| name | PETase 2024–2025 Literature Scan |
| description | Use PubMed & Scholar Gateway to extract PETase (and PET hydrolase) variants and effects from 2024–2025 papers into a standardized table with citations. |
| version | 1.0.0 |
Goal
Create a 2024–2025 PETase variants & effects evidence table using PubMed and Scholar Gateway connectors, with strict, citable provenance.
When to use
- The user asks for PETase or PET hydrolase variant scouting, benchmarking, or zero-shot hypothesis generation focused on 2024–2025.
Operating rules
- Always use connectors (PubMed first; Scholar Gateway for Wiley/paywalled content). Prefer PMC for full text when available.
- Restrict the search window to 2024-01-01 .. 2025-10-21.
- For each paper, extract mutations, assay comparability, performance endpoints, thermostability, expression notes, rationale, and citations.
- Deduplicate by DOI; include PMID/PMCID when present.
- Use the Output schema exactly (see
resources/output-schema.csv).
Query seeds
(See resources/query-strings.md for adaptable queries.)
Output format
- Primary: table matching the schema (CSV in a fenced code block).
- Secondary: ranked shortlist (5–10 variants) + zero-shot hypotheses.
Steps
- Search PubMed with Boolean + fielded queries; filter 2024–2025; sort by date.
- For promising records, fetch abstracts/full text (PMC if available). Cross-check in Scholar Gateway to access Wiley content.
- Extract data into the schema; convert/standardize units carefully.
- Deduplicate by DOI; verify all rows have at least one citation (PMID/PMCID/DOI).
- Produce the CSV table, then a ranked shortlist and 2–3 hypotheses.
Safety & provenance
- Cite rigorously (PMID/PMCID/DOI). No hallucinated values.
- If a metric is missing, leave it blank.
- Do not train or store proprietary datasets; this is a literature-only workflow suitable for Zero‑Shot reasoning.
