Category Archives: Open Research Repository

Open Research Repository

Zenodo: The Open Repository Reshaping Global Research

Leave a comment

1. A Platform Born from Open Science Ideals

At its core, Zenodo is a general-purpose open repository developed under the European OpenAIRE program and operated by CERN. Its founding vision is clear: Built and developed by researchers, to ensure that everyone can join in Open Science.

2. The Institutional Roots: CERN and OpenAIRE

The technical backbone comes from CERN, where physicists and engineers use the world’s largest and most complex scientific instruments to study the basic constituents of matter – fundamental particles. The policy framework, meanwhile, was shaped by OpenAIRE, a non-profit, community-driven initiative shaping the policies, infrastructures, and services for Open Science in Europe and beyond.

3. Why Zenodo Was Created

The historical context is important. The OpenAIRE project, in the vanguard of the open access and open data movements in Europe was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. From Wikipedia we learn that Zenodo was launched on 8 May 2013, as the successor of the OpenAIRE Orphan Records Repository to let researchers in any subject area comply with any open science deposit requirement absent an institutional repository.

4. Scale and Reach

The growth has been remarkable. Also in 2021, Zenodo reported it had crossed 1 petabyte in hosted data and 15 million yearly visits. This expansion reflects a universal need: The need for a catch-all is not restricted to one funder, or one nation, so the concept caught on, and Zenodo rapidly started welcoming research from all over the world, and from every discipline.

5. Persistent Identifiers and Citability

A key technical feature is that for each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable. This aligns with the mission of DataCite, a global community that shares a common interest: to ensure that research outputs and resources are openly available and connected so that their reuse can advance knowledge across and between disciplines, now and in the future.

6. Compliance with FAIR Principles

Equally essential is adherence to data standards. The GO FAIR Foundation guides people and organisations on solutions for making data Findable, Accessible, Interoperable, Reusable [FAIR] for both people and machines. Zenodo embeds these principles directly into its workflow, ensuring that no one is left behind through lack of access to the necessary tools and resources, Zenodo makes the sharing, curation and publication of data and software a reality for all researchers.

7. The Publisher Ecosystem

Major publishers now reinforce this infrastructure. PLOS is a non-profit organization on a mission to drive open science forward with measurable, meaningful change in research publishing, policy and practice. Similarly, the strength of Science and its online journal sites rests with the strengths of its community of authors, who provide cutting-edge research, incisive scientific commentary, and insights on what’s important to the scientific world.

8. Scholarly Communication and Community

Beyond repositories, broader communities drive change. FORCE11 has spent 15 years of bringing together a global community dedicated to improving scholarly communication, research practices, and knowledge sharing.

9. Researcher Identity and Attribution

To connect outputs with individuals, ORCID is a free, unique, persistent identifier (PID) for individuals to use as they engage in research, scholarship, and innovation activities. This ensures that every deposit on Zenodo can be unambiguously attributed.

10. European Policy Context

At the policy level, the EU ranks second worldwide in scientific output, while 57% of its scientific publications involve international collaboration. Zenodo operates as a direct instrument of this open-science strategy.

11. Looking Forward

Ultimately, Zenodo stands at the intersection of world-class computing infrastructure, European open-access policy, and the practical needs of researchers across every discipline. Its continued evolution will remain central to the global effort to make knowledge freely accessible, permanently citable, and genuinely reusable for generations to come.
Open Research Repository

Zenodo and the Place of Research Repositories in Open Science

Leave a comment

Origins and Purpose

ZENODO, an open data repository, was commissioned and funded by the EC and built by CERN to support this.

From that beginning, its reach widened. Zenodo was launched in May 2013.

Its place within open science is clear. Among its flagship offerings are: Zenodo (CERN), a trusted repository that enables researchers to share and preserve publications, datasets, and software.

Access is central to that purpose. Free to upload and free to access, Zenodo makes scientific outputs of all kinds citable, shareable, and discoverable for the long term.

A Home for Different Kinds of Research

Zenodo is not confined to one field. Generalist repositories like Dryad, Figshare, and Zenodo tend to accept any kind of data from any discipline.

This distinguishes generalist repositories. Multidisciplinary/generalist repositories are not focused on a particular field and typically accept all types of data.

