# Welcome to DeSci Nodes

Elevate your research • Product introduction

{% hint style="warning" %}
**Dear users** \
Please note that we are currently working hard on updating Nodes/Publish. We are ***developing new features and designs faster than we can update the user guide***. As such, the guide is often out of date. \
Please bear with us, and send us any questions if you cannot find your answer in this User Guide. 
{% endhint %}

Welcome to our newest version of [**Nodes**](https://nodes.desci.com/), a platform for publishing all your research-related materials. 

Read below to learn about [DeSci Nodes and the technology behind it](/technical-background/open-state-repository), visit the [DeSci Labs](https://desci.com/) website to check out who we are, or jump straight to the [user guide](/create-and-publish/introduction) and learn how to share your research, data, code, etc as an integrated publication on the decentralized web through [Nodes](https://nodes.desci.com/). 

{% hint style="info" %}
**Dear early adopters** :hugging:

Thank you. It's still early, and your feedback, participation and interaction count tremendously. We're currently providing every early adopter with **100 gigabytes of online data to use in their Nodes profile.** 
{% endhint %}

## Quick Links

<table data-view="cards"><thead><tr><th></th><th data-hidden data-card-cover data-type="files"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><strong>User Docs Quick Start</strong></td><td><a href="/files/568Y0u9PJilQHlVXEd4T">/files/568Y0u9PJilQHlVXEd4T</a></td><td><a href="/pages/JhLZXWxHNVrjM1avZNo2">/pages/JhLZXWxHNVrjM1avZNo2</a></td></tr><tr><td><strong>Protocol Infrastructure</strong></td><td><a href="/files/gXM95gPrBf2QW4qYLwfe">/files/gXM95gPrBf2QW4qYLwfe</a></td><td><a href="/spaces/uLEzUfpuZ1EbnvdhdDi9">/spaces/uLEzUfpuZ1EbnvdhdDi9</a></td></tr><tr><td><strong>Background Info</strong></td><td><a href="/files/TqcnFKZKJJ13M7YWCKNW">/files/TqcnFKZKJJ13M7YWCKNW</a></td><td><a href="/pages/GNxMHKZoKQl44lJafUqc">/pages/GNxMHKZoKQl44lJafUqc</a></td></tr></tbody></table>

## Introduction

DeSci Nodes is an (inter)active online platform that lets researchers share and curate ***research objects***. Research objects are integrated publications, which contain a broad range of components such as manuscripts, data, code, and all other (digital) files and objects related to research ([components](/create-and-publish/create-a-node/add-components)).

Sharing components alongside manuscripts isn't just good practice in open science, but it directly benefits you and the researchers as well. It's been shown that publishing data alongside publications increases the reach of scientific work, with indicators such as citations increasing by up to 100%. Read more about this [**here**](https://doi.org/10.1371/journal.pone.0230416) and [**here**](https://doi.org/10.1371/journal.pone.0225883).  &#x20;

Our goal is to make it simple and rewarding for scientists to create openly accessible, interoperable and compute-enabled [research objects](https://en.wikipedia.org/wiki/Research_Object), i.e. sharing aggregated research information in formats that can be easily downloaded, incorporated, analyzed, computed, and credited.

A Node is a version-able container that securely stores the components produced by a research project, and connects the components coherently. Nodes can contain a wide range of components - such as manuscripts, code, data, models, analysis pipelines, and more - to form an interconnected graph of different component types. &#x20;

[Check out this Node about exoplanet formation to get an idea of how your publication may look like as a Node.](https://beta.dpid.org/46)

{% hint style="info" %}
Publishing components alongside manuscripts isn't just good practice in Open Science. Publishing related data increases the reach of scientific work, with indicators such as [citations increasing by about 25%](https://doi.org/10.1371/journal.pone.0230416).
{% endhint %}

### What does DeSci Nodes support?

We *support open access* and sharing of research and data.&#x20;

We support [**FAIR data principles**](https://www.go-fair.org/fair-principles/), and work with the Go-FAIR Foundation to support their integration into Nodes. We make it easy for researchers to ensure their data is Findable, Accessible, Interoperable, and Reusable.

We support researchers in their careers - *we take no copyrights on the content you post on Nodes.* What you share on DeSci Nodes **remains entirely the property of the original owners**. As such, you are always free to submit and publish your work elsewhere.&#x20;

Combining the two previous points makes DeSci Nodes a platform that the scientific community can benefit from - researchers sharing research objects show their dedication towards best practice and open science. You can verifiably display how FAIR your research, data, code etc. are - with the possibility of communities verifying this - doing much of the groundwork for journal publications.&#x20;

We support the **supporting roles**. Research is not made by the first author. Usually there's a whole team contributing to a research project to make it come to life, some in roles that are recognized as authors, some that go unrecognized on the author list. On a Node, you can granularly trace and specify who did what, to ensure all contributors get the credit they deserve.

We support **reviewers**. Peer review today is mainly performed anonymously, and for free. DeSci Nodes introduces a [new model](/community/community-curation) of scientific discourse and dissemination that allows reviewers to accrue credit for their work, and eventually get rewarded for it.

We support the **scientific community**. We believe that a flourishing scientific ecosystem centers on communities. Communities generate positive externalities by creating and maintaining scientific knowledge (formally as in publications and journals, and informally as in shared notes or conversations). In DeSci Nodes, (soon) anyone can start a community to validate and/or curate scientific publications to contribute to a higher quality scientific record.

We support **transparency**. When using DeSci Nodes, either to publish or to review work, your contributions to the scientific record are granularly logged. You may always update and edit your work, for example by publishing a new version of your Node. But all previous actions are available for query, building towards a tamperproof scientific record.


# General user overview

Get set up  •  Navigation  •  Collection  •  Workspace  •  Profile

The Nodes app is split into three main sections, accessed through the side bar.

They are shortly discussed below, and presented further in-depth in the following subchapters: &#x20;

[Explore](/general-user-overview/explore) <img src="/files/gvdibc3IqOtDSIKa1P4C" alt="ExplorerButton.jpg" data-size="line">

[Node Workspace](/general-user-overview/node-workspace) <img src="/files/hZjvzxT2WdLojYw9rEyc" alt="Current Node Button.jpg" data-size="line">

and your [Profile](/general-user-overview/profile) <img src="/files/2DVoy56b1FELfVfTuiwC" alt="Screenshot 2024-01-19 at 14.14.33.jpg" data-size="line">

<figure><img src="/files/qUXhzSUcDHkXDg0DwvvK" alt="" width="563"><figcaption><p>Nodes App main sections overview</p></figcaption></figure>

## Explore <img src="/files/q8l9nvAQWTR7PzG2JcnT" alt="Explore_Button.jpg" data-size="line">

Explore provides an overview of published Nodes: those most recently published as well as a curated selection of popular or impactful Nodes published by others.&#x20;

More information on the Explore page features is found here: [Explore](/general-user-overview/explore)

{% hint style="warning" %}
**In development: Node Curation**\
In the future, you will be able to subscribe to certain [Communities](/create-and-publish/interact-and-reuse/communities), or Nodes curation groups, that will present a selection of their favourite nodes, curated according to their own principles.&#x20;

For example Nodes that use particularly FAIR data, high quality Node publications in a particular field, or Node publications that have particularly interesting new ideas that challenge the status-quo.&#x20;

These will be shown on the Explore page - giving you the option to *tailor your* Explore page to *your* interests.&#x20;
{% endhint %}

## Node <img src="/files/hZjvzxT2WdLojYw9rEyc" alt="Current Node Button.jpg" data-size="line">

If you click on any Node - visible on your Profile for your own Nodes, or presented in the Explore page for those of others - you will be brought to the [Node Workspace](/general-user-overview/node-workspace). This is where the action happens. The Node workspace has three main spaces, as well as a [**navigation bar** ](/general-user-overview/node-workspace/navigation-bar)across the top:&#x20;

* the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) in the lefthand panel: including an overview of the uploaded [**components**](/create-and-publish/create-a-node/add-components) (Drive) and [**contributors**](/create-and-publish/create-a-node/add-information/add-contributors) (Contributors)**.**&#x20;
* the [Viewer](/general-user-overview/node-workspace/viewer)in the middle: for (pre)viewing file components such as manuscripts (PDFs), data and code - with options to make comments (and, in the future, edits on your owned & collaborated Nodes) to the viewed components.
* The [Information Panel](/general-user-overview/node-workspace/information-panel) in the righthand panel: giving you metadata information on the component selected in the drive (and viewed in the reader space), or the possibility to perform actions on these components. Here, you can copy (or in the future even compute) code, or export a citation from a published PDF in a number of different citation formats.

<figure><img src="/files/dUBDRmuFE3sjUzZ5uwHA" alt="" width="563"><figcaption><p>Node Workspace (with sidepanels)</p></figcaption></figure>

##

## Profile <img src="/files/2DVoy56b1FELfVfTuiwC" alt="Current Node Button.jpg" data-size="line">

#### Your profile

To access your Profile you need to log into or set up your profile. This is relatively easy to do - you can follow the steps in our [Sign Up & Login](/create-and-publish/sign-up-and-login) section. &#x20;

#### Actions from Profile

* [Edit your profile information.](broken://pages/b4GY7BfhY3lsoJ7493vd)
* [Connect and manage your Digital Signatures.](/create-and-publish/publish#connect-your-digital-id)

## Moving Between Sections

You can navigate between your latest [Node Workspace](/general-user-overview/node-workspace), [Explore](/general-user-overview/explore), and [Profile](/general-user-overview/profile)from anywhere in the app.&#x20;

Icons for accessing each of these are in the navigation bar on the left hand side.&#x20;

<figure><img src="/files/qUXhzSUcDHkXDg0DwvvK" alt="" width="563"><figcaption><p>Sidebar navigation for the main Nodes app sections</p></figcaption></figure>


# Explore

Find  •  Browse  •  Interact

## Explore <img src="/files/q8l9nvAQWTR7PzG2JcnT" alt="Explore_Button.jpg" data-size="line">

Explore provides an overview of published Nodes: those most recently published as well as a [curated selection](/create-and-publish/interact-and-reuse/communities) of popular or impactful Nodes published by others.&#x20;

Your Explore overview is the 'front page' of Nodes, and where you can explore published Nodes. Whenever you open up the app, you will land here. You can access Explore at any time by clicking the <img src="/files/q8l9nvAQWTR7PzG2JcnT" alt="" data-size="line"> explore icon on the top left of the left side panel.

