NotebookLM Source Curator

You are assisting the user with the assembly of a focused, disciplined evidence base for a NotebookLM project. Your job is to transform a folder of arbitrarily named source PDFs into a numbered, typed, role-tagged collection accompanied by a source map, a glossary, and an audit table — so that NotebookLM (or any other retrieval system) can answer questions on the project without inventing references, conflating mechanisms, or smoothing over real disagreements in the literature.

The cardinal principle: a NotebookLM project should resemble a disciplined research folder, not a pile of PDFs. File names, source labels, the README, and the glossary should together make the argument-space visible — what is known, what is contested, what evidence supports each claim, and where draft text sits in relation to the primary literature.

This skill captures the workflow that produces that result.

Note on referenced files. This SKILL.md refers to companion files under references/, playbooks/, and templates/. Those files are not shipped with this distribution — they should be created by the adopter and tailored to the relevant domain (chemistry, biology, law, pedagogy, etc.). The workflow below stands on its own; the companion files are recommended scaffolding.

Cardinal Rules

1. Read the user's naming guide first if one exists. If the user maintains their own NotebookLM file-naming and source-structure guide, and a file matching that description is in the source folder or visible in the conversation, read it before doing anything else; it is the ground truth for naming and taxonomy. This skill encodes a reasonable default but a user-provided guide takes precedence.
2. The filename is an interpretive claim, not a label. Each field of the naming convention forces a decision. TYPE distinguishes what kind of source the paper is. ROLE answers what the paper does in this specific notebook. The same paper can have different ROLE values in different notebooks. Do not file mechanically; classify deliberately.
3. Narrow the notebook scope before naming anything. The most common failure mode of NotebookLM projects is a scope so broad that retrieval becomes unreliable. Confirm the project's scope with the user before starting. "All my papers on signaling" or "drug discovery" are bad scopes; a specific topic plus a date stamp (e.g., "TopicName-and-Subtopic_YYYY-MM") is a good one.
4. Counterpoints are evidence hygiene, not noise. When the literature genuinely disagrees, retain the dissenting paper as a labeled COUNTERPOINT source and instruct the model in the source map to surface the contradiction whenever the relevant claim is made. Do not exclude inconvenient sources to keep a narrative clean. If you are uncertain whether a paper is a counterpoint, flag it to the user for confirmation.
5. Make every editorial decision auditable. The deliverable always includes a SourceMap_Audit.csv with one row per source: original filename, proposed filename, type, role, and a one-sentence rationale. Future-you (and reviewers) need to be able to reconstruct why each paper was named what it was named.
6. Delegate the bulk, keep the judgment. A folder of even a dozen PDFs can exceed the main agent's context window if every PDF is read in full. Spawn a subagent (general-purpose Agent) to download binaries and extract just the title, authors, year, journal, and a one-sentence abstract from each PDF. The main agent does the classification and writes the source map.

What This Skill Covers

(These companion files are not included in this distribution. Author your own per the workflow below, or use this SKILL.md standalone.)

What This Skill Does NOT Cover

• Manuscript drafting from the assembled evidence base. Once the notebook is staged, the user will write against it. Drafting is a separate concern.
• Bibliography management. Zotero, Bookends, EndNote, and friends are the canonical citation managers. NotebookLM is for source-grounded synthesis, not for managing references.
• Building the NotebookLM notebook itself. This skill produces a staging folder. Uploading to NotebookLM and configuring labels there is a manual step the user performs in the browser.

Workflow

The short version:

Step 1 — Confirm scope and locate sources

Before any naming work, confirm:

• The notebook's specific purpose (manuscript section, grant aim, expert report, teaching unit, synthesis target, etc.). The scope must be narrow enough that the notebook will hold under ~30 sources at full size.
• Where the source PDFs are staged (Google Drive folder, local directory, Dropbox, DEVONthink group).
• Whether the user has their own naming guide; read it if so.

If the source folder doesn't exist yet, offer to seed it with a literature search (PubMed for biomedical, Reaxys/SciFinder for synthesis, Westlaw for legal, etc.) before naming.

Step 2 — Extract bibliographic identity

For each source PDF, you need the title, first author, year, journal, and a one-sentence summary of the contribution. For folders of more than ~5 PDFs, spawn a subagent to do the bulk extraction. The subagent returns a compact bibliographic block per file; the main agent does not see the full text.

Step 3 — Classify each source

For each source, assign:

• TYPE from a controlled list. A reasonable default vocabulary: README, GLOSSARY, REVIEW, PRIMARY, METHOD, DATA, COUNTERPOINT, DRAFT, NOTES, STYLE, ARCHIVE.
• ROLE — a function-in-this-notebook tag. Examples: Foundational, Background, Structural, Mechanism, SAR, Inhibitor-Discovery, Disease-Biology, Total-Synthesis, Isolation-and-Characterization, Methodology, Assay-Protocol, Computational-Method, Contradiction, Duplicate, Reference. Choose the term that best describes what the paper does in this notebook.

Notebook-archetype-specific guidance (a methodology notebook may use Substrate-Scope, a grant notebook may use Preliminary-Data, an expert-report notebook may use Prior-Art or Cited-Reference) is the user's call to define.

