paper-capture

name	paper-capture
description	Resolve a paper from a DOI, arXiv id, URL, or Author-Year-keyword into the Obsidian vault. Fetches metadata, downloads PDF, writes 30_Literature/CITEKEY.md.

Paper Capture (Desktop)

Turn a reference into a vault entry: metadata, PDF, structured note. Idempotent -- captures the same paper twice will update the existing note, not duplicate it.

This skill is identical to the Code variant -- it has no Agent tool dependency. The only difference is invocation: Desktop has no /capture-paper slash command. The user invokes by free text ("capture this paper: 10.1038/...", "save this DOI") or by pasting a DOI. Recognize and trigger proactively when a DOI / arXiv id appears in the conversation, since there is no paper-mention-detect hook on Desktop.

Inputs accepted

• DOI: 10.1038/s41586-021-03819-2 or https://doi.org/10.1038/...
• arXiv id: 2103.04822 or arXiv:2103.04822 or https://arxiv.org/abs/2103.04822
• URL: any publisher URL -- extract DOI from the page if needed
• Title-author-year: "Kim 2023 ionic transistor" -- looser, requires Semantic Scholar resolution

Workflow

1. Resolve to a paper id. Prefer DOI > arXiv id > Semantic Scholar paperId. If only a title is given, search Semantic Scholar; if 0 or >1 high-confidence hits, escalate to user.
2. Fetch metadata (Semantic Scholar first, then paper-mcp fallback). Required fields: title, authors (full), year, venue, DOI, abstract.
3. Generate citekey per references/citekey_rules.md. De-dupe against existing 30_Literature/*.md (use obsidian MCP search by frontmatter citekey:).
4. Download the PDF per references/source_priority.md: university-paper-access -> arxiv -> scihub. PDF lands at {vault}/80_Attachments/papers/{citekey}.pdf. If all paths fail, write the note anyway with pdf: null in frontmatter and report the failure.
5. Write the vault note at {vault}/30_Literature/{citekey}.md from 70_Templates/literature.md. Populate frontmatter:
   • citekey, authors (list), year, venue, doi, arxiv, s2_id
   • status: unread
   • tags: [] (user adds)
   • projects: [] (user adds, or auto-tag if invoked from a known project)
   • added: {today}
   • pdf: 80_Attachments/papers/{citekey}.pdf (or null)
6. Confirm to user: one line -- Captured: {citekey} ({title trunc 60}) -> 30_Literature/{citekey}.md.

Re-capture / update behavior

If 30_Literature/{citekey}.md already exists:

• Re-fetch metadata; update frontmatter fields except status, tags, projects, body sections (those are user-edited).
• Don't re-download PDF if file already exists at the expected path.
• Report: Updated: {citekey} (metadata refreshed; status/tags preserved).

When invoked from deep-research

The deep-research investigator agent calls this skill automatically for every paper it reads at the full level. The projects field is auto-tagged with the active project slug if one is detectable from ~/.claude/projects/.../memory/ or the working directory.

Errors

• Metadata not found -> don't write a note; report and stop.
• PDF download failed across all sources -> write note with pdf: null, status unread (no pdf). User can manually drop a PDF later.
• Citekey collision with a different paper (same firstauthor/year/keyword for two real papers) -> suffix with -b, -c, etc., and note the collision in the body.

What this skill does NOT do

• Annotate the paper. The user reads and writes their own takeaways.
• Auto-add to the active project's MOC. The hook can suggest, but the user promotes.
• Write to the bibtex file. (Possible future hook; out of scope here.)