papers-query-knowledge-base

name	papers-query-knowledge-base
follows	rf-obsidian-markdown
status	active-local-query
description	Queries the local `obsidian-vault/analysis/` notes for research. Finds papers by title, task path, technique tags, venue, or year; summarizes methods and evidence across papers; cites core_operator and primary_logic from analysis frontmatter. When present, `obsidian-vault/index/index.jsonl` serves as the fast filter layer and `obsidian-vault/index/` pages serve navigation and backlink exploration.

Paper Knowledge Base

Use this skill to query the local paper corpus across conversations and projects. The main evidence layer is obsidian-vault/analysis (analysis notes with TL;DR, semantic method/evidence sections, and PDF links). When it exists, obsidian-vault/index/index.jsonl is the fast filter layer for large vaults, while the Markdown pages in obsidian-vault/index/ remain useful for Obsidian jumps and backlink-friendly browsing.

Where the knowledge base lives: Under the current repository root that contains obsidian-vault/analysis/ and obsidian-vault/paperPDFs/. obsidian-vault/index/ is a generated companion layer created by papers-build-index.

Paths

• Use repo-relative paths rooted at the folder that contains obsidian-vault/analysis/ and obsidian-vault/paperPDFs/.
• When invoking from another workspace, replace these with the correct absolute repository path for your machine.

Where things live

Relative to the repository root:

• Analysis notes: obsidian-vault/analysis/<Topic>/<Venue_Year>/<Year>_<Title>.md or flat venue folders such as obsidian-vault/analysis/ICLR_2026/<Title>.md; PDF path in frontmatter pdf_ref.
• Generated index / navigation: obsidian-vault/index/index.jsonl, obsidian-vault/index/paper_index.md, _AllPapers.md, by_topic/, by_method/, by_dataset/, by_venue_year/.
• Public placeholder: obsidian-vault/index/README.md is tracked as a stable explanation file and is not overwritten by index generation.

All paths use forward slashes.

How to use for research

1. Find papers — Search obsidian-vault/analysis/ directly by title, task folder, tags, venue, year, core_operator, or primary_logic. If obsidian-vault/index/index.jsonl is present, use it first to narrow a large candidate set, then read the matching notes for evidence.

2. Read an analysis — Open the matched analysis note directly. Each note has: Frontmatter (title, venue, year, tags, aliases, pdf_ref, core_operator, primary_logic, claims; no category, modalities, or frontier); Quick Links & TL;DR; method/problem/evidence sections such as 问题与动机, 整体框架, 核心模块与公式推导, 实验与分析, and 局限性与启发; and Local Reading (PDF). Older notes may still use legacy mixed headings, so match semantically rather than by one exact title string.

3. Use obsidian-vault/index/ when helpful — index.jsonl is for fast filtering; the Markdown pages are for coarse topic / method-family / dataset / merged venue-year overview pages, statistics, Obsidian jumps, or backlink exploration. Use venue, year, and venue_year fields for structured filtering; use methods for exact method names and method_groups for low-cardinality method-family filtering.

4. Cite in answers — Use core_operator and primary_logic from frontmatter for one-line method summary; Summary and Key Performance from TL;DR for comparison. Link to note: [[analysis/.../file.md|Title]]; to PDF: [[paperPDFs/.../file.pdf|PDF]].

Index frontmatter (for tooling)

Collection pages: type: paper-index, dimension: topic | method | dataset | venue_year | all, and optional topic: / method: / dataset: / venue_year:.

For exact paths and frontmatter schema, see references/structure.md.

Regenerating the collection (optional)

If you want refreshed obsidian-vault/index/index.jsonl and the Obsidian navigation pages, from the repository root:

python .claude/skills/papers-build-index/scripts/build_paper_index.py

The public repository may produce an empty index until local paper rows or analysis notes are added. Notes with clear paper evidence in frontmatter, body metadata rows, or venue/year paths can be indexed even when pdf_ref still needs repair.

Output style

• KB-grounded answers to research questions
• evidence-backed cross-paper summaries in prose
• direct pointers to relevant obsidian-vault/analysis/... notes and local PDFs when useful

Boundaries

• This skill handles both text summaries and comparison requests. When comparing papers, provide honest text-based analysis that acknowledges metric incomparability (different datasets, evaluation protocols, etc.) rather than forcing misleading tabular comparisons.
• This skill can point out evidence-backed research gaps, but it does not generate systematic idea candidates, scope cuts, or experimental roadmaps. Use research-brainstorm-from-kb or idea-focus-coach for that.
• This skill does not issue reviewer-style acceptance or rejection risk verdicts. Use reviewer-stress-test.
• If the retrieval goal is to support an upcoming code change, use this skill in code-context mode rather than the legacy code-context-paper-retrieval alias.