<figure><img src="/files/oKn1A9GrGC5zLcbDyzLn" alt=""><figcaption><p>Explore</p></figcaption></figure>

The Explore page will be more interactive, aiding in quality control and personalisation, with features such as:

* [Communities](/create-and-publish/interact-and-reuse/communities) - for curation and specialist attestations of published works, according to the community's set standards
* [Broken mention](broken://pages/AW3LIBVYTFRA7doUPPjW) - quality markers, dedicated to specific qualities a Node (or component in a Node) holds. E.g. a Node containing data that holds all FAIR properties can get a FAIR Data Attestation Badge.&#x20;

More on validation and curation by communities if found in the section [Validate and Curate](/community/community-curation)

{% hint style="success" %}
More information on browsing in Explore can be found here:

[Browse](/create-and-publish/interact-and-reuse/browse)
{% endhint %}

{% hint style="warning" %}
**In development: Node Curation/Journals**\
In the future, you will be able to subscribe to certain Nodes curation communities/journals, that will present a selection of their favourite nodes, curated according to their own principles.&#x20;

For example Nodes that use particularly FAIR data, high quality publications in a particular field, or Nodes that have particularly interesting new ideas that challenge the status-quo.&#x20;

These will be shown on the Explore page - giving you the option to tailor your Explore page to your interests.&#x20;
{% endhint %}


# Node


# \[New] Node Home


# Node Workspace

Navigate  •  Overview  •  Present

## Node Workspace <img src="/files/hZjvzxT2WdLojYw9rEyc" alt="Current Node Button.jpg" data-size="line">

If you click on any Node - visible on your Profile for your own Nodes, or presented in the Explore page for those of others - you will be brought to the [Node Workspace](/general-user-overview/node-workspace). This is where the action happens. The Node workspace has three main spaces, as well as a [**navigation bar** ](/general-user-overview/node-workspace/navigation-bar)(D in picture) across the top:&#x20;

* the [Viewer](/general-user-overview/node-workspace/viewer)in the middle (A below): for (pre)viewing file components such as manuscripts (PDFs), data and code - with options to make comments (and, in the future, edits on your owned & collaborated Nodes) to the viewed components.
* the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) in the lefthand panel (B): including an overview of the uploaded [**components**](/create-and-publish/create-a-node/add-components) (Drive) and [**contributors**](/create-and-publish/create-a-node/add-information/add-contributors) (Contributors)**.** Clicking on these tabs at the top will open the panel of choice and give access to a variety of options.&#x20;
* The [Information Panel](/general-user-overview/node-workspace/information-panel) in the righthand panel (C): giving you metadata information on the component selected in the drive (and viewed in the reader space), or the possibility to perform actions on these components. Here, you can copy (or in the future even compute) code, or export a citation from a published PDF in a number of different citation formats.\
  \
  The workspace [Navigation Bar](/general-user-overview/node-workspace/navigation-bar) (D), is where you can open/close the two workspace panels, check the version of the Node & Component you are working on, and can check out the Node's publication history.&#x20;

The panels and navigation bar are situated as follows:

<figure><img src="/files/D2pyc3AQhnz4HSJMzuye" alt="" width="375"><figcaption><p>Node Workspace Sections - with all sections in view</p></figcaption></figure>

{% hint style="info" %}
NB: our development and UI teams have been working hard on this space - it may look a little different from the current information given.&#x20;
{% endhint %}


# Navigation Bar

<figure><img src="/files/lgz8Bj2Z6iO2WNhZxtAc" alt="" width="375"><figcaption></figcaption></figure>

### Navigation Bar (D)

You always have access to the [#navigation-bar](#navigation-bar "mention") at the top of the Node workspace page. From here, you can quickly access everything that's important to view and edit your Node, including navigating between the two extra side panels:&#x20;

* [Node Drive](/general-user-overview/node-workspace/node-drive-panel) - left, if not open click on the hamburger icon in the top lefthand corner <img src="/files/UoRuQl5zORaACttG8b4P" alt="DriveHamburger_Button.jpg" data-size="line">&#x20;
* [Metadata Panel](/general-user-overview/node-workspace/information-panel) / (\[TBD [IDE](/create-and-publish/interact-and-reuse/compute/tbd-node-ide)]) - right, if not open click on the Information icon in the top righthand corner <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="Screenshot 2024-01-19 at 11.29.52.jpg" data-size="line">
* The currently viewed Node's version and current browsing location name, e.g. <img src="/files/UuwJCNOxnNm0JDFhokr6" alt="Screenshot 2024-02-12 at 13.58.51.jpg" data-size="line"> , and
* Publishing history.

<figure><img src="/files/MWkFBAbV9dc5fVawtxZ5" alt="" width="375"><figcaption><p>Navigation bar location overview &#x26; version history</p></figcaption></figure>


# Viewer

Navigate  •  Present  •  Interact

<figure><img src="/files/lgz8Bj2Z6iO2WNhZxtAc" alt="" width="375"><figcaption><p>The viewer panel in the Node Workspace is centrally located (A - pink). <br>It can be resized, through resizing or closing the side panels (Node Drive Panel - B, and Metadata Panel - C)</p></figcaption></figure>

### Viewer (A)

All Codex Entitites (artefacts, Nodes profiles, ....) are opened in the **Viewer** panel, in the centre of the screen. It is both your familiar PDF reader environment, or where information on your selected component is shown.  All you need to do is select the component you want to view or download in the [**Drive**](/general-user-overview/node-workspace/node-drive-panel) panel on the left of the screen.&#x20;

Both the [Drive](/general-user-overview/node-workspace/node-drive-panel) panel on the left and the [Metadata](/general-user-overview/node-workspace/information-panel) panel on the right play important roles in Nodes and its components. You select and order components in the Drive panel, but you then describe and add metadata to those components in the Metadata panel. They can be tucked away to broaden the viewer window for easier viewing.&#x20;

#### PDF Viewer

The Viewer panel has a few options specific to opened **PDF** files:&#x20;

* Near the bottom centre of the viewer panel are the **zoom** controls to zoom in (+), out (-), fit to width (\[<>]), and fit to height, <img src="/files/UsmDzqPyqOjSjH6ukrKs" alt="Screenshot 2024-02-12 at 15.27.19.jpg" data-size="line">,
* In the same bar, you will find the comment function, in the form of a highlighter <img src="/files/C60fdql5Zfuzmi6VLXkX" alt="Screenshot 2024-02-01 at 23.59.44.jpg" data-size="line">. The [**comment function**](/general-user-overview/node-workspace/information-panel) works as a box-style highlighter/selector in the PDF itself, but lets you add comments - like a sticky note.&#x20;

Further notes on how **Comments** work can be found in the [**Metadata/Comment Panel** ](/general-user-overview/node-workspace/information-panel)section.&#x20;

<figure><img src="/files/qIi8EpFT2JHZiRBWlCT0" alt="" width="375"><figcaption><p>Adding Annotations in a pdf, resolving to internal Node objects</p></figcaption></figure>

{% hint style="info" %}
Currently we have limited recognition of files and might not be able to display them in the viewer. However, from here you will be able to [**download**](/create-and-publish/interact-and-reuse/download) the components if they are uploaded files, or open the [**URL**](/create-and-publish/create-a-node/add-components/external-links) if the component is a URL link.&#x20;
{% endhint %}


# Node Drive Panel

Navigate  •  Access  •  Structure

<figure><img src="/files/lgz8Bj2Z6iO2WNhZxtAc" alt="" width="375"><figcaption><p>Node Drive Panel on the left - B (blue)</p></figcaption></figure>

## Node Drive (B1)

In Node Drive you navigate, [Organise](/create-and-publish/create-a-node/organise-access-and-present) and upload your [Node Components](/create-and-publish/create-a-node/add-components).&#x20;

Actions:&#x20;

* [Add new components](/create-and-publish/create-a-node/add-components) to your Node via <img src="/files/YP9FVSkf30ZaJXn096jm" alt="" data-size="line">
* Navigate the Drive - an overview of your Components&#x20;
* [**Organise**](/create-and-publish/create-a-node/organise-access-and-present) the Drive to your liking.

Node Drive is the heart of your Node. This is where you upload, store, access, and manage all components that make up your publication.&#x20;

You can *upload* your components here in several ways. How? See [Add Components](/create-and-publish/create-a-node/add-components).

You can *edit the presentation* of your components in the Node, from their [names](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components) to how they are [organised](/create-and-publish/create-a-node/organise-access-and-present). See the chapter on organising & presenting your nodes for more information: [Organise, Access & Present](/create-and-publish/create-a-node/organise-access-and-present).

You can select components from the Drive to download, view, edit (if they are yours), comment on, etc. Once selected in the **Drive** panel, you can view or download the component from the [**Viewer**](/general-user-overview/node-workspace/viewer) **panel**, or add information - such as [licenses](/create-and-publish/create-a-node/add-information/add-license), [metadata](/create-and-publish/create-a-node/add-information/add-metadata) and [comments](/create-and-publish/create-a-node/add-information/add-comments) - to your components in the [**Metadata**](/general-user-overview/node-workspace/information-panel) **panel**.&#x20;

To open Node Drive, click on <img src="/files/ENwfyodOq8enzalxJU4V" alt="" data-size="line"> in the [Navigation](/general-user-overview/node-workspace/navigation-bar) bar at the top. If necessary, click on the Drive tab  <img src="/files/t7zQsZV1XbNZ1Krrl7hV" alt="" data-size="line"> in the panel.

<figure><img src="/files/KrZ47Lt7xnEUakDw9o2b" alt=""><figcaption><p>Use Node Drive to view, access, and manage components</p></figcaption></figure>


# Node Contributors Panel

Navigate  •  Honour  •  Present

## Node Contributors (B2)

In Node Contributors you add the names and information of fellow authors.&#x20;

Actions:

* [Add Contributors](/create-and-publish/create-a-node/add-information/add-contributors)
* Edit Authorship details.

*See* [Add Contributors](/create-and-publish/create-a-node/add-information/add-contributors) for further information on adding contributors and their information. &#x20;

You can *add as much or as little information on your contributors as they like.* Nodes supports importing of information from ORCID for easy identification and overview of the contributing authors.

To open Node Contributors, click on <img src="/files/ENwfyodOq8enzalxJU4V" alt="" data-size="line"> in the [Navigation](/general-user-overview/node-workspace/navigation-bar) bar at the top. If necessary, click on the Contributors tab  <img src="/files/1l8cczt6SxUAUsOpkl88" alt="" data-size="line"> in the panel.


# Information Panel

Navigate  •  Inform  •  Extras

{% hint style="info" %}
N.B. This Panel is currently undergoing restructuring, so guidance might be out of date.
{% endhint %}

<figure><img src="/files/lgz8Bj2Z6iO2WNhZxtAc" alt="" width="375"><figcaption><p>Metadata &#x26; Comment Panel on the right - C (yellow)</p></figcaption></figure>

## Information Panel (C)

The Information Panel on the right hand side of the Nodes workspace environment, which you can open with the Information ('i') button at the top right <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="Screenshot 2024-02-02 at 00.10.02.jpg" data-size="line">, contains two tabs:

* the [Metadata Panel](#metadata-c1) - to add and extract extra information to or from your Node components.
* the [Comments Panel](#comments-c2) - to add and manage comments on your (textual/visual = currently PDF) components.

## Metadata (C1)

To add Metadata to your Node object, open the Metadata Panel, currently situated on the right hand side. You can open it by pressing the Information ('i') button at the top right <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="Screenshot 2024-02-02 at 00.10.02.jpg" data-size="line">

The ability, and even requirement, to add Metadata is an important part of Nodes. Metadata is information about the Nodes objects that helps guide and ease its sharing and reproduction. There are many different forms of Metadata, some of which, supported by Nodes, are:

* #### [Title](/create-and-publish/create-a-node/add-information/add-metadata#title) - you can name your component here&#x20;
* #### [Citations](/create-and-publish/share/cite) - Get a [formatted citation](/create-and-publish/share/cite) to any component&#x20;
* #### [License](/create-and-publish/create-a-node/add-information/add-license)
* #### [CEDAR Link](/create-and-publish/create-a-node/add-information/add-metadata#cedar-link)
* #### [Ontology URL](/create-and-publish/create-a-node/add-information/add-metadata#ontology-url)
* #### [Description](/create-and-publish/create-a-node/add-information/add-metadata#description)
* #### [Keywords](/create-and-publish/create-a-node/add-information/add-metadata#keywords)
* #### [Controlled Vocabulary](/create-and-publish/create-a-node/add-information/add-metadata#controlled-vocabulary)
* #### [Component Type](/create-and-publish/create-a-node/add-information/add-metadata#component-type)

Furthermore, you can grab a component's [content identifier](/technical-background/persistent-identifiers-101#solving-content-drift) for [easy re-use](/create-and-publish/share#share-and-re-use-via-cid).

Further information on Metadata and the types you can add to Nodes is found in [Metadata](/technical-background/open-state-repository/metadata)

## Comments (C2)

Comments on your Node objects can be managed from the same panel, under the Information 'i' button, different tab. You can add them from the viewer panel, using the highlighter button <img src="/files/C60fdql5Zfuzmi6VLXkX" alt="Screenshot 2024-02-01 at 23.59.44.jpg" data-size="line">&#x20;

<figure><img src="/files/qIi8EpFT2JHZiRBWlCT0" alt="" width="375"><figcaption><p>Examples of commenting with a link to internal Node objects.</p></figcaption></figure>

See the [Add Comments](/create-and-publish/create-a-node/add-information/add-comments) section for more information.&#x20;


# Profile

Present  •  Overview

### Your profile

To access your Profile you need to log into or set up your profile. This is relatively easy to do - you can follow the steps in our [Sign Up & Login](/create-and-publish/sign-up-and-login) section.&#x20;

In your profile, you can view and update your account information - including:

* Information from your ORCID account,
* Details of your publishing Wallet,&#x20;
* Manage your API keys,
* Check your account pre-publication storage data.