Zenodo also accepts varied outputs. Zenodo is an open-source, open-access, open-data platform for all fields of research.

Those outputs include code. The repository archives data, code, and GitHub materials.

They can include documents as well. CODATA uses Zenodo as a repository for our most important reports, statements and some presentations.

This breadth serves different researchers. Zenodo caters to researchers across all scientific fields, specializing in secure long-term preservation and free access to data sets.

Choosing Where to Deposit

Breadth does not remove the need to choose carefully. Be sure to check for size limits, licensing options, fees for larger deposits and other policies or features important to you.

A disciplinary repository may come first. If there are no discipline specific repositories you can always use a more generalist repository such as Zenodo.org.

Other institutions offer a similar path. If certain materials are not eligible for deposit in a disciplinary repository, Cornell researchers can explore sharing via our Institutional Repository, eCommons, or in the Cornell University Research Data collection in Zenodo.

Cost can also influence the choice. Dryad charges a data publication fee, but Zenodo and Figshare both allow registered users to deposit data free of charge.

Capacity remains a practical consideration. Zenodo accepts datasets of up to 50GB.

Making Research Citable

After deposit, identification matters. A digital object identifier (DOI) is automatically assigned to all Zenodo files.

That identifier supports references. DataCite DOIs should be displayed as the full URL when bibliographic information about content is displayed.

Researchers also need usable citations. Many data repositories generate a formatted citation for you.

Visibility follows from sharing. Publishing data through a creditable repository allows for information and files to be discoverable.

These aims extend beyond individual datasets. Zenodo builds and operates a simple and innovative service that enables researchers, scientists, EU projects and institutions to share, preserve and showcase multidisciplinary research results (data and publications) that are not part of the existing institutional or subject-based repositories of the research communities.

Software, Versions, and Preservation

Software makes preservation especially important. There also exist more generalized archival research repositories such as Zenodo.org.

GitHub and Zenodo can work together. Zenodo archives your repository and issues a new DOI each time you create a new GitHub release.

A fixed release can then be cited. Freeze your repository, get a DOI, and make your code citable.

Funders also recognize this distinction. GitHub can easily deliver a static, citable version to a generalist repository like Zenodo, which will mint a DOI, with metadata reported to ADC and/or USAP-DC.

A permanent identifier helps future readers. To help others repeat your results, put your code in a repository that gives it a permanent identifier (DOI/PID), such as Zenodo or Code Ocean.

Research services apply the same approach. The repository can be published in Zenodo and the DOI of the repository should be given to the NERC Data Centre for reference and to link it to any data being published from that code.

Use Across Research Communities

The repository appears in institutional guidance. All NIH-funded researchers may use Zenodo, which is especially good for data with links to GitHub.

It is also listed by public agencies. Zenodo.

Universities identify its broader role. Some examples of code repositories include GitHub, Zenodo, and Code Ocean.

Research organisations use it directly. A general purpose open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts.

It can complement other services. As part of that shift, the OSF Projects workflow – the part of the OSF used for project collaboration, file management, and storage – is being phased out as an active workflow.

Responsible Sharing

Open sharing still requires judgment. Grantholders must make sure their shared outputs: are discoverable.

Some material needs controlled access. Restricted and Closed content is also supported.

Repository selection therefore remains part of research practice. General-purpose data repository: e.g. Dryad, Figshare, Zenodo.

Together, these sources describe a practical role. Zenodo is a general-purpose, free and open-access repository operated by the European Organization for Nuclear Research (CERN).

Open Research Repository

Figshare: A Comprehensive Research Repository Platform

Leave a comment

Overview and Purpose

Figshare is an online open access repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos. Figshare is City St George’s institutional repository and publishing platform for digital research outputs like data, images, video and audio recordings. Figshare is a provider of open research repository infrastructure. Figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.

Technical Capabilities and File Support

figshare is a general-purpose file repository that accepts all forms of research output from data files to presentation files (eg Powerpoint presentations). Figshare accepts the upload of any file type or format. We accept any file format and aim to preview all of them in the browser. Upload files up to 20GB. Flexibility and Ease of Use – Figshare accepts all file formats in order to keep the barriers to data sharing low for researchers.

