researchstyle

Personal Survey Registry

Turn an existing paper collection into a structured survey registry (summary.md + references.bib). The output uses the same registry format as the survey skill — so personal and topic registries can be merged.

Step 1 — Locate the source. Ask which source to index:

"Where are your papers?"

• (a) Zotero library
• (b) A PDF folder (give me the path)
• (c) Google Scholar profile (give me the URL)

Step 2 — Index the collection.

Zotero:

1. Locate zotero.sqlite — check in order: ~/Zotero/, ~/Library/Application Support/Zotero/, ~/snap/zotero-snap/common/Zotero/. If not found, use find ~ -maxdepth 4 -name "zotero.sqlite" as fallback. If still not found, ask for the path.

2. Run the bundled script:

python3 <skill-base-dir>/parse_zotero.py <path-to-zotero.sqlite> <output_dir>

The script handles: copying the DB to avoid locking, pivot queries to avoid cartesian products, author extraction, cite key deduplication, topic classification, and generating both summary.md and references.bib.

3. Review the output — the script's topic classification uses keyword matching and may need manual adjustment. Check the topic distribution it prints and offer to re-classify if the user's field isn't well covered by the default patterns.

4. For papers missing abstracts or DOIs, find the PDF via the itemAttachments table. PDFs are at <zotero-data-dir>/storage/<key>/<filename>.pdf. Read them to extract the abstract.

PDF folder:

1. List all PDFs in the given path.
2. Read each PDF — extract title, authors, year, abstract, DOI/URL from the content.
3. For bulk keyword search: pdfgrep -r -i "KEYWORD" <folder> (install via package manager if missing, e.g., apt install pdfgrep or brew install pdfgrep).

Google Scholar:

Note: Google Scholar actively blocks automated access — WebFetch may hit CAPTCHAs or rate limits. If scraping fails, suggest alternatives: export BibTeX manually from the Scholar profile page (Scholar → select all → export BibTeX), use ORCID or DBLP profiles instead (both have machine-friendly APIs), or switch to the PDF folder method with downloaded papers.

1. Fetch the profile page.
2. Extract paper titles, years, citation counts.
3. For each paper, search for the DOI and abstract via WebSearch.

Step 3 — Produce the registry. Output to the global registry path at <global-registry-root>/personal/ (e.g., ~/.claude/survey/personal/), containing:

1. summary.md — all papers listed by topic cluster, with BibTeX cite keys (e.g., [AuthorYear]) as indices.

2. references.bib — BibTeX entries. Only include entries that have at least a DOI or URL — skip the rest. Every included entry must contain:

• abstract — the paper's abstract
• doi or url — at least one identifier for retrieval

Processing tips:

• Always use bundled scripts (parse_zotero.py for Zotero). Don't try to do it inline with shell commands — even for small libraries, a script is more reliable and easier to debug.
• Topic classification in the script uses keyword matching ordered most-specific-first. The default patterns cover quantum computing, physics, CS, and math. For other fields, modify TOPIC_PATTERNS in the script or ask the user to provide keywords for their domain.