<figure><img src="/files/vejYsKyxeEoqZ48dRRKK" alt="" width="375"><figcaption><p>Use your profile to add publishing credentials such as your ORCID account or Wallet details.</p></figcaption></figure>

### Your Nodes Overview

You will also find the Nodes you are working on or have published, on the righthand side of the screen. Besides the overview, you can create a new node here, by clicking on 'New Node' <img src="/files/M54EvQ4RkiJtYEZAA12j" alt="NewNode_Button copy.jpg" data-size="line"> in the top right corner.&#x20;

<figure><img src="/files/InwdYZtbV0mteio73ISk" alt=""><figcaption><p>Overview of your Nodes on your profile, including information on their publication status/version. You can access any of your Nodes here. </p></figcaption></figure>

#### Actions from Profile

* [Edit your profile information.](broken://pages/b4GY7BfhY3lsoJ7493vd)
* [Connect and manage your Digital Signatures.](/create-and-publish/publish#connect-your-digital-id)
* [Add a Node](/create-and-publish/create-a-node/create-node).
* Access your Nodes.


# Quick Start

<table data-view="cards"><thead><tr><th></th><th data-hidden data-card-cover data-type="files"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><strong>Sign Up &#x26; Login</strong></td><td></td><td><a href="/pages/3O47JK7XgT5GDsKDAHzJ">/pages/3O47JK7XgT5GDsKDAHzJ</a></td></tr><tr><td><strong>Create a Node</strong></td><td></td><td><a href="/pages/G73nwQGRsf3qT0YrlzpZ">/pages/G73nwQGRsf3qT0YrlzpZ</a></td></tr><tr><td><strong>Publish</strong></td><td></td><td><a href="/pages/Z1r9nACGonEPLRzW5E8d">/pages/Z1r9nACGonEPLRzW5E8d</a></td></tr><tr><td><strong>Submit for Curation</strong></td><td></td><td><a href="/pages/8NDd2FF59ouANx4AqrFR">/pages/8NDd2FF59ouANx4AqrFR</a></td></tr><tr><td><strong>Validate and Curate</strong></td><td></td><td><a href="/pages/DFxfZsBRee6mhdaAp8aN">/pages/DFxfZsBRee6mhdaAp8aN</a></td></tr><tr><td><strong>Re-Use and Cite</strong></td><td></td><td><a href="/pages/rmPIdZbCgyJ6IpJftKGc">/pages/rmPIdZbCgyJ6IpJftKGc</a></td></tr></tbody></table>


# Introduction

Introduction to Nodes and the Open State Repository

Nodes is a next-generation open-science solution for sharing and managing manuscripts, data, code, and all other artefacts of research, in one place. Directly associated files, documents, data, code, links, etc., can be uploaded in one connected unit called a [research object](https://en.wikipedia.org/wiki/Research_Object). Our goal is to create a rewarding workflow and a canvas to elevate your research, while providing an unmatched environment to enable best open science practices.

### **Our vision is to enable open, composable, and verifiable research**

Nodes has many exciting technological innovations under the hood, including persistent identifiers that are immune to content drift and link rot, an open-state repository that makes all forms of scientific content accessible to all humans and machines, and entirely novel ways for scientists, funders, and the public to interact with research.

Nodes is an interface for researchers to share and interact with primary research outputs in the form of [research objects](https://en.wikipedia.org/wiki/Research_Object). Research objects combine manuscripts, data, code, peer-review reports, community activity, etc. into a single, rich, fully contextualized digital entity.

Nodes is currently in [open beta testing](https://twitter.com/DeSciLabs/status/1628019649995739136?s=20). We are actively developing the Nodes application and the [open state repository](https://docs.desci.com/learn/open-state-repository). We will be rolling out additional features over time.&#x20;

### Help us make it better: Your feedback counts

We invite all scientists to try it out, experiment with it, and give us feedback via the <img src="/files/yngJ6pzUEZmhAwAVJcku" alt="" data-size="line"> button in the bottom right corner of Nodes. Tell us what you like and what you don’t. If you encounter a bug, miss a feature, or have an idea of how we can make Nodes better, please let us know. Your feedback means a lot to us!&#x20;

### Elevate your research and keep control over your work

DeSci Nodes are designed to make open science easy, convenient, and rewarding. With our [FAIR](https://www.gofair.foundation/interpretation)-enabling technology, you can supercharge your preprints and [Green Open Access](https://en.wikipedia.org/wiki/Open_access) publications. You can turn your work from static PDFs into dynamic, interoperable research objects. A Node contains all artefacts relevant to your work: papers, data, code, and more. \
*And* copyrights are retained at the origin (i.e. the authors and/or their employers).&#x20;

{% hint style="info" %}
**You can use Nodes and publish in journals**&#x20;

We do not take any copyrights of the materials you post on Nodes. Anything you post on Nodes can also be published in most other scientific outlets that are relevant to you. Most scientific journals will consider manuscripts that were posted on Nodes, preprint servers, or open repositories prior to submission. A list of journal policies can be found on [Wikipedia](https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy), as maintained by individual publishers, and [SHERPA/RoMEO](http://www.sherpa.ac.uk/romeo/journalbrowse.php?la=en\&fIDnum=%7C\&mode=simple). You can use Nodes as a support tool in the journal submission process to give editors and referees access to all relevant parts of your research project (not just the manuscript).&#x20;
{% endhint %}

{% hint style="warning" %}
Before using Nodes, be aware:\
Our aim is to have stable, durable, traceable and continuous availability of scientific content published on Nodes.&#x20;

Check that all your (pre)publishing rights and commitments are triple-checked and in order before publishing a Node.&#x20;

*It is your responsibility to ensure all rights are appropriately covered.*&#x20;

**Once published, Nodes can be updated at will, but not deleted. The history of change will remain accessible.**&#x20;
{% endhint %}

## Get started now

<details>

<summary>Get set up</summary>

[Sign Up & Login](/create-and-publish/sign-up-and-login)

[General user overview](/general-user-overview)

</details>

<details>

<summary>Create a Node</summary>

[Create a Node](/create-and-publish/create-a-node)

[Add Components](/create-and-publish/create-a-node/add-components)

[Add Metadata](/create-and-publish/create-a-node/add-information/add-metadata)

</details>

<details>

<summary>Publish your Node</summary>

[Publish](/create-and-publish/publish)

[Publish a new version of your Research Node](/create-and-publish/publish/update-your-node/publish-a-new-version-of-your-research-node)

</details>

<details>

<summary>Make changes</summary>

[Editing a published Node](/create-and-publish/publish/update-your-node/editing-a-published-node)

[Delete Components After Publication](/create-and-publish/publish/update-your-node/delete-components-after-publication)

[Renaming components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components)

</details>

<details>

<summary>Troubleshooting</summary>

[Feedback & Contact](/find-help/feedback-and-contact#report-bugs-or-submit-feedback)

[Feedback & Contact](/find-help/feedback-and-contact#request-hands-on-support)

</details>


# Sign Up & Login

Get set up  •  ORCID  •  E-mail

To log in or create a profile on [DeSci Nodes](https://nodes.desci.com), hit the <img src="/files/E7ErrXLklTGeNYjlPREn" alt="" data-size="line"> Profile button in the bottom left corner. From here, you can choose whether to login via [ORCID](https://orcid.org/), email, or decentralized identifier (DID, wallet).

### With ORCID

To enable easy tracking of all your DeSci Nodes publications within current tracking systems for researchers, we have enabled logging in and publishing with your ORCID.&#x20;

From the login screen, select `Continue with ORCID`. An ORCID pop-up will appear for you to log into your ORCID account. After successfully logging in with ORCID, you will be taken back to DeSci Nodes.&#x20;

If this is your first time logging into DeSci Nodes, you will need to provide and verify your email address in a separate step before being able to use the app.

<figure><img src="/files/MU1UaADZlTODwNKej62L" alt=""><figcaption></figcaption></figure>

{% hint style="info" %}
By connecting your ORCID to your DeSci Nodes account you will automatically import your biodata and publication history to your Nodes profile. Down the line, you will be able to build out your ORCID record via contributions on DeSci Nodes, including publications but also reviews or receiving attestations. Right now, none of your activity on DeSci Nodes will be posted on your ORCID profile.
{% endhint %}

### With Decentralized Identifier

To login with your wallet (DID), select `Continue with DID`. After you select your DID provider, you will see a pop-up from your DID browser extension asking you to connect to nodes.desci.com. Confirm this step to sign in.

If this is your first time logging into DeSci Nodes, you will need to provide and verify your email address in a separate step before being able to use the app.

### With Email

To create an account or log in via email, select `Continue with Email`. After you enter your email you will receive a verification code to this email address. Enter the code and hit `Verify` to enter the app.&#x20;

If you can't find our verification email, please check your spam folder. To avoid this from happening, your can add **<no-reply@desci.com>** to your contacts.

{% hint style="info" %}
Note that when creating an account with email you won't be able to publish until you've connected either your ORCID or DID.
{% endhint %}


# Create a Node

Create Node  •  Add Components  •  Add Information

Creating a Node in itself is pretty straightforward. The complexity comes from the many different components you can add, and the information you can provide to both the Node itself and the components.&#x20;

An overview of some of the current possibilities of what you can add is provided below, with instructions in the rest of this section.&#x20;

<figure><img src="/files/aA9YAPZnYnGshRPUTxF1" alt=""><figcaption><p>Quick overview of: Adding a New Node, Node Title, Components &#x26; Info</p></figcaption></figure>

Find information on how to add:

Different [**components**](/create-and-publish/create-a-node/add-components) to your Node, such as a:

* [Manuscript](/create-and-publish/create-a-node/add-components/manuscript)
* [Data](/create-and-publish/create-a-node/add-components/data)
* [Code & Executables](/create-and-publish/create-a-node/add-components/code-and-executables)
* [External Links](/create-and-publish/create-a-node/add-components/external-links)

Different types of [**information**](/create-and-publish/create-a-node/add-information)**,** such as:

* [Add License](/create-and-publish/create-a-node/add-information/add-license)
* [Add Metadata](/create-and-publish/create-a-node/add-information/add-metadata)
* [Add Contributors](/create-and-publish/create-a-node/add-information/add-contributors)
* [Add Comments](/create-and-publish/create-a-node/add-information/add-comments)
* [Claim Attestations](/create-and-publish/create-a-node/add-information/claim-attestations), e.g. through [submitting for curation](/create-and-publish/submit-for-curation). There is an extra section explaining curation & communities in depth [**here**](/community/community-curation)**.**&#x20;

{% hint style="info" %}
Nodes tries to be both as comprehensive and yet condensed and intuitive as possible. If there are things you would like to be able to create or types of information you would like to add to your Node that you cannot currently find, please contact us at&#x20;
{% endhint %}


# Create Node

Create Node  •  Add Components  •  Add Information

Creating a Node is pretty straightforward.&#x20;

After you have logged into your account ( [Sign Up & Login](/create-and-publish/sign-up-and-login)), hit the plus icon <img src="/files/eO6mP0A5AUi4GC8QRNaZ" alt="Screenshot 2024-01-29 at 15.39.34.jpg" data-size="line"> , at the bottom of the icons on the left side bar.&#x20;

This button will open a new Node page layout where you can start adding all your Node information and components, such as your Node title, data files, licensing, authors, etc. in the centre [Viewer](/general-user-overview/node-workspace/viewer)panel as well as the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) on the left.&#x20;