Research Benefits and Metrics

This article outlines the usage metrics measured and displayed on item pages in Figshare: views, downloads, citations, and Altmetrics. Assigns a persistent and unique digital object identifier (DOI) to support accurate citation and Data availability statements. Researchers benefit from openly publishing/sharing their work in Swinburne figshare in multiple ways, including: wider reach – Google scholar indexing. Sharing research data on Figshare can help promote your research and raise your profile as a researcher.

Sharing and Access Options

Research outputs can be shared privately with collaborators or made public in the name of open research or to comply with funder and publisher requirements. The primary aim of the service is to showcase research outputs to the world by making them more discoverable and accessible. Open research infrastructure​​ Figshare.com is free to use for individual researchers, any scholarly research outputs up to 20GB can be shared openly and freely.

Platform Integration and Workflow

simplify your research workflow. Upload Manage Share Publish. Figshare helps organizations share, showcase and manage research outputs in a discoverable, citable, reportable and transparent way. Figshare’s repository solutions help researchers and organizations manage their research outputs in a discoverable, citable, reportable and transparent way.

References Used:

Figshare overview description City St George’s institutional repository description
Figshare provider infrastructure statement Repository purpose statement Organizational management description Repository solutions statement Data management file acceptance File format flexibility statement Workflow and file format acceptance File type upload policy Usage metrics documentation Open research infrastructure statement DOI assignment benefits Researcher benefits including Google Scholar indexing Sharing options description Service primary aim statement Research promotion benefits

Open Research Repository, Research

Zenodo an open repository for all research

Leave a comment

Zenodo serves as an open repository for all research outputs, governed by clear policies.

Its scope includes all fields of research and all types of research artifacts, from any stage of the research lifecycle. Anyone may register as a user, and all users are allowed to deposit content for which they possess the appropriate rights. A key operational point is that by uploading content, no change of ownership is implied and all uploaded content remains the property of the parties prior to submission. The repository accepts all data file formats, even those considered preservation unfriendly, with a total file size limit of 50GB per record.

Files deposited on Zenodo can have different levels of accessibility

Users may specify a license for all publicly available files and can deposit files under closed, open, or embargoed access. For embargoed status, the repository will restrict access to the data until a provided end date, after which the content becomes publicly available automatically. In all cases, the metadata for records is licensed under CC0 and is always publicly accessible.

The platform ensures long-term preservation through specific technical measures.

All data files are stored in CERN Data Centres, primarily in Geneva, with replicas in Budapest, and are kept in multiple replicas in a distributed file system. Items will be retained for the lifetime of the repository, which is currently tied to the host laboratory CERN and its experimental programme defined for the next 20 years at least. If the repository were to close, best efforts would be made to integrate all content into suitable alternative institutional and/or subject based repositories.

Uploading research to Zenodo is a structured process.

Users begin by creating a new upload and can add files by clicking an upload button or using drag and drop, with a limit of up to 100 files and a total of 50GB. They must then fill in minimal required metadata fields, including resource type, title, publication date, and creators. A critical step is managing the Digital Object Identifier (DOI); if the upload already has a DOI, it must be declared, but if not, one can be reserved through the platform. After setting the visibility (public or restricted) and optionally applying an embargo, the user can publish the record.

Research communities, such as the SEARRP, implement specific curation policies on Zenodo.

Researchers are required to deposit their datasets and metadata within twelve months of data collection, or immediately post-publication. The metadata for submitted data will be publicly available, and there are several routes to publication: linking to already open access data, submitting as new open access, using Zenodo’s embargo mechanism for up to two years, or setting terms and conditions for restricted sharing. Users of open access data from such communities are expected to cite the relevant researchers and, for certain intensive datasets, include the data collectors as co-authors on manuscripts.

Extracting data from digital sources for repositories is a distinct challenge, often addressed with specialized tools.

Web scraping tools are designed to automate data extraction from websites. A key consideration when choosing a tool is its ability to handle JavaScript-heavy websites, CAPTCHAs, IP bans, and large-scale tasks. Solutions range from full APIs like ScraperAPI, which handles proxies and CAPTCHAs, to no-code browser extensions like Web Scraper, which uses a point-and-click interface and can export data in CSV, XLSX, and JSON formats. Other platforms, like Browse AI, offer AI-powered scraping and monitoring with features like human behavior emulation and geo-based data extraction.

