eyedatahub 0.2.2

Versioned, source-term-aware command-line access tool for ophthalmology datasets.

EyeDataHub

EyeDataHub is a versioned, community-extensible, license- and access-aware command-line tool backed by a manually curated ophthalmology dataset snapshot. It helps users find, inspect, cite, preflight, and acquire supported resources from their official sources.

EyeDataHub does not host or redistribute the indexed third-party datasets. It does not accept source terms for users or determine legal permission, ethical acceptability, data quality, clinical validity, or scientific suitability.

One-minute overview

The current catalog contains 251 manually source-checked records across 18 primary categories. At the final catalog update on 25 July 2026:

• 171 routes were anonymous direct;
• 34 required immediate self-service authentication;
• 11 required user click-through;
• 27 required controlled or manual access;
• 8 required author contact.

Acquisition support is separate from access: one official deposit completed an end-to-end transfer test, 13 routes passed partial API or file-listing checks, and all other loader states are labelled by their actual test scope.

Install

python -m pip install "git+https://github.com/pooyakhosravi/EyeDataHub.git@v0.2.2"

For development:

git clone https://github.com/pooyakhosravi/EyeDataHub.git
cd EyeDataHub
python -m pip install -e .

Optional platform clients are available through .[kaggle], .[huggingface], .[synapse], or .[full].

Safe command-line workflow

# Read-only discovery
eyehub search --modality oct --access anonymous_direct
eyehub search --task segmentation --source-terms standard-no-nc --json

# Read-only record and citation inspection
eyehub show fives --json
eyehub cite fives --type dataset --format bibtex

# Read-only acquisition preflight
eyehub download fives --data-dir ./data --dry-run --json

# Explicit transfer from the represented official source
eyehub download fives --data-dir ./data --json

Search, show, cite, Python queries, JSON, JSON-LD, and the optional MCP server are read-only. Only an explicit non-dry-run download command may start transfer. Manual, controlled, author-contact, unavailable, and unsupported routes return structured status and instructions instead of imitating success.

What “license-aware” means

Before acquisition, EyeDataHub displays:

• the raw source-stated terms and evidence URL;
• whether the terms appear to apply to data, metadata, code, a publication, challenge participation, mixed components, or an unknown scope;
• registration, authentication, token, click-through, manual approval, agreement, author-contact, and institutional restrictions;
• route-verification date and loader test scope;
• warnings for unknown, research-only, noncommercial, no-derivatives, or mixed terms.

The tool blocks manual authorization routes, never accepts agreements, and writes a provenance manifest after successful transfer. This behavior is not legal advice. The descriptive standard-no-nc filter means only that the normalized source label contains no explicit noncommercial clause; it does not establish permission for a proposed use.

Python

from pathlib import Path

from eyedatahub.acquisition import acquire_dataset, preflight_dataset
from eyedatahub.datasets.registry import REGISTRY

dataset = REGISTRY.get_dataset("ophthalwechat")
data_dir = Path("./data")

plan = preflight_dataset(dataset, data_dir)       # read-only
result = acquire_dataset(dataset, data_dir)       # explicit transfer request
print(result.status, result.manifest_path)

REGISTRY is the retained internal Python class name. Public-facing release artifacts use catalog and snapshot because EyeDataHub is not a data repository.

Credentials and security

Copy .env.example to a private .env file or use each platform's supported credential mechanism. EyeDataHub records only an authentication category or credential presence, never credential values. .env and acquired data directories must not be committed.

Supported backends include official Figshare, Zenodo, Mendeley Data, Dryad, Kaggle, Hugging Face, PhysioNet, Dataverse, Synapse, GitHub, Google Drive, and direct-file routes. Support varies by record and is exposed through acquisition_support and loader_test_scope.

Release record

The release DOI is doi:10.5281/zenodo.21614657. The Zenodo record contains a README that directs users to this repository; software and catalog files are distributed from GitHub.

See CONTRIBUTING.md for reviewed additions and CLAUDE.md for the canonical agent guide.

Citation and licences

Use CITATION.cff for the software citation and cite each acquired dataset from its official source. EyeDataHub code is MIT licensed; the catalog metadata are CC BY 4.0. Third-party data remain under their source-specific terms and access controls.