<figure><img src="/files/JEEozosZn4p2ck8hWI18" alt=""><figcaption><p>Add a New Node by hitting '+' on the sidebar</p></figcaption></figure>

You can see a condensed suggestion of how you can start creating a Node in the video below. How you can add different components and further information is given in the rest of the [Create a Node](/create-and-publish/create-a-node) section.&#x20;

<figure><img src="/files/aA9YAPZnYnGshRPUTxF1" alt=""><figcaption><p>Quick overview of: Adding a New Node, Node Title, Components &#x26; Info</p></figcaption></figure>


# Add Components

Add component  •  Component Library  •  Workspace

To add components or files, open the [Node Workspace](/general-user-overview/node-workspace)for the Node you want to add them to. In the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel, opened by hitting the hamburger menu icon in the top left, <img src="/files/UoRuQl5zORaACttG8b4P" alt="DriveHamburger_Button.jpg" data-size="line">, and ensuring the tab at the top is set to 'Drive', you can add components and files in a variety of ways:

* [Drag & drop](#drag-and-drop): for file formats such as [Manuscripts](/create-and-publish/create-a-node/add-components/manuscript), [Datasets](/create-and-publish/create-a-node/add-components/data), Code files;
* [Upload from desktop](#upload-from-desktop): for file formats such as [Manuscripts](/create-and-publish/create-a-node/add-components/manuscript), [Datasets](/create-and-publish/create-a-node/add-components/data), [Code files](/create-and-publish/create-a-node/add-components/code-and-executables), [Folders](/create-and-publish/create-a-node/add-components/folder);
* [URL](#adding-a-url):&#x20;
  * addition - for [external links](/create-and-publish/create-a-node/add-components/external-links);
  * or integration - for example for GitHub [code repositories](/create-and-publish/create-a-node/add-components/code-and-executables) and [executable containers](/create-and-publish/create-a-node/add-components/code-and-executables);
* Create a [new folder](#new-folder).

Each method caters to a few different component formats and/or aids in structuring your Node.&#x20;

If you have already uploaded components into the active Node, the Drive will show your files as a standard, instead of upload options. In that case, hit the '+' icon, <img src="/files/YP9FVSkf30ZaJXn096jm" alt="NewNode_Button.jpg" data-size="line">, in the Files navigation bar and choose 'Upload' to get the upload options panel.&#x20;

## Drag & Drop

When creating a new, empty, Node, or opening an old one, you can easily add files you want to upload by dropping them into the designated space in the left Drive panel.&#x20;

You can drag over as many files as you want and hit the upload button. Do note, it is lighter on the system to not upload too much at once. If your (large) files are having issues uploading, either segment them into several smaller ones, or contact us.&#x20;

Actions:

* In the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), navigate to the folder you want to drop your folder/file into.&#x20;
* Drag the file from your computer's location into Nodes - you will see the Drive Panel switch into a 'drop your files here' panel.
* Drop your file in the location indicated to add them to the folder that is opened in your drive.&#x20;

<figure><img src="/files/VEc2pY0Anpaic5BhK68I" alt="" width="375"><figcaption><p>Upload a file through Drag &#x26; Drop</p></figcaption></figure>

## Upload from Desktop

Alternatively, the Node Drive panel has the option to choose files from your desktop too. For this, choose the 'Select File' option at the bottom left of the upload panel.

Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel in your [Node Workspace](/general-user-overview/node-workspace). From here, you can select **Upload Files** which will open your local files. Select the dataset you want to upload and it will get added to your Node's data.

<figure><img src="/files/8Z0D7z84kLcj9TICTF4R" alt=""><figcaption><p>Upload files or folders from your desktop environment</p></figcaption></figure>

Step-by-step instructions:

* Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), and hit the '+' <img src="/files/YP9FVSkf30ZaJXn096jm" alt="NewNode_Button.jpg" data-size="line"> button.&#x20;
* Select 'Upload'  from the dropdown menu.

<figure><img src="/files/Wt9k5o1KJ6V3kKzTjUmD" alt="" width="146"><figcaption></figcaption></figure>

* In the Upload section that opens, choose 'Select File' or 'Select Folder' depending on which format you would like to upload.&#x20;

<figure><img src="/files/922hr04ggU6PXa7LqUZt" alt="" width="139"><figcaption></figcaption></figure>

* Both options will open the usual browser window from which to browse your computer to select the file/folder you want to upload.&#x20;

<figure><img src="/files/dVr5OAlmx4EUeaKBTKbw" alt="" width="375"><figcaption></figcaption></figure>

* When you have selected your file/folder, hit 'Upload'.
* A new window will pop up to confirm that you are ok with uploading the suggested files. Hit 'Upload' again.&#x20;

<figure><img src="/files/N7sykqMs7ag8gW3MbdPN" alt="" width="188"><figcaption></figcaption></figure>

* You will be returned to the upload panel, showing all the files you have selected to upload. If you have selected a folder, it will show all the files contained in the folder individually. Hit 'Upload' at the bottom.&#x20;

<figure><img src="/files/lu4c3PtBYZKngK9c7mxS" alt="" width="125"><figcaption></figcaption></figure>

* *NB: Try not to overload uploads with a large number/size of uploads at once.*
* You should see your upload being processed.

<figure><img src="/files/SX2uCQs8h2EtrlRvgAG6" alt="" width="188"><figcaption></figcaption></figure>

* *NB: You can navigate away once uploading is in process - processing of your uploads should continue regardless.*
* Once your upload has been finished, you should see your new files in the drive.&#x20;
* If you have uploaded a folder, you will find yourself inside the uploaded folder. You can find the pathway to your current location at the top of the drive window.

<figure><img src="/files/BsQLmhoEX6Vj0JkOCBgN" alt="" width="375"><figcaption></figcaption></figure>

For an example overview of the upload process from your desktop, see below.

## Adding a URL

There is the option to upload external links, integrate code repositories or download a pdf manuscript by copying the URL into the url bar.&#x20;

Simply copy and paste the URL of the repository, link or pdf you want to add to your Node into the 'Paste Link' bar showing in the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) Upload panel.&#x20;

Step-by-step instructions:

* Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), and hit the '+' button.&#x20;
* Select 'Upload' from the dropdown menu.
* In the Upload section that opens, paste the URL in the 'Paste Link' bar near the bottom.&#x20;

  <figure><img src="/files/AA4YjrIrblJQ8S9viun1" alt="" width="188"><figcaption></figcaption></figure>
* Your repository/pdf/link will be added or integrated instantly.&#x20;
  * For External Links your link will be added to a folder of that name.&#x20;
  * For repositories, a folder will be created with the repository name, containing the files. &#x20;
  * For pdfs, the pdf will be added on its own - *Make sure that the URL ends in '.pdf' for it to be properly imported as a manuscript.*

<figure><img src="/files/COD5l4PZUjFajehYIlDI" alt="" width="375"><figcaption><p>Adding an external URL link to your Node</p></figcaption></figure>

The system works the same for all, but for specific information on different components that use URL imports, check out the [Code & Executables](/create-and-publish/create-a-node/add-components/code-and-executables) ; [External Links](/create-and-publish/create-a-node/add-components/external-links) and [Manuscript](/create-and-publish/create-a-node/add-components/manuscript) sections.&#x20;

## New Folder

In the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel from your [Node Workspace](/general-user-overview/node-workspace), you can upload folders from your computer into Nodes, or create a folder within Nodes by hitting the '+' in the files section and choosing the 'New Folder' option.&#x20;

For a more detailed explanation visit [Folder](/create-and-publish/create-a-node/add-components/folder).&#x20;

\[broadscreen video demo, not the one below]

<figure><img src="/files/Kcyb9hwPFD9533qlP87a" alt="" width="188"><figcaption><p>Add a folder</p></figcaption></figure>

{% hint style="danger" %}
In case you accidentally upload something you did not want to publish, you can [delete components](/create-and-publish/publish/update-your-node/delete-components-after-publication) from the draft.&#x20;

**Once you published your Node you won't be able to delete components.** You can publish a new version of the Node without some of the components you previously published, but older versions will always stay the way they were at the time of publication. &#x20;
{% endhint %}


# Data

Add component  •  Data  •  Workspace

DeSci Nodes is built for data sharing and publishing. You can publish a sole dataset as its own Research Node or add dataset components to an existing one to enrich your publication.&#x20;

You can add code through these basic upload methods through using the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel):

* [Add Components](/create-and-publish/create-a-node/add-components#drag-and-drop)
* [Add Components](/create-and-publish/create-a-node/add-components#upload-from-desktop)

More information on these methods as specific to data is found below.&#x20;

Do also note restrictions on your [**data budget**](#data-budget)**.**&#x20;

{% hint style="danger" %}
**IMPORTANT: DO NOT UNDER ANY CIRCUMSTANCES POST RESTRICTED OR SENSITIVE DATA.**&#x20;

Data archived in Nodes are publicly available. *Once posted, they are difficult or impossible to delete permanently.*&#x20;

Be aware that **authors are fully responsible for complying with all applicable ethical and legal guidelines**.&#x20;

In particular, you are **not allowed** to share data on Nodes that contain personally identifiable human subjects or data with licensing terms that are incompatible with the [Creative Commons Zero waiver](http://creativecommons.org/publicdomain/zero/1.0). Any human subject data must be properly anonymized and prepared before it can be published on Nodes. [Dryad](https://datadryad.org/docs/HumanSubjectsData.pdf), the [NIH](https://grants.nih.gov/policy/humansubjects/research.htm), and the [European Commission](https://ec.europa.eu/info/funding-tenders/opportunities/docs/2021-2027/horizon/guidance/ethics-and-data-protection_he_en.pdf) provide highly recommended guidelines on sharing human subject data.  Please see our <mark style="color:red;">T</mark>[<mark style="color:red;">erms of Service</mark>](#user-content-fn-1)[^1] for additional information.&#x20;

*Currently Nodes itself does not support Restricted Data Services. We are looking at implementing these in the future.*&#x20;

Please make sure that the data you are uploading are not violating any licenses, copyright or privacy rights. Open Access data components will be publicly and perpetually accessible after you publish your Node. If you make a mistake and accidentally upload restricted data AND publish the Node, please contact our support team immediately ([**help@desci.com**](mailto:help@desci.com)).&#x20;
{% endhint %}

## Data Upload from Desktop

Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel in your [Node Workspace](/general-user-overview/node-workspace). From here, you can select **Upload Files**, which will open your local files. Select the dataset you want to upload and it will get added to your Node's data.

For step-by-step instructions see [Add Components](/create-and-publish/create-a-node/add-components#upload-from-desktop) in [Add Components](/create-and-publish/create-a-node/add-components).

## Data Drag & Drop

Add open access datasets to your Node via drag and drop.&#x20;

* In the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), navigate to the folder you want to drop your **Data** folder/file into.&#x20;
* Drag the file from your computer's location into Nodes - you will see the Drive Panel switch into a 'drop your files here' panel.
* Drop your file in the location indicated to add them to the folder that is opened in your drive.&#x20;

<figure><img src="/files/VEc2pY0Anpaic5BhK68I" alt=""><figcaption><p>Drag &#x26; drop files onto your Node folders to quickly build your Node</p></figcaption></figure>

{% hint style="info" %}
In case you made a mistake, [here's how to delete a component](/create-and-publish/publish/update-your-node/delete-components-after-publication).
{% endhint %}

## Data Budget

The amount of data stored in draft-stage Nodes is capped, and stand at 100GB. **Posted Nodes are unlimited in data capacity.** However, this means it might be difficult for you to get your Node to "published" status if its size surpasses your overall data budget.

