Nagomi

Clinical research, with the evidence trail still visible.

Nagomi is the research verification layer for clinical evidence work. It helps search PubMed, structure questions, check references, inspect papers, and export what was found.

It is built as a Gemini CLI extension, so the workflow can live close to writing, teaching, coding, and evidence review.

Open extension View repo

PubMed search PICO structure Reference checks Evidence export

Gemini CLI extension
Research tool
Not medical advice

Install

gemini extensions install https://github.com/avivlyweb/pubmed-gemini-extension

Requires Gemini CLI, Node.js 18+, and Python 3.9+.

Evidence trail

PICO Verify Audit Export

Why it exists

Evidence work breaks when the source trail becomes too easy to fake or too hard to inspect.

Clinical research tools should not only retrieve papers. They should help users understand whether a source is real, relevant, and usable.

Nagomi was built around that problem. It combines PubMed search, PICO structure, evidence weighting, reference verification, single-paper audit, and export into a small command set.

The goal is practical: make research faster without making the evidence trail disappear.

How to use it

Five commands cover the core research workflow.

Search, synthesize, verify, analyze, and export. The surface stays small so the workflow stays teachable.

`/nagomi:search`

Turns a clinical question into a more structured PubMed search with PICO logic.

/nagomi:search what is the most effective treatment for Achilles tendinopathy

Synthesis

`/nagomi:synthesis`

Brings multiple papers into a weighted evidence view instead of a loose abstract list.

/nagomi:synthesis yoga vs meditation for neuroplasticity in seniors

Verify

`/nagomi:verify`

Checks references for broken, mismatched, or fabricated citation patterns.

/nagomi:verify ~/Downloads/final_submission.pdf

Analyze

`/nagomi:analyze`

Inspects one PubMed record for methodology, study design, and trust signals.

/nagomi:analyze 34580864

Export

`/nagomi:export`

Exports evidence trails into formats that can move into reference managers or writing workflows.

/nagomi:export "chronic heart failure telemonitoring" format=bibtex

What it checks

A research workflow needs structure, skepticism, and clean output.

Nagomi is useful because it treats verification as part of the product, not as something to remember at the end.

PICO

Clinical questions become searchable structure.

Nagomi helps move from a broad clinical question to population, intervention, comparison, and outcome logic.

Compass

Evidence needs weight, not just volume.

The Evidence Compass idea helps separate stronger sources from weaker signals before a conclusion is trusted.

Verification

References are checked before they are reused.

The verification flow is built to catch mismatched DOI records, impossible metadata, and stitched-together citation errors.

Retractions

Pulled papers should not quietly remain in the trail.

A research workflow is stronger when it can flag papers that have changed status after publication.

Audit

Single papers can be inspected more deeply.

The analyze command is useful when one source matters enough to inspect study design, bias, and practical relevance.

Export

The trail should move with the work.

BibTeX and RIS export make the output easier to reuse in writing, teaching, and reference workflows.

Where it fits

Nagomi sits next to EBPcharlie, Practice Shift, and CRISP Live.

EBPcharlie is the product surface for clinicians. Practice Shift translates evidence into short learning. CRISP Live shows reasoning as a replayable team process. Nagomi is the research verification layer underneath that mindset.

Fast path

/nagomi:search shoulder impingement diagnosis clusters
/nagomi:synthesis chronic low back pain exercise
/nagomi:verify references.pdf

Boundary

Nagomi supports scholarly exploration and evidence checking. It is not medical advice.

Open extension See EBPcharlie