For data trapped within documents, AI-powered extraction software provides a solution.

Tools like Parseur use AI to automatically convert PDFs, emails, and images into structured data, aiming to save up to 98% on manual data entry costs. Similarly, Amazon Textract is a machine learning service that goes beyond simple optical character recognition (OCR) to automatically extract text, handwriting, layout elements, and data from scanned documents.

The automated identification of dataset references in literature is an active area of research.

Researchers note that datasets are critical for replication and reproducibility, but citing them is not yet a common or standard practice, which affects our ability to track their usage. Automated systems like Data Gatherer leverage large language models to identify and extract dataset references from scientific publications, aiming to reduce the time required for dataset discovery. Other research focuses on using specific neural network models, such as a Bi-LSTM-CRF architecture, to achieve automatic dataset mention extraction from scientific articles.

📚 References

  1. Zenodo. Policies
  2. Marini, P., Santos, A., Contaxis, N., & Freire, J. (2025). Data Gatherer: LLM-Powered Dataset Reference Extraction from Scientific Literature. In Proceedings of the Fifth Workshop on Scholarly Document Processing (SDP 2025). Association for Computational Linguistics.
  3. ScraperAPI. 16 Best Web Scraping Tools In 2025 (Pros, Cons, Pricing)
  4. Zeng, T. (2024). Dataset Mention Extraction in Scientific Articles Using Bi-LSTM-CRF Model. arXiv.
  5. Web Scraper. Web Scraper – The #1 web scraping extension
  6. Zenodo. Create new upload
  7. Parseur. AI data extraction software | Parseur®
  8. Browse AI. Browse AI: Scrape and Monitor Data from Any Website with …
  9. Zenodo. Curation policy for the SEARRP Community
  10. Amazon Web Services. Amazon Textract
Open Research Repository, Research

A Guide to Free Open Access Sites for Publishing Research

Leave a comment

For discovering legitimate open access publications, comprehensive directories are essential starting points. The Directory of Open Access Journals (DOAJ) is a unique and extensive index of diverse open access journals from around the world, committed to ensuring quality content is freely available online for everyone. Similarly, the Directory of Open Access Repositories (OpenDOAR) is a quality-assured global directory of academic open access repositories. Other major directories include the Directory of Open Access Books and the Directory of Open Access Dissertations.

General-purpose repositories allow researchers to share various outputs, from datasets to preprints. Key platforms include:

  • Zenodo: A general-purpose open-access repository developed by CERN and backed by the European Commission. It is free, has no upper data limits, and supports all research outputs.
  • Figshare: An open-access repository that allows researchers to store and share a wide range of research outputs including datasets, presentations, videos, and code. It offers free storage up to 20GB for individuals.
  • Open Science Framework (OSF): A free, open-source repository and project management tool supporting collaborative research, data sharing, and reproducibility.
  • Harvard Dataverse: An open-source repository application for research data, free for all researchers worldwide with generous storage limits.

The table below compares some major free generalist repositories:

Repository Primary Cost for Standard Use Key Limits for Free Tier Notable Features
Zenodo Free 50 GB per record Backed by CERN, supports all output types, versioning
Open Science Framework (OSF) Free 50 GB for open projects Integrated project management, preregistration, collaboration tools
Harvard Dataverse Free 2.5 GB per file, 1 TB total per researcher Tiered access controls, integrated data analysis tools
Figshare Freemium (Free tier available) 20 GB of private storage Wide file format support, strong journal integration
Dryad Data Publishing Charge (DPC) applies $120 DPC for up to 50 GB Curated, requires link to publication, enforces CC0 license

Subject-specific and preprint repositories cater to disciplinary norms. Preprint repositories like arXiv, bioRxiv, and SocArXiv allow rapid sharing of manuscripts before peer review. Field-specific repositories also exist, such as SSRN for social sciences, ICPSR for social science data, and RePEc for economics.