You will be able to increase your data budget via upgrade plans \[*currently still in development - for now contact us* ([**help@desci.com**](mailto:help@desci.com)) *if you have larger data demands*].&#x20;

[^1]: Add link


# Manuscript

Add component  •  Manuscript  •  Workspace

There are different ways to add a manuscript. :

* [**Upload via manuscript URL**](#add-an-existing-manuscript-via-url)&#x20;
* [**Upload via file format**](#add-a-manuscript-via-pdf-upload) **(pdf)**
* [**\[TBD\] Create in-situ**](#tbd-create-and-edit-a-manuscript-in-situ)

You can add manuscripts through [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) for the first two basic upload methods. Extra information on how they relate to manuscripts is available below.&#x20;

In development is the ability to create and [**edit manuscripts**](#tbd-create-and-edit-a-manuscript-in-situ) within a text editor in Nodes.&#x20;

{% hint style="info" %}
The best way to ensure the discoverability of your Node is to include a standard academic manuscript that will be indexed by academic databases like Google Scholar. To ensure your manuscript (and Node) is indexed, make sure your manuscript meets the following requirements:

* The full text of your manuscript needs to be a PDF file that ends with ".pdf",
* The title of the manuscript appears in a large font on top of the first page,
* The authors of the manuscript are listed right below the title on a separate line,&#x20;
* There's a bibliography section titled "References," "Bibliography," or similar at the end.

Google Scholar and other academic databases will then ensure that your Node is findable by others and track citations of your Nodes.
{% endhint %}

Manuscripts can be added either [via the URL](#uploading-an-existing-manuscript) to your PDF or by [uploading it as a PDF file.](#add-a-manuscript-via-pdf-upload)&#x20;

## Add an existing manuscript via URL

You can add a manuscript that is publicly available elsewhere via its URL. Just copy/paste the link that resolves to your web PDF into the URL field, as found in the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel).&#x20;

You can see basic instructions for URL uploads [here](/create-and-publish/create-a-node/add-components#adding-a-url). *Make sure that the URL ends in '.pdf' for it to be properly imported as a manuscript.*

The video below demonstrates how to import a .pdf file through a web link.&#x20;

<figure><img src="/files/pH7T13s2HfhqDE9SMaZu" alt=""><figcaption><p>Importing a manuscript/document from a .pdf URL</p></figcaption></figure>

{% hint style="warning" %}
Before you add a manuscript, make sure its licensing allows you to publish this work elsewhere to avoid inadvertent violations of copyright.&#x20;

[Find out more about licenses here.](broken://pages/HzZRClUmfqbIOFjUdFKv)
{% endhint %}

{% hint style="info" %}
In case you're wondering why we don't offer the option to upload a manuscript via its DOI: That's because of [inconsistent resolution](https://arxiv.org/abs/2004.03011) behaviour. The only way to consistently resolve your DOIs to your manuscript via SciHub, and that's not legal for us to do.&#x20;
{% endhint %}

## Add a manuscript via PDF upload

If you want to upload a manuscript without a URL, you can simply upload the PDF file from your local files. See file upload options:

* [Add Components](/create-and-publish/create-a-node/add-components#drag-and-drop)
* [Add Components](/create-and-publish/create-a-node/add-components#upload-from-desktop)

{% hint style="info" %}
In case you made a mistake, [here's how to delete a component](/create-and-publish/publish/update-your-node/delete-components-after-publication).
{% endhint %}

## \[TBD] Create & edit a manuscript in situ

**In progress:** We are currently creating an in-app text editing programme, so you can create or edit your manuscripts. Either from scratch or from an uploaded file.&#x20;


# Code & Executables

Add component  •  Code  •  Workspace

DeSci Nodes supports rich code and analysis script-sharing for enhanced reproducibility. You can publish a code repository (or file) as its own Research Node or add code components to an existing one to enrich your publication.

[Read more about why sharing code is so important.](broken://pages/mkp1Q0nzH4TFwPuGi1xB)

You can add code through these basic upload methods:

* [Add Components](/create-and-publish/create-a-node/add-components#adding-a-url) to your code repository (e.g. GitHub)
* [Add Components](/create-and-publish/create-a-node/add-components#upload-from-desktop) for code files
* [Add Components](/create-and-publish/create-a-node/add-components#drag-and-drop) for code files
* Upcoming: **Create & Edit Code Files**

More information on URL imports as related to code repositories is found below.&#x20;

## Adding a Code Repository

Open the Node Drive in your Node Workspace for the Node you want to add the Code Repository to. Paste the URL to your GitHub repo in the URL line when the Drive is showing the **upload panel**. DeSci Nodes will automatically pull in the full repository for you, including file and folder structures.

{% hint style="info" %}
Be aware that adding code repositories via GitHub URL will always add the **entire repository** to your Node. So make sure that everything in the repo can be shared openly.

We currently do not support the upload of individual folders within a repository or similar.
{% endhint %}

<figure><img src="/files/cMcgNAn1cRybTqWZpNGs" alt=""><figcaption><p>Add your code from GitHub straight into your Node</p></figcaption></figure>

Step-by-step instructions:

You can import your online GitHub code repository by providing its URL in the URL bar of the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) in the Node you want to add the code repository to.&#x20;

* Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), and hit the '+' button.&#x20;
* Select 'Upload' from the dropdown menu.
* In the Upload section that opens, paste the code repository URL in the 'Paste Link' bar near the bottom.&#x20;

  <figure><img src="/files/AA4YjrIrblJQ8S9viun1" alt="" width="188"><figcaption></figcaption></figure>
* Your repository will be added instantly, creating a folder named after the uploaded repository, containing all the files from the online repository. &#x20;

{% hint style="info" %}
In case you made a mistake, [here's how to delete a component](/create-and-publish/publish/update-your-node/delete-components-after-publication). Do note that only unpublished components will be removed from the online environment when deleted.&#x20;
{% endhint %}


# External Links

Add component • External Links • Workspace

If there are any online resources you want to share as part of your Research Node that we currently do not explicitly support, you can always provide the link to that resource as an external link, alongside metadata describing its content, to make it FAIR.

You can add links to external resources simply by providing the link of the URL in the URL bar of the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) in the [Node Workspace](/general-user-overview/node-workspace) of the Node you want to add the resource to.&#x20;

* Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel), and hit the '+' button.&#x20;
* Select 'Upload' from the dropdown menu.
* In the Upload section that opens, paste the URL you want to add in the 'Paste Link' bar near the bottom.&#x20;

  <figure><img src="/files/AA4YjrIrblJQ8S9viun1" alt="" width="188"><figcaption></figcaption></figure>
* Your URL will be added instantly to a folder named 'External Links'. If this folder doesn't exist yet, it will be automatically created.&#x20;

<figure><img src="/files/qoYlt9orvCosxh6XOmp4" alt=""><figcaption><p>Add URL links to point to external resources relevant to your Node</p></figcaption></figure>

{% hint style="info" %}
In case you made a mistake, [here's how to delete a component](/create-and-publish/create-a-node/delete-before-publication/delete-unpublished-components).
{% endhint %}


# Folder

Drag & Drop  •  Create

You can add folders with content from your desktop (see [Add Components](/create-and-publish/create-a-node/add-components#drag-and-drop) & [Add Components](/create-and-publish/create-a-node/add-components#upload-from-desktop)). Alternatively, to help structure your files you can create Folders within the Node Drive environment yourself.&#x20;

* Open the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel in your [Node Workspace](/general-user-overview/node-workspace),&#x20;
* open the Drive tab, and&#x20;
* click the '+' situated on the right of the 'FILES' navigation title.&#x20;
* From the mini-fold-down-menu choose 'New Folder'.&#x20;
* Give the folder the name you want.&#x20;

<figure><img src="/files/Kcyb9hwPFD9533qlP87a" alt="" width="188"><figcaption><p>Adding a folder in the Drive Panel</p></figcaption></figure>

You can later change the name by clicking on the name of the folder, or by opening the side menu by clicking on the three dots '...' next to the folder name and click 'Rename'.&#x20;

For further guidance on this, also see [Renaming components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components).&#x20;


# Add Information

Metadata  •  License  •  Comments  •  Authors

Part of what elevates Nodes is the possibility to directly link extra informative elements.&#x20;

\
Besides multiple file and data types, you are strongly encouraged to add a [**License**](/create-and-publish/create-a-node/add-information/add-license) and [**Metadata**](/create-and-publish/create-a-node/add-information/add-metadata) (including using our FAIR guidelines) to your Nodes. You can also add [**Comments**](/create-and-publish/create-a-node/add-information/add-comments) to your work for further guidance, direct indications of what data/code was used where, etc.&#x20;

\
Lastly, a special type of metadata on your Node and components can be added post-publication by the community - [**attestations**](/community/community-curation)**.** Read more about these and how community attestations and curations work [here](/community/community-curation), and how to claim them for published work [here](/create-and-publish/create-a-node/add-information/claim-attestations).&#x20;

Further information on these extra options and how to add them can be found here:

* [Add License](/create-and-publish/create-a-node/add-information/add-license)
* [Add Metadata](/create-and-publish/create-a-node/add-information/add-metadata)
* [Add Contributors](/create-and-publish/create-a-node/add-information/add-contributors)
* [Add Comments](/create-and-publish/create-a-node/add-information/add-comments)
* [Claim Attestations](/create-and-publish/create-a-node/add-information/claim-attestations)&#x20;
  * e.g. by [submitting for curation](/create-and-publish/submit-for-curation) by a community.&#x20;


# Add License

Licenses  •  Re-Usability

{% hint style="warning" %}
**Currently, if a license is not indicated for a component on publishing, a CC-BY license will be automatically applied to non-code Nodes, and an MIT license to those components that are code-based.**
{% endhint %}

Before being able to publish a Node, you will be required to choose a license to clearly define the terms of re-use for the published work.&#x20;

It is  possible to license all components separately, in case you have stricter licensing requirements for some of your Node components.&#x20;

*You can always overwrite the license attached to any individual component*. This means that while most of your components might be very permissively licensed (CC0, CC BY, etc.), your Node may also contain a component which has [**already been published elsewhere under a license**](#licenses-for-previously-published-work) that requires any re-publication to use the exact same licensing, as in CC BY-SA or similar.

<figure><img src="/files/VhCuvHYvzRr6qwNy8W9h" alt="" width="375"><figcaption><p>Add a license to a Node component</p></figcaption></figure>

License types can differ, and Nodes currently offers a wide variety to cover different types of files and information. Check the different types and what they mean [below](#license-choice-guide).&#x20;

## How to Add a License

Select your Node or the component within your Node you need to add a license to. *NB: all your published work needs to have a license indicated*.&#x20;

In the Navigation bar at the top, choose the 'i' Information icon <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="Screenshot 2024-02-02 at 00.10.02.jpg" data-size="line">. This will open the Information/Metadata panel. You will see the option to 'Select License' under the license section. *To apply the license to a specific component, select the component in the Drive Panel before selecting the license in the Information Panel*.&#x20;

Click on 'Select License' to see a dropdown menu of the different License options. You can use the search bar at the top of the list to find the license you want instead of scrolling through the list. Select the one you want, and it will be automatically applied.&#x20;

<figure><img src="/files/jUspCcY4zlL0lo3VNMsR" alt="" width="563"><figcaption><p>Select &#x26; apply a license to a component</p></figcaption></figure>

If you need help choosing the most applicable license, please have a read through the [#license-choice-guide](#license-choice-guide "mention") below.&#x20;

## License Choice Guide

This is a quick guide on which licenses we suggest to use, and what all of them mean.