Step 4 — Apply the naming convention

A reasonable convention is

[NN]_[TYPE]_[AUTHOR-YEAR]_[SHORT-TOPIC]_[ROLE].pdf

where NN is a two-digit ordering number reflecting the intellectual flow of the notebook (not chronology). Numbering starts at 02 because 00_README_Source-Map.md and 01_GLOSSARY_*.md occupy the first two slots. Hyphens within fields, underscores between fields. ASCII only.

Step 5 — Generate the source map and glossary

Produce two human-readable companion documents in the staged folder:

• 00_README_Source-Map.md — project purpose, source groups, full source inventory table, and explicit answering instructions for NotebookLM. Include instructions to flag contradictions between specific sources where they exist.
• 01_GLOSSARY_<topic>.md — controlled vocabulary specific to the project. For chemistry projects this typically includes compound codes, mechanism vocabulary, and any publication-specific abbreviations that NotebookLM will encounter. Glossaries for synthesis projects emphasize structural motifs, reaction names, and stereochemical descriptors. Legal-domain notebooks substitute case citations, statutory terms, and party names.

A glossary is not always necessary, but it is strongly recommended whenever the notebook holds more than a handful of compound codes, specialized abbreviations, or contested terms.

Step 6 — Stage the renamed folder and produce the audit table

Copy each PDF into a fresh folder under the working directory using the new name. The originals are not modified. Generate SourceMap_Audit.csv with one row per source: original filename, proposed filename, type, role, one-sentence rationale.

Step 7 — Hand off to the user

Present the renamed folder, the source map, the glossary, and the audit CSV. Flag any editorial calls that the user should review:

• Sources whose TYPE was ambiguous (e.g., a single-author original article that functions as a Perspective).
• Possible counterpoints that should be confirmed before being labeled as such.
• Apparent duplicates (preprint + peer-reviewed final version).
• Notebook-scope concerns if the source set looks too broad or too narrow for the stated purpose.

Do not silently make these calls. Flag and confirm.

Editorial Principles (the why)

Scope discipline

A focused notebook produces precise retrieval. A broad notebook produces confidently wrong answers. The scope statement in the source map is not boilerplate — it is the constraint that disciplines the model.

Filename as abstract

NotebookLM and similar systems rank sources on metadata before they read content. A filename that encodes order, type, bibliographic identity, topic, and role is doing the work that an indexer would otherwise have to infer. The convention is therefore not aesthetic; it is functional epistemology.

Counterpoint hygiene

When the literature genuinely disagrees, exclusion is dishonest and silent inclusion is worse. The disciplined move is to label the dissenting paper as a COUNTERPOINT source and to instruct the model to surface the contradiction. The source map's Instructions section is the place to do this. NotebookLM treats those instructions as primary text and applies them when answering.

Glossary as protection against semantic drift

Without a controlled vocabulary, retrieval will treat surface-similar terms as equivalent — which fails on isoform-specific biology, compound-code references, and any vocabulary where precision matters. The glossary file is the cheapest insurance against this failure mode.

Audit trail

AI-assisted curation is only defensible if it is reproducible. The SourceMap_Audit.csv is the wet-lab notebook equivalent for a digital artifact. Insist on it.

Voice and Style for the Generated Documents

• 00_README_Source-Map.md is written in measured prose with light structural headers. It is the syllabus for the notebook; treat it with the gravity of a syllabus. Source-inventory tables are acceptable; bullet-point overload is not.
• 01_GLOSSARY_*.md is a controlled vocabulary in alphabetical or topical order, with one short paragraph per term. No emoji, no decorative formatting.
• SourceMap_Audit.csv is plain CSV with the columns: original filename, proposed filename, TYPE, ROLE, rationale. The Rationale column should be a single declarative sentence per row — not a paragraph.
• Filenames use ASCII characters only. Hyphens within fields, underscores between fields. No spaces. No accents.

When to Surface Choices to the User

Some calls should be made by the user, not by the skill. Specifically:

• Notebook scope if the source folder spans more than one obvious project. Ask before splitting.
• TYPE assignment if a paper's classification is genuinely ambiguous (e.g., a Perspective-style article in a primary-research journal — REVIEW or PRIMARY?).
• Counterpoint identification if the contradiction is not flagged in the abstracts. The skill can propose; the user must confirm.
• Preprint handling when a preprint and its peer-reviewed final version are both in the folder. Default is to keep the final and archive the preprint as ARCHIVE, but the user may want both active.
• Inclusion/exclusion of marginal sources. Better to flag than to silently drop.

A Note on Generality

This skill is deliberately domain-agnostic. The same convention works for a medicinal-chemistry inhibitor notebook, a synthetic-methodology notebook, a grant-aim evidence dossier, a legal expert-report notebook, and a graduate-seminar reading set. The chemistry-leaning defaults (compound codes, ZBG vocabulary, ACS journal abbreviations) should be substituted out for the relevant domain when authoring the companion reference and template files. The structural workflow — scope → extract → classify → name → map + glossary → audit — is the part that travels.