A wealth of open data is available for reuse and analysis from governmental and institutional sources. Notable sources include:

  • Government & Global Data: Data.gov, U.S. Census Bureau, World Bank Open Data, and UNICEF.
  • Health & Scientific Data: NIH repositories, World Health Organization (WHO), CDC, NASA Earth Data, and Dryad Digital Repository.
  • Academic & Social Science Data: ICPSR, Pew Research Center, Google Dataset Search, and Google Scholar.

Tools exist to help you find the right repository. The Registry of Research Data Repositories (re3data) is a searchable listing of data repositories worldwide. FAIRsharing is a curated portal describing standards, databases, and data policies. Experts also recommend checking guidelines from your institution or funder and, when possible, using a domain-specific repository to enrich metadata and discoverability within your field.

References

  1. DOAJ: Directory of Open Access Journals. doaj.org.
  2. Literature Review Made Simple: Comparing 4 open access repositories. Enago Academy.
  3. Data Repositories. Harvard Medical School Data Management.
  4. Institutional Repositories: Platforms. Atla LibGuides.
  5. 43 Free Open Data Sources You Shouldn’t Ignore. Crawlbase Blog.
  6. FAIRsharing | re3data.org. re3data.org.
  7. Open Access Dataset and Data Repositories. McMaster University MIRA.
  8. Data repositories | Digital Education Resources. Vanderbilt Libraries Digital Lab.
  9. Find a FAIR repository. International Neuroinformatics Coordinating Facility (INCF).
  10. Freely Available and Open Access Resources. UCLA Library Guides.
Alternatives, Open Research Repository

Figshare and Open Research Repository Alternatives

Leave a comment

Figshare Overview

Figshare is an online open access repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos. Figshare is a provider of open research repository infrastructure. Our solutions help organizations and researchers share, showcase and manage their research. figshare is a general-purpose file repository that accepts all forms of research output from data files to presentation files (eg Powerpoint presentations). Figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.

Open Alternatives Landscape

Major Open Repository Options

Dryad is a nonprofit, community-governed open-access repository and publishing platform dedicated to the curation, preservation, and reuse of research data. Zenodo is a general-purpose, free and open-access repository operated by the European Organization for Nuclear Research (CERN). The Open Science Framework (OSF) is a free and open free, open repository and platform to enable collaboration and support the entire research lifecycle.

Zenodo Features

Zenodo provides leading features such as versioning and metrics such as usage statistics. The integration with GitHub allows automatic archival of software. It allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts. Zenodo is a general-purpose research repository designed to facilitate the sharing, preservation, and dissemination of research outputs across all scientific disciplines.

Dryad Capabilities

The Dryad Digital Repository is a curated resource that makes research data discoverable, freely reusable, and citable. Dryad has several important features: Content is free to download and re-use under a Creative Commons Zero (CC0) license. Dryad curates and preserves the data, applying advanced metadata and regularly refreshing and migrating the data to updated versions of its platform.

Open Science Framework (OSF) Platform

OSF is a free and open source project management tool that supports researchers throughout their entire project lifecycle. As a flexible repository, it can store and archive research data, protocols, and materials. Open Science Framework (OSF) is a cloud-based open-source research project management tool that supports researchers throughout the active research stage. OSF Registries are scholarly repositories built for archiving, sharing, searching, and aggregating research plans, designs, data, and outcomes.

Repository Comparison Context

Some other generalist repositories are listed in brief at the bottom including Dryad, Figshare, Mendeley Data, Open Science Framework (OSF), and Zenodo. You may want to look into Dryad Digital Repository, FigShare, or Zenodo. All three of these data repositories are recommended by high-profile journals. These platforms provide essential infrastructure for open science and research data management across diverse academic disciplines.

References Used:

Figshare overview description
About Figshare infrastructure
figshare data management features
Figshare research outputs repository
Dryad nonprofit repository description
Zenodo CERN repository
OSF research lifecycle support
Zenodo features and GitHub integration
Zenodo research artefacts
Zenodo general-purpose repository
Dryad Digital Repository description
Dryad advantages and licensing
Dryad curation and preservation
OSF project management tool
OSF flexible repository capabilities
OSF cloud-based research tool
OSF Registries scholarly repositories
Generalist repositories list
Journal-recommended repositories