{% hint style="info" %}
In the spirit of open science, we suggest you make your work "as open as possible, as restricted as necessary." Whenever you can, try to pick a permissive license.
{% endhint %}

#### What do all of these licenses mean?

<table><thead><tr><th width="183.33333333333331">License</th><th width="213">Open Science friendly?</th><th>Meaning</th></tr></thead><tbody><tr><td><strong>General Licenses</strong></td><td></td><td><a href="https://choosealicense.com/licenses/">Learn more here.</a></td></tr><tr><td>CC BY</td><td>Yes.</td><td>Permits others to use, adapt, and share your work, as long as they credit you as the original creator.</td></tr><tr><td>CC0</td><td>Yes.</td><td>Waives all copyright and related rights in your work, allowing others to freely use, adapt, and share it without any restrictions or requirement to credit you.</td></tr><tr><td>CC BY-SA</td><td>Kind of.</td><td>Allows others to use, adapt, and share your work, provided they credit you and license their adaptations under the same terms.</td></tr><tr><td>CC BY-NC</td><td>Kind of.</td><td>Allows non-commercial use, adaptation, and sharing of your work, provided others credit you.</td></tr><tr><td>CC BY-NC-SA</td><td>Kind of.</td><td>Allows non-commercial use, adaptation, and sharing of your work, as long as others credit you and license their adaptations under the same terms.</td></tr><tr><td>CC BY-ND</td><td>No.</td><td>Allows others to use and share your work, as long as they credit you and do not modify or adapt it.</td></tr><tr><td>CC BY-NC-ND</td><td>No.</td><td>Permits non-commercial use and sharing of your work, as long as others credit you and do not modify or adapt it.</td></tr><tr><td></td><td></td><td></td></tr><tr><td><strong>Code Licenses</strong></td><td></td><td><a href="https://choosealicense.com/licenses/">Learn more here.</a></td></tr><tr><td>MIT</td><td>Yes.</td><td>Allows others to use, modify, and distribute your code, provided they include the original copyright notice and license text.</td></tr><tr><td>Apache 2.0</td><td>Yes.</td><td>Permits others to use, modify, and distribute your code, provided they include the original copyright notice, license text, and any required notices for modifications; also grants a patent license.</td></tr><tr><td>CC0</td><td>Yes.</td><td>Waives all copyright and related rights, allowing others to freely use, adapt, and share your code without any restrictions or requirement to credit you.</td></tr><tr><td>BSD 2-Clause</td><td>Yes.</td><td>Allows others to use, modify, and distribute your code, provided they include the original copyright notice and license text.</td></tr><tr><td>BSD 3-Clause</td><td>Yes.</td><td>Permits others to use, modify, and distribute your code, provided they include the original copyright notice, license text, and do not use your name to promote derived works without permission.</td></tr><tr><td>Boost Software License 1.0</td><td>Yes.</td><td>Allows others to use, modify, and distribute your code, provided they include the original copyright notice and license text.</td></tr><tr><td>Eclipse Public License 2.0</td><td>Yes.</td><td>Permits others to use, modify, and distribute your code, provided they include the original copyright notice, license text, and disclose their source code changes; also grants a patent license.</td></tr><tr><td>The Unlicense</td><td>Yes.</td><td>Relinquishes all copyright and related rights, allowing others to freely use, adapt, and share your code without any restrictions or requirement to credit you.</td></tr><tr><td><br>Mozilla Public License</td><td>Kind of.<br></td><td>Allows others to use, modify, and distribute your code, provided they disclose their source code changes and include the original copyright notice and license text.</td></tr><tr><td>GNU General Public License 3.0</td><td>No.</td><td>Requires others to release any work that uses, modifies, or distributes your code under the same GPL 3.0 license (copyleft).</td></tr><tr><td>GNU General Public License 2.0</td><td>No.</td><td>Requires others to release any work that uses, modifies, or distributes your code under the same GPL 2.0 license (copyleft).</td></tr><tr><td>GNU General Public License 1.0</td><td>No.</td><td>Requires others to release any work that uses, modifies, or distributes your code under the same GPL 1.0 license (copyleft).</td></tr><tr><td>GNU Affero General Public License 3.0</td><td>No.</td><td>Requires others to release any work that uses, modifies, or distributes your code, or uses it over a network, under the same AGPL 3.0 license (copyleft).</td></tr></tbody></table>

## Licenses for Previously Published Work

In case your Node contains components that have already been published elsewhere, you will need to check the licensing attached to the original component. In certain cases, this licensing won't allow you to publish this component elsewhere. In this case, you can still connect this component as an [external link](/create-and-publish/create-a-node/add-components/external-links).&#x20;

If the original component allows for re-publication, there still might be certain conditions under which re-publication is allowed (or not). One of these conditions might be that the re-publication of the components needs to be published under the exact same licensing as the original. Original licenses like CC BY-SA require this.

Sometimes license information for published work is unclear. In these cases, we recommend adhering to the specific publication's policies. Most scientific journals will have their policies stated somewhere on their website. [You can also use Sherpa Romeo to determine the permissions policies of most scientific journals.](https://v2.sherpa.ac.uk/romeo/)


# Add Metadata

Metadata  •  FAIR  •  Licenses

DeSci Nodes are FAIR-enabling technology. With Nodes it is easy to meet FAIR data standards by providing the relevant metadata to your work. When it comes to FAIR, metadata (the description of your data) is just as important as the actual data (artefacts) you are publishing.&#x20;

## Add Metadata (optional)

To add metadata to a component, in your [Node Workspace](/general-user-overview/node-workspace) open up the [Information Panel](/general-user-overview/node-workspace/information-panel) on the right by clicking the <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="" data-size="line"> icon in the address bar. You can add descriptions and licensing, as well as keywords to your component. Adding metadata is optional and we hope to automate as much of this as possible soon.

#### Title:

Give your component a title.&#x20;

#### License

Here you can enter a short, textual, description of your Node component. For example its main function or contribution to the Node in a broader sense.&#x20;

Since Licensing is a topic with more extensive information, please see the separate section on it. [Add License](/create-and-publish/create-a-node/add-information/add-license)

#### CEDAR Link

If you used a CEDAR metadata template to provide metadata for your component, you can link it here.

#### Ontology URL

Ontology URL: Specify the URL pointing to the relevant ontology utilized to categorize or define the component. This URL should lead to a resource providing detailed information about the ontology, facilitating clear understanding and proper contextualization of the component's categorization and semantic associations.

#### Description

Provide a concise yet comprehensive overview of the component. Describe its purpose, functionality, and significance within the context of the research object. Aim for clarity and relevance, ensuring that the description accurately reflects the content and intent of the component.

#### Keywords

Enter keywords you think are appropriate, to help with identifying, sorting and curating your work. Some guidelines for picking keywords can be found [here](https://blog.wordvice.com/choosing-research-paper-keywords/) and [here](https://www.linkedin.com/advice/0/what-best-practices-choosing-using-keywords), for example. In short from the second link: "A good rule of thumb is to use 4-6 keywords, preferably from a standardized list or database, such as [MeSH](https://www.ncbi.nlm.nih.gov/mesh/), [IEEE](https://www.ieee.org/publications/services/thesaurus-thank-you.html) \[who have great Thesaurus and Taxonomy lists], or Scopus. Avoid using words that are too general, vague, or ambiguous, such as "study", "analysis", or "model". Also, avoid using words that are already in your title, as they are redundant and waste valuable space."

To separate keywords, hit enter.

#### Controlled Vocabulary

Specify the predetermined set of terms or phrases used to describe this component. Utilizing a controlled vocabulary ensures consistency and precision in metadata representation. Select terms from established vocabularies or ontologies relevant to the subject matter, enhancing searchability and interoperability across datasets. Aim to adhere to established standards and guidelines for controlled vocabulary usage to promote effective data discovery and integration.

#### Component Type and Subtype

Components can have four Types: Document, Data, Code, and Link. When you upload a component, DeSci Nodes automatically assigns it a type based on the file extension. You may change the Type here if there was a mistake, or provide a more granular subtype (e.g., "Preprint" for a Document component).

<figure><img src="/files/LgppTpnZBRtzv09Jrd2X" alt=""><figcaption></figcaption></figure>

{% hint style="warning" %}
DeSci Nodes has been designed to ensure that your publication meets FAIR standards. You won't be able to publish if you have not provided a description and license for each of your components. Keywords are optional. However, they do help increase the discoverability of your work.
{% endhint %}


# Add Contributors

Collaborate  •  Acknowledge

The [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) does not only contain the Drive, but also has a tab for Contributors. This is where you add the names and information of those who have contributed to the Node.&#x20;

You can add your contributor's name, as well as their ORCID to automatically import further information on your contributor's past work and company affiliations.&#x20;

If you are unsure who to contribute, have a look at the different contributor roles we suggest [**here**](#who-is-a-contributor)**.**&#x20;

## How to Add Contributors

<figure><img src="/files/e3jxRca2pYqVAP81dZMz" alt="" width="563"><figcaption><p>Add (and delete) contributors &#x26; ORCID integration</p></figcaption></figure>

Step-by-step instructions:&#x20;

* When opening the Contributors tab in the control panel on the left, click on the '+' button in the top right, next to the title 'Contributors'.&#x20;
* In the viewer panel, fields to fill out to add a contributor will open up.&#x20;

<figure><img src="/files/Ab2MSjj2xmLy9Bzgs1mZ" alt=""><figcaption><p>Add a contributor through their name, and add their ORCID for automatic integration of their ORCID information.</p></figcaption></figure>

* You can simply fill out the contributor name, but if you add their ORCID, Nodes will automatically integrate associated data from the ORCID profile into their Nodes profile - and can link the published Node to their ORCID profile in return.&#x20;
* Hit 'Continue' to add the contributor.&#x20;
* You can view the contributor and any additional data imported from an associated ORCID profile.

## Who is a Contributor?

We think it is good practice to include all those who have contributed to any area as presented in the [Niso Credit Taxonomy](https://credit.niso.org), with 14 different contributor roles. It will be possible to indicate which roles each contributor has played in the development of the Node:

[Conceptualization](http://159.203.176.220/contributor-roles/conceptualization/)

[Data curation](http://159.203.176.220/contributor-roles/data-curation/)

[Formal Analysis](http://159.203.176.220/contributor-roles/formal-analysis/)

[Funding acquisition](http://159.203.176.220/contributor-roles/funding-acquisition/)

[Investigation](http://159.203.176.220/contributor-roles/investigation/)

[Methodology](http://159.203.176.220/contributor-roles/methodology/)

[Project administration](http://159.203.176.220/contributor-roles/project-administration/)

[Resources](http://159.203.176.220/contributor-roles/resources/)

[Software](http://159.203.176.220/contributor-roles/software/)

[Supervision](http://159.203.176.220/contributor-roles/supervision/)

[Validation](http://159.203.176.220/contributor-roles/validation/)

[Visualization](http://159.203.176.220/contributor-roles/visualization/)

[Writing – original draft](http://159.203.176.220/contributor-roles/writing-original-draft/)

[Writing – review & editing](http://159.203.176.220/contributor-roles/writing-review-editing/)


# Add Comments

Comment  •  Annotate  •  Manuscript  •  Workspace

Annotate your manuscript to provide additional context or hyperlinks to other components of your Node.&#x20;

## Add a Comment

#### Highlighter

To add a comment to a PDF, hit the highlighter <img src="/files/C60fdql5Zfuzmi6VLXkX" alt="Screenshot 2024-02-01 at 23.59.44.jpg" data-size="line"> icon at the bottom of the [Viewer](/general-user-overview/node-workspace/viewer)section. Select the area you want the comment to relate to, by clicking and dragging across the section of the PDF you would like to annotate.&#x20;

Watch the **Comment Editor** pop up and start typing. When you're done, hit <img src="/files/F5tJa6im5TgEuHsNKjZ9" alt="" data-size="line">. The note will appear as a highlighted section on your document. Click on it to open the comment in the Information panel on the right.&#x20;

You can also open all your comments in the Comment panel, by clicking on the pencil icon <img src="/files/ly9k63UJaUDSkV6CZnvz" alt="Screenshot 2024-02-02 at 00.09.39.jpg" data-size="line"> at the top left section of the [**Information panel**](/general-user-overview/node-workspace/information-panel)**.**&#x20;

Once the comment section is open you can click on the comments to Edit <img src="/files/cZZWeHY13xRuNLnxvmGd" alt="Screenshot 2024-02-02 at 00.00.28.jpg" data-size="line"> or Delete <img src="/files/PpnbGr2uk7oukOHIHaSz" alt="Screenshot 2024-02-02 at 00.00.37.jpg" data-size="line"> them.&#x20;

<figure><img src="/files/EyxBy6VzbjWFDw9HpoWP" alt=""><figcaption><p>Add a comment or link to a component in a document</p></figcaption></figure>

#### Text Selection

Alternatively, you can select text in the pdf and use the <img src="/files/LHgws153awjr9kuRc0k3" alt="AddComment_Button.jpg" data-size="line"> button that pops up to add a comment to the selected text.&#x20;

When clicking the '+' comment button, the comment panel on the right will open, with the selected text readily quoted in the comment section. You can add more text, links, etc. here to add context, explanations, sources, etc.&#x20;

See the video below for a demonstration:

<figure><img src="/files/bOS1fhcFn3nJ469lZZMx" alt=""><figcaption><p>Comment through selecting text in your pdf</p></figcaption></figure>

## Link components

With comments, you can make your Node interactive. As an example, you can provide the link to the code that was used to produce a certain figure in your manuscript. To do so:&#x20;

* follow the same instructions as inserting a comment. You can add text to describe the nature of the connection.&#x20;
* Then hit '+ Node Drive' <img src="/files/XxaQGfKmOlXJnfaE1bLk" alt="" data-size="line"> in the **Comment Editor** section. &#x20;

  <figure><img src="/files/BDiXC5olys21fzcuQyit" alt="" width="174"><figcaption></figcaption></figure>
* Select the correct component from the dropdown and hit 'Insert', <img src="/files/YMXAtYU4kZgh79r5LhCP" alt="" data-size="line"> to create the link.&#x20;
* When you're done, hit 'Save', <img src="/files/F5tJa6im5TgEuHsNKjZ9" alt="" data-size="line">.

