (timestamped):
  • {baseDir}/artifacts/phenosnap_outputs/phenotypes_<YYYYMMDD_HHMMSS>.json
• Third-party download cache:
  • {baseDir}/third_party/phenosnap_main.zip
  • {baseDir}/third_party/get-pip.py

Detection heuristic (activation check)

Trigger if the user message contains any of:

• phenotype cues: symptom(s), phenotype(s), Dx, diagnosis, PMH, Hx, history of, or a symptom-like list
• medication cues: meds, medications, taking, prescribed, plus patterns like:
  • dosages: \b\d+(\.\d+)?\s?(mg|mcg|g|ml|units)\b
  • frequencies: qd, q.d., bid, b.i.d., tid, t.i.d., qhs, qAM, qPM, daily, weekly

Do not trigger for purely informational questions without user-provided phenotype/medication content.

Procedure