This data was taken/derived from https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast and is associated with the following article: Janesick, A., Shelansky, R., Gottscho, A.D. et al. High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis. Nat Commun 14, 8353 (2023). https://doi.org/10.1038/s41467-023-43458-x
This policy outlines the guidelines and best practices for the collective management and storage of test datasets used in Galaxy tool development within our Zenodo community. We aim to ensure the integrity, accessibility, and discoverability of these essential resources.
\nThe Galaxy Tool Developers Community on Zenodo serves as a centralized repository for test datasets required for the development and testing of Galaxy tools. By collectively managing these files, we aim to:
\n\n
Facilitate Reproducibility: Ensure that tool tests can be consistently run and validated by the community.
\nPromote Collaboration: Provide a shared resource that reduces redundant data generation and fosters collaboration among developers.
\nMaintain Data Integrity: Establish standards for data quality, documentation, and version control to ensure accurate and consistent data.
\nEnhance Discoverability: Make it easy for developers to find and utilize relevant test datasets.
\nAll datasets submitted to this community must adhere to the following guidelines:
\nRelevance: Only submit datasets directly relevant to the testing of Galaxy tools. This includes input files, expected output files, and any other data necessary for tool validation.
\nNo Personal Data: Do not upload any sensitive, confidential, or personally identifiable information. ONLY public data will be permitted.
\nLicensing: All submitted datasets should have an appropriate open license (e.g., Creative Commons Zero, MIT License) to ensure their free use and distribution within the community. Explicitly state the license in the Zenodo record.
\nComprehensive Metadata: Provide detailed and accurate metadata for each dataset. This includes:
\nTitle: A clear and concise title describing the dataset's purpose.
For example: Snapatac2 test-data
Authors/Contributors: List all individuals or groups involved in the creation or curation of the dataset.
\nDescription: A thorough description of the dataset, its origin, and how it is used in tool testing. Include information on file formats, data types, and any specific characteristics.
\nKeywords: Use relevant keywords and tags to improve discoverability (e.g., tool name, data type, analysis method).
\nRelated Identifiers: Link to any related Galaxy tools, workflows, or publications using persistent identifiers (e.g., DOIs, GitHub repositories).
\nREADME Files: For complex datasets or collections, include a README.md or README.txt file within the Zenodo record. This file should provide:
\nInstructions on how to use the dataset for testing.
\nDetails on the structure and content of the files.
\nAny specific requirements or dependencies.
\nVersion history, if applicable.
\nStandard Formats: Prefer widely accepted and open file formats (e.g., FASTA, FASTQ, BED, VCF, GFF, tabular text). Avoid proprietary formats where open alternatives exist. In cases where the data can be zipped, it would be appreciated (for eg, .gz, bz2, etc)
\nClear Naming Conventions: Use consistent and descriptive file names that indicate the content and purpose of each file.
\nLogical Structuring: For datasets containing multiple files, organize them into logical subdirectories within the Zenodo submission to enhance clarity.
\nVersioning: When a dataset is updated or modified, submit a new version on Zenodo. Do not overwrite existing versions. Clearly document changes in the version description.
\nChange Log: Maintain a change log in the dataset's description or README file, detailing significant modifications between versions.
\nPeer Review (Informal): While there is no formal peer review process, community members are encouraged to review submitted datasets for accuracy, completeness, and adherence to this policy. Issues should be communicated respectfully to the submitter.
\nReporting Issues: If you identify any issues with a dataset (e.g., incorrect data, missing metadata, policy violation), please contact the community administrators.
\nMaintenance: Dataset owners are responsible for the ongoing maintenance and updates of their submitted datasets.
\nThe community administrators are responsible for:
\n\n
Policy Enforcement: Ensuring adherence to this curation policy.
\nDispute Resolution: Mediating any disputes or concerns related to datasets.
\nSpam/Irrelevant Content Removal: Removing any submissions that are clearly outside the scope or violate the terms of service.
\nGuidance and Support: Providing assistance and guidance to community members regarding data submission.
", "description": "We collectively manage and store (test) datasets used in Galaxy tool development.", "page": "This Zenodo community is a collaborative space dedicated to supporting the vibrant ecosystem of Galaxy tool development. Our primary goal is to provide a robust and reliable infrastructure for storing and managing the essential test datasets that underpin the quality and reproducibility of Galaxy tools.
\n\n
As Galaxy tool developers, we understand the critical need for consistent and well-documented test data. By pooling our resources and adhering to a shared curation policy, we aim to:
\n\n
Accelerate Development: By providing readily available and validated test data, developers can focus more on tool implementation and less on data generation.
\nImprove Tool Quality: Standardized test data leads to more thorough and consistent testing, ultimately resulting in higher-quality Galaxy tools.
\nFoster a Shared Resource: This community acts as a living archive of test datasets, reflecting the collective effort and expertise of the Galaxy tool development community.
\n\n
We encourage all Galaxy tool developers to contribute their test datasets to this community and actively participate in its growth and maintenance. Your contributions are vital to building a stronger, more reliable, and more collaborative Galaxy ecosystem.
", "title": "Galaxy Tool Developers", "type": { "id": "organization" }, "website": "https://galaxyproject.org/iuc/" }, "revision_id": 12, "slug": "galaxy_tool_dev_sig", "updated": "2025-12-09T22:53:15.890948+00:00" } ], "ids": [ "46d6497b-683a-4ddd-b90d-d7f734710d74" ] }, "id": "19053875", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.19053875", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.19053876", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:19053876", "provider": "oai" } }, "revision_id": 3, "stats": { "all_versions": { "data_volume": 38899700528.0, "downloads": 109, "unique_downloads": 109, "unique_views": 54, "views": 60 }, "this_version": { "data_volume": 10223956031.0, "downloads": 23, "unique_downloads": 23, "unique_views": 10, "views": 11 } }, "status": "published", "swh": {}, "updated": "2026-03-16T17:42:49.353181+00:00", "versions": { "index": 1, "is_latest": false } }