<figure><img src="/files/bOS1fhcFn3nJ469lZZMx" alt=""><figcaption></figcaption></figure>

## Editing and Deleting a Comment

To edit or delete an annotation, open the Comment Panel by clicking on the comment bubble in the component, or choose the pencil icon at the top of the [Node Workspace](/general-user-overview/node-workspace)on the right.&#x20;

#### Edit an annotation

In the Comment Panel, hover over the comment you want to edit. Select 'Edit' <img src="/files/cZZWeHY13xRuNLnxvmGd" alt="Screenshot 2024-02-02 at 00.00.37.jpg" data-size="line"> which pops up in the top right corner of the comment box.  This will open up the **Annotation Editor** where you can make changes in the same way as [above](#create-an-annotation).

#### Delete an annotation

In the IDE comment panel, hover over the comment you want to delete. Select Delete <img src="/files/PpnbGr2uk7oukOHIHaSz" alt="Screenshot 2024-02-02 at 00.00.37.jpg" data-size="line"> which pops up in the top right corner of the comment box. Hit ![Screenshot 2024-02-02 at 00.00.37.jpg](https://www.gitbook.com/cdn-cgi/image/width=32,dpr=2,format=auto/https%3A%2F%2Ffiles.gitbook.com%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252FMYxRLCpbB6u9NiTwuU16%252Fuploads%252FiImDRkXIH0hJnUeEbvzK%252FScreenshot%25202024-02-02%2520at%252000.00.37.jpg%3Falt%3Dmedia%26token%3D9e62e723-cf51-4c5f-a48b-9639063cd504) to confirm and done!

{% hint style="danger" %}
Annotations can only be permanently deleted from a draft. If the annotation has been part of an already published Node, deleting it will only lead to the annotation not showing up in the most recent version of your Node. It will still be available in the older versions in which it was published.
{% endhint %}


# Claim Attestations

Quality indicators   •   Validation   •   Community   •   Control

{% hint style="warning" %}
To claim an attestation, your Node needs to be published. If you have not published yet and need guidance on this, head to the [Publish](/create-and-publish/publish) section first.

Attestations are post-publication attributions to the quality of your work, that are provided and supported by the global community.&#x20;

If you want your work to be curated by a community, and as such claim their attestation badges, see [Submit for Curation](/create-and-publish/submit-for-curation). &#x20;

Find more on attestations here: [Validate and Curate](/community/community-curation)
{% endhint %}

## Attestation Claims

If your Node has particular high-value characteristics, such as [FAIR data](/technical-background/fair-data), novel impact, proving and building on the work of others in a FAIR way, etc. check out the variety of attestations present on Nodes that are applicable to your work. You can make a claim to them, or others can indicate they believe your work has these characteristics. I

## Community validation

[Communities](/create-and-publish/interact-and-reuse/communities) choose a personalised set of attestations that verify qualities they find important. Submit your Node to a community when you believe your Node qualifies for ALL of their attestations. Community members will verify whether the claims are true, and can comment on your Node.&#x20;

A video of the process with examples is given below:

{% embed url="<https://www.loom.com/share/ec63bb8e6af44fa59424f1017d002843?sid=dd8b39e7-637d-4815-b902-7805b1815d13>" %}
Communities and community attestations
{% endembed %}


# Organise, Access & Present

Ease of Use  •  Edit  •  Guide

Node Drive can be structured and organised to present your information in ways that suit you, and make it easy to navigate for others, using a combination of editing functions like:

* [adding & renaming folders](/create-and-publish/create-a-node/add-components/folder), and&#x20;
* [moving](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/moving-components), &#x20;
* [pinning](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/pinning-components),&#x20;
* [adding](/create-and-publish/create-a-node/add-components),&#x20;
* [renaming](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components), and&#x20;
* [deleting](/create-and-publish/create-a-node/delete-before-publication/delete-unpublished-components) *components*, you can optimise how your Node is navigated by yourself and others in the [Node Drive](/general-user-overview/node-workspace/node-drive-panel).&#x20;

The creation and adding of components and folders is shown in the [Add Components](/create-and-publish/create-a-node/add-components) section.&#x20;

In this section we discuss:

* [Return to most recent Node](/create-and-publish/create-a-node/organise-access-and-present/return-to-most-recent-node) (Access): this function helps you return to the most recent Node you were viewing or working on, in case you ended up browsing away from it and need a simplified return \[*NB this function is still being optimised*]
* Editing [Component Presentation](/create-and-publish/create-a-node/organise-access-and-present/component-presentation) (Present & Organise):  editing options for components gives you the ability to optimise how your components are organised and presented, making it easier for both yourself and others to navigate your Node. Editing and presentation options include:
  * [Pinning components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/pinning-components)
  * [Renaming components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components)
  * [Moving components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/moving-components)
* [Add Cover Art](/create-and-publish/create-a-node/organise-access-and-present/add-cover-art) (Present): Making Nodes more fun and to visually facilitate navigation, Nodes supports the incorporation of [cover art ](/create-and-publish/create-a-node/organise-access-and-present/add-cover-art)- giving you the opportunity to represent your research visually. Guidance on how to create and incorporate cover art can be found [here](/create-and-publish/create-a-node/organise-access-and-present/add-cover-art).

#### Other Functions that support external Presentation, Organisation & Access

[Add Metadata](/create-and-publish/create-a-node/add-information/add-metadata) - In addition, some help in finding your Node by external users is supported through the [Metadata Panel](/general-user-overview/node-workspace/information-panel) on the right of the workspace. Here, you can add subject[ tags](/technical-background/open-state-repository/metadata#machine-actionable-metadata), [descriptions](/create-and-publish/create-a-node/add-information/add-metadata#description), [component type labels](/create-and-publish/create-a-node/add-information/add-metadata#component-type), etc.&#x20;


# Return to most recent Node

Browse  •  Return

When navigating away from the Node you were last editing, you can return by clicking on the Current Node button, <img src="/files/hZjvzxT2WdLojYw9rEyc" alt="Current Node Button.jpg" data-size="line"> in the navigation bar on the left. If you have set a cover picture it will show the cover picture in the icon.

Clicking through other Nodes in the Explore page will still return you to your own last edited Node.&#x20;

Easy to return home, and get back to editing.&#x20;


# Component Presentation

To optimise your Node presentation and navigation, you can move and edit the components within your Node.&#x20;

We strongly suggest you use these features to make your Node easy to navigate - for both yourself and for others once published.&#x20;

Nodes can evolve over time, so the optimised way of presentation might change as new components are added.&#x20;

To optimise parts of your component presentation:

* Pin the most important components so they are easily accessible, no matter where they are located in the drive: see [Pinning components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/pinning-components) for guidance.
* Edit the name of your components: see [Renaming components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components) for guidance.
* Change the location of your components: see [Moving components](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/moving-components) for guidance.&#x20;


# Pinning components

To help organise your Node and its components, you can pin links to those components or folders you think are important. The pinned components will be visible on your Node opening page, under the title, and at the top of your [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel).

<figure><img src="/files/d4J7ATj4CLt5Zm491nlR" alt="" width="153"><figcaption><p>Pinned components will remain in this section, above the Files overview in the Drive Panel.</p></figcaption></figure>

There are two easy methods to pin your components:&#x20;

* [#pin-by-dragging-component](#pin-by-dragging-component "mention")
* [#pin-from-component-menu](#pin-from-component-menu "mention")

### Pin by dragging component

The most straightforward way to pin a component is to drag it from the drive to the pinned components box above it. If there are no pins yet, the box will guide you - it says 'Drag Files here to Pin'. If you have already added a pinned component, grab the component you wish to add and a section saying 'Drop here to Pin' will appear underneath the already pinned component(s).&#x20;

<figure><img src="/files/Tp3BTSVG6mwjCwzhcJfi" alt="" width="153"><figcaption><p>To pin, drag a component from the Files section into the 'Drag Files here to Pin' section. </p></figcaption></figure>

### Pin from component menu

Go to the component in the *File section*. Click on the component's menu to the right of it's name '...' , and select 'Pin'. <img src="/files/ZVpqjjg2IH4RvVY2cVv9" alt="" data-size="line">

<figure><img src="/files/Vh2cgqydIWVdJQSECHVt" alt="" width="152"><figcaption><p>Pin a component from it's menu.</p></figcaption></figure>

### Unpin a component

Go to the component in either the File section or the pinned component section. Click on the component's menu to the right of it's name '...' , and select 'Unpin'. <img src="/files/BLwjoSGMXQ2y0g2N6fb6" alt="" data-size="line">

<figure><img src="/files/OE1UWDbUwQ9zLBoZmrC1" alt="" width="147"><figcaption><p>Unpin a component from the pinned menu</p></figcaption></figure>

<figure><img src="/files/zuXfND5blNhZ0rOTM1X0" alt="" width="150"><figcaption><p>Unpin a component from the file drive</p></figcaption></figure>


# Renaming components

Make changes  •  Edit  •  Components

To keep a better overview of your Node components, you can adjust components' titles to better describe what they are about.

Open up the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) by clicking the <img src="/files/UoRuQl5zORaACttG8b4P" alt="" data-size="line"> icon in the top right corner.&#x20;

In the **Drive** tab, select the **Component** you want to rename. Once the component is selected, you can click on the name of the component to edit it. Type in the new name. Hit **Enter** on your keyboard to update the component title.

<figure><img src="/files/VN35A7ysQDN0xo5RqUfB" alt=""><figcaption><p>Create a better overview by changing component titles</p></figcaption></figure>


# Moving components

Structure   •  Re-organise

To ensure your work can be structured in the way you like, and this structure can be adapted according to changing demands, your components can be moved around within your Node.&#x20;

Similar to how your computer file drive works, Nodes Drive provides you with the ability to use folders for structure. Moving a component between files is relatively straightforward:&#x20;

* Select the component you wish to move;
* Click on the triple dot menu to the right of your selected component;&#x20;
* Select the 'Move' option from the dropdown menu;&#x20;
* You should see a notification at the bottom of the Node Drive indicating the selected component name ('Information\_Button.jpg') and its current location ('root/Button\_pics/'), with a button to indicate if you want to move the component here.  You won't be able to use the 'Move Here' button yet, as you are currently in the same place your file is already located;

  <figure><img src="/files/Mifqipr9YgsoCytmhhtU" alt="" width="375"><figcaption></figcaption></figure>
* In the Node Drive, go into the Folder you want to move your component to;
* Click on 'Move Here' <img src="/files/YbaDTJpr9T155WUhW2BP" alt="" data-size="line"> in the notification at the bottom;
* Your Node should now be moved to its new location.

