Evidence map›Paper›PMID 41402353›Full record

ArticleScientific data2025

Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools.

Jeremy F Magland, Ryan Ly, Oliver Rübel, Benjamin Dichter

Abstract readDataset
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Review
  2. SpikeLab: Agentic tools for spike data analysis.bioRxiv : the preprint server for biology · 2026
    Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Jeremy F MaglandFlatiron Institute, New York, NY, USA. jmagland@flatironinstitute.org.
Ryan LyLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Oliver RübelLawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0001-9902-1984
Benjamin DichterCatalystNeuro, Casper, WY, USA.

Funding

DANDI: Distributed Archives for Neurophysiology Data IntegrationR24MH117295 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Satrajit Sujit Ghosh, Yaroslav O Halchenko · 2019 to 2026
$11.6M
Evaluation and optimization of NWB neurophysiology software and data in the cloudU24NS120057 · NINDS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI DICHTER, BENJAMIN K, RUEBEL, OLIVER · 2021 to 2025
$5.9M
NIMH NIH HHS R24 MH117295NINDS NIH HHS U24 NS120057U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R24MH117295U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24NS120057
6 · The paper itself

Abstract

The DANDI Archive is a key resource for sharing open neurophysiology data, hosting over 400 datasets in the Neurodata Without Borders (NWB) format. While these datasets hold tremendous potential for reanalysis and discovery, many researchers face barriers to reuse, including unfamiliarity with access methods and difficulty identifying relevant content. Here we introduce an AI-powered, agentic chat assistant and a notebook generation pipeline. The chat assistant serves as an interactive tool for exploring DANDI datasets. It leverages large language models (LLMs) and integrates with agentic tools to guide users through data access, visualization, and preliminary analysis. The notebook generator analyzes dataset structure with minimal human input, executing inspection scripts and generating visualizations. It then produces an instructional Python notebook tailored to the dataset. We applied this system to 12 recent datasets. Review by neurophysiology data specialists found the generated notebooks to be generally accurate and well-structured, with most notebooks rated as "very helpful." This work demonstrates how AI can support FAIR principles by leveraging data standards and lowering barriers to data reuse and engagement.

Indexed as

Databases, FactualNeurophysiologyHumansLanguageLarge Language ModelsProgramming LanguagesSoftware

Identifiers

PMID41402353
PMCPMC12727687

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.