Guide

AI Research Assistant Workflow: From Sources to Citations (2025)

August 23, 2025 - By notebooklm

AI Research Assistant Workflow, From Sources to Citations 2025

A powerful model does not guarantee a trustworthy result. What matters is a workflow that starts with a clear question, moves through transparent retrieval, and ends with claims that are easy to verify. The following end to end process is tuned for students, researchers, and analysts who want speed without sacrificing rigor. It works with any mix of tools, from web-first assistants and grounded notebooks to reference managers and writing apps.

Step 1, Frame a Decision Question

Translate a vague topic into a decision or testable claim. Good questions fit on one line.

Weak, climate policy in Europe.
Strong, did the 2023 ETS revision increase allowance price volatility compared to 2021.

Add a measurable outcome or comparison when possible. This keeps your search and extraction focused.

Step 2, Build a Starter Corpus

Aim for three to six sources that you can actually read in a day.

One overview or review article for context.
Two to three primary studies or reports.
One dissenting or critical perspective.
Anything your advisor or instructor requires.

Store PDFs in your reference manager first. Use consistent names and tags, for example ETS_2023_revision_summary.pdf. Your library remains the source of truth.

Step 3, Index And Verify

Upload the packet to your source-grounded notebook. Run a smoke test.

Ask for a table of contents with page numbers.
Ask for definitions of two uncommon terms you know are present.
Click citations. If they fail, fix the PDFs or run OCR before you continue.

Document what you did in a short log. This becomes part of your methods.

Step 4, Extract Structure Before Prose

Pull out the bones of the argument first. Two artifacts cover most projects.

Study or clause matrix

Columns depend on field. Examples, sample size, inclusion criteria, model, outcome metrics, confidence interval, page. For policy, stakeholder, obligation, threshold, deadline, section.

Claims and evidence list

One row per claim with a short paraphrase, a quoted sentence, and a page anchor. Keep quotes under 25 words for readability.

Export both artifacts to CSV or Sheets. Version them in your repository.

Step 5, Ask For Agreements, Contradictions, And Gaps

This is where AI shines as a reader’s assistant. Ask targeted questions.

What do these sources agree on, with citations.
Where do they disagree, and why, show page anchors.
Which variables are missing for a strong conclusion.
What alternative explanations appear in the Discussion sections.

Keep everything anchored. If a claim lacks a page number, do not accept it.

Step 6, Draft In Your Own Voice

Use the structure you extracted to write prose for a specific audience.

Start with a one paragraph abstract in plain English.
Expand each claim into a short section with evidence and context.
Use your assistant for clarity edits, not for writing from scratch.
Insert citations as you write, not after. Your reference manager handles the format.

If you need a figure, ask the model to propose the simplest chart that supports your point, then build it in your plotting tool with data from your matrix.

Step 7, Run Verification Passes

Treat verification like a checklist.

Citation audit, click a sample from each section, confirm they land on the right passages.
Numerical audit, reproduce any numbers from your matrix or notes.
Assumption audit, list assumptions the conclusion depends on, confirm they appear in sources.
Scope audit, ensure you did not import claims from outside the corpus.

If anything fails, fix the source or narrow the claim.

Step 8, Reproduce And Package

Someone else should be able to recreate your result.

Export the study matrix and claims list to CSV.
Save prompts, tool versions, and dates in a methods note.
Keep PDFs and exports with the project in your library and repository.
Generate a short Read Me that explains the folder layout and how to rerun the steps.

If you shared AI generated summaries, include the anchored report alongside any audio or video overviews so reviewers can inspect the evidence.

Worked Example, Policy Change Brief

Question

Did the revision to Policy X increase administrative burden for small firms.

Corpus

Policy text, regulator summary, two industry reports, one academic paper.

Structure extraction

Table of obligations with party, action, deadline, section.
Claims list with quotes that mention forms, fees, and reporting frequency.

Analysis

Agreement, all sources show quarterly reporting added for firms above a threshold.
Contradiction, one report claims monthly reports for a subset, citation reveals an older draft.
Gap, unclear guidance on exemptions for firms below a revenue floor.

Draft

One page brief with three findings, each followed by two citations. A figure shows the old and new timelines.

Verification and package

Clicked every citation in the brief. Saved CSVs and prompts. Committed the lot to the repository with a README.

Prompts You Can Paste

Matrix maker

From the uploaded PDFs, build a table with columns, Stakeholder, Obligation, Trigger, Deadline, Section, Citation with page number. Return as Markdown and keep each cell under 20 words.

Contradiction finder

Identify statements that disagree about [topic] across sources. Show each pair with citations and a short reason for the difference, for example draft vs final, or sample differences.

Evidence backed summary

Write five bullets that answer [question] using only the corpus. After each bullet, include a citation with page number in parentheses.

Methods note

Write a short methods paragraph that describes the sources used, indexing steps, and prompts. Include the date for reproducibility.

Templates To Reuse

Study matrix columns

Study, Year, Sample Size, Inclusion Criteria, Method, Outcome Metric, Result, Limitations, Citation with page.

Claim row fields

Claim paraphrase, Quote under 25 words, Page, Source name, Confidence, Notes.

README outline

Question, Corpus, Tools and versions, Steps to reproduce, Exports, Contact.

Common Pitfalls

Over summarization. Section summaries lose nuance. Always keep a claims list for precision.
Citation drift. Edits and re-indexing can change anchors. Freeze versions before final export.
Shiny tool syndrome. A new interface will not fix a vague question. Tighten scope first.
One giant notebook. Break work into projects per question so retrieval stays sharp.

Conclusion

A clean workflow beats a flashy model. Start with a decision question, build a small high quality corpus, extract structure, write in your voice, then verify with citations you can click. Keep prompts and exports with the project so another researcher can reproduce the result. You will move faster, argue more clearly, and spend less time in citation hell.