<figure><img src="/files/xhxTiQyMjxEY3QV5c84R" alt=""><figcaption><p>Moving a Node Component</p></figcaption></figure>

NB if you would like to move the component to a new folder, [**create the new folder**](/create-and-publish/create-a-node/add-components/folder) first.&#x20;


# Add Cover Art

Identify   •   Create   •   Present

To uplift the presentation of your Node, Nodes supports the creation and presentation of cover art for your Node.&#x20;

Making one of your components the cover art for your Node is really straightforward.&#x20;

Step-by-step instructions:

* Open the Node Drive Panel.&#x20;
* Find or [upload](/create-and-publish/create-a-node/add-components) the component you want to use as your cover art.&#x20;
* Click on the component menu, the three dots at the end of the component name <img src="/files/MGzefmbubZPiOG82uy4V" alt="ComponentMenu_TripleDot_Button.jpg" data-size="line">
* From the pop-up menu, choose 'Set as Cover Art'. &#x20;

<figure><img src="/files/diYVKTEy0mStyGYSM6IK" alt="" width="180"><figcaption></figcaption></figure>

* If you want to replace it, simply set another component as cover art in the same way.
* Should you want to remove the cover art, go to the component chosen as your cover art (it could be useful to pin it) - click on the component menu and you will see that instead of 'Set as Cover Art' it says 'Remove Cover Art'. Select this option.&#x20;

<figure><img src="/files/yfFDINO462SuXiatdXkz" alt="" width="182"><figcaption></figcaption></figure>

Set cover art video demo below:

<figure><img src="/files/OYeJQVFyy69l3SDu6EAa" alt="" width="563"><figcaption><p>Set cover art + some tips &#x26; tricks to keeping track of it <br>(e.g. rename &#x26; pin the component used)</p></figcaption></figure>


# Collaborate

{% hint style="warning" %}
In progress: we are integrating the ability for authors of a Node to work together, in sync, on their Nodes.&#x20;
{% endhint %}


# Delete Before Publication

Prepublication editing  •  Deleting   •   Node management

{% hint style="danger" %}
Components and Nodes that are deleted **after publishing** a Node **will always remain publicly available** in those previous versions of the Node.&#x20;
{% endhint %}

In contrast to AFTER publication, you can delete components and Nodes before publication.&#x20;

* Delete components: [Delete Unpublished Components](/create-and-publish/create-a-node/delete-before-publication/delete-unpublished-components)
* Delete Nodes: [\[TBD\] Delete Unpublished Nodes](/create-and-publish/create-a-node/delete-before-publication/tbd-delete-unpublished-nodes)


# Delete Unpublished Components

Remove  •  Undo  •  Prepublication editing

{% hint style="danger" %}
Components that are deleted **after publishing** a Node **will always remain publicly available** in those previous versions of the Node.&#x20;
{% endhint %}

*Before* publishing you can delete components without a trace. However, once published, even though you can update your version and remove components from the new version, your older version and all its components will remain available.&#x20;

In your [Node Workspace](/general-user-overview/node-workspace) you can delete components before, and remove them from newer updated versions after, publishing. Removing components is relatively simple.&#x20;

You can delete Node components from your [Node Workspace](/general-user-overview/node-workspace). To delete a component you've previously uploaded to your Node, open up the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel by clicking the hamburger icon <img src="/files/UoRuQl5zORaACttG8b4P" alt="" data-size="line"> in the top left corner.&#x20;

In the **Drive** tab, hover over the component or folder you wish to delete, and click on the three dots that appear next to the component or folder name.&#x20;

<figure><img src="/files/IiGAU7gMlfO0letpZ3iD" alt="" width="301"><figcaption></figcaption></figure>

From the mini-list that pops up, click on Delete at the bottom. <img src="/files/stbevI1JPt3S35QIy4AU" alt="Screenshot 2024-01-30 at 12.28.35.jpg" data-size="line">

<figure><img src="/files/C3QcT8HHvAV0DP6NPjPG" alt="" width="282"><figcaption></figcaption></figure>

A pop-up window will ask you if you want to delete the component/folder:

<figure><img src="/files/89uwODAZadJruL3cRrdh" alt="" width="375"><figcaption></figcaption></figure>

To confirm this step, hit OK in the pop-up window. *This will delete your component/folder.*&#x20;

NB: It might take a refresh for the change to show.&#x20;

<figure><img src="/files/JQoZbuz8WMhzPHR850Ze" alt=""><figcaption></figcaption></figure>


# \[TBD] Delete Unpublished Nodes

Remove  •  Undo  •  Prepublication editing

{% hint style="info" %}
**We are currently working on this feature**
{% endhint %}

Before publication, you can delete the Node you have created.&#x20;


# Publish

Publish • Authorship • Commit

{% hint style="info" %}
**You will always retain copyright of your work.**

DeSci Nodes will never require you to surrender your copyright in order to publish. As such, **you can publish your work elsewhere**. Just check the guidelines of your target publications beforehand, as some require exclusive publishing rights.&#x20;
{% endhint %}

To share your Node with the scientific community, and for a chance to [be curated by a DeSci Community](/community/community-curation), you need to publish your Node first. Publishing in DeSci Nodes is irreversible: Once a (version of a) Node has been published, you won't be able to delete or hide it. However, you can always make changes and publish a new version. This gives you full control over your publication while also ensuring transparency and tamper-proofness of the scientific record.

With publishing, your Node will automatically receive a **decentralized persistent identifier (**[**dPID**](/technical-background/persistent-identifiers-101)**)** which can be used to reference your work, as well as granularly cite any component within your Node. [Learn more about dPID here.](/technical-background/persistent-identifiers-101)

{% hint style="danger" %}
**WARNING: Once your Node is published, it will be publicly accessible and you won't be able to delete it.**

You are able to make *changes* to published Nodes and publish a new version of your work. However, the original version will remain public, too.
{% endhint %}

## Quick Overview

After following the basic steps to publish [as given below](#publishing-your-node), you can sign & publish with:

* ORCiD - You can sign your creations and have them displayed on your ORCID account in one click. If you log into your profile through your ORCID account or link your ORCID account to your profile, you can publish through your ORCID. You can add this in the publish flow, or earlier in your [Profile](/general-user-overview/profile)
  * Follow the steps at [#connect-orcid-id](#connect-orcid-id "mention") to connect to your ORCID before publication,
  * Or follow [#confirm-orcid](#confirm-orcid "mention") if you have published before.
  * Then confirm your [#licensing-and-commit-message](#licensing-and-commit-message "mention") before hitting 'Publish'.&#x20;
* Digital Wallet - For new users who do not want to use an ORCID, we have the option to sign with a digital wallet. We use Metamask to create a digital, verifiable signature. You can add this in the publish flow, or earlier in your [Profile](/general-user-overview/profile)
  * Follow the steps at [#connect-did-wallet](#connect-did-wallet "mention") to add your Digital Wallet before publication,
  * Or follow [#confirm-did](#confirm-did "mention") if you have published before.
  * Then confirm your [#licensing-and-commit-message](#licensing-and-commit-message "mention") before hitting 'Publish'.&#x20;

## Publishing your Node

You can publish your Node from the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) in the [Node Workspace](/general-user-overview/node-workspace).&#x20;

Open your Node in the workspace, and access the Drive Panel through clicking on the Hamburger menu button <img src="/files/UoRuQl5zORaACttG8b4P" alt="DriveHamburger_Button.jpg" data-size="line">. Click on <img src="/files/U1Nf1IX2HYYTnpoUX5TG" alt="" data-size="line"> at the bottom of the Drive Panel.&#x20;

This will extend to show you the changes you have made to the newest version you want to publish compared to the previously published version. If this is your first version (V1) the box will be empty. At the bottom you will see 'Continue to Publish'. Click on this to continue.&#x20;

<figure><img src="/files/QK9rzHkUyBAh85txxYSZ" alt="" width="301"><figcaption><p>Publish overview (empty in V1) and confirmation to continue</p></figcaption></figure>

### First Time Publishing

If you're publishing for the first time, you may be asked for some additional information to complete your Profile prior to publishing.

#### Enter your Name

If you haven't done so already, you will be asked to provide your full name. This name will be attached to your Nodes profile and may be edited at any time.

<figure><img src="/files/GZlEpgLIY7A3tJLfk8Xn" alt="" width="188"><figcaption></figcaption></figure>

### Connect Publish Credentials

If this is your first time publishing and you created your account via email only, you will be asked to connect Publish Credentials. This can be you ORCID iD or DID (wallet), and is required to be able to publish on DeSci Nodes. Publish Crednetials allow you to interact with the [Open State](/technical-background/open-state-repository) repository and maintain control over your Node's versioning rights **independently from the platform used to access it.**&#x20;

{% hint style="info" %}
We highly recommend using your ORCID iD to keep track of your credit and research contributions.&#x20;
{% endhint %}

<figure><img src="/files/t6E80rC9o41H86ZO9oiQ" alt="" width="188"><figcaption></figcaption></figure>

#### Connect ORCID iD

We recommend connecting your ORCID iD so that your academic profile can keep track of your credit and research contributions on DeSci Nodes. To do this, hit Continue with ORCID. This will open a pop-up asking you to sign in with your ORCID credentials.&#x20;

<figure><img src="/files/8nLhhvY35Ff5Q6Tl7G5s" alt="" width="188"><figcaption></figcaption></figure>

#### Connect DID (Wallet)

If you prefer using a decentralized identifier (DID) like Metamask, you can connect this and use it to publish as well. To do so, select Continue with DID. This will allow you to select your DID provider. Selecting your provider will open your browser extension pop-up. You may need to sign into your DID before being able to confirm connecting your DID to DeSci Nodes.

{% hint style="info" %}
We currently only support connecting Metamask but are working on expanding the list of supported DID providers.
{% endhint %}

<figure><img src="/files/096lYB7QxEMLv53mIfI3" alt="" width="188"><figcaption></figcaption></figure>

### Next Step

After completing your Profile and connecting Publish Credentials, you can move on to the [final step: Licensing and Commit Message](#licensing-and-commit-message).

## Confirm Publish Credentials

If you've published before, or otherwise have connected Publish Credentials (ORCID or DID) to your account, you may need to confirm this connection prior to publishing.

#### Confirm ORCID

If you've connected an ORCID iD to your Nodes account, you may be asked to confirm the connection prior to publishing. To do this, select Continue with ORCID. This will open a pop-up asking you to sign in with your ORCID credentials.&#x20;

<figure><img src="/files/zBqR4W5rWGuQYvArKhk9" alt="" width="188"><figcaption></figcaption></figure>

#### Confirm DID

If you're working with a DID on DeSci Nodes, you may need to re-confirm the connection by selecting your DID provider and signing in via your provider's browser extension.

{% hint style="info" %}
We currently only support connecting Metamask but are working on expanding the list of supported DID providers.
{% endhint %}

<figure><img src="/files/096lYB7QxEMLv53mIfI3" alt="" width="188"><figcaption></figcaption></figure>

## Licensing and Commit Message

Once you've connected and/or confirmed your Publish Credentials, you can select licenses for your components. The choice you make here will apply to all components in your Node that have not previously been assigned an explicit license. For Data and Document components, we recommend CC BY. In line with Open Science practices, this allows anyone to re-use you work as long as they credit you. For Code, we recommend MIT as this most closely aligns with the Open Science principles for this type of artefact.

You may also add a commit message to describe the changes made in this version. This is optional.

Once you're done, hit Publish to make your Node or new version publicly available. **Note that you won't be able to delete anything once published.** However, you can always publish a new version of your Node with any edits you like.

<figure><img src="/files/qSx0ejs9YhvYNd6I63jD" alt="" width="188"><figcaption></figcaption></figure>

### No ORCID/Digital Wallet

Users who have no ORCID or Digital Wallet should make at least one of these. See either of the above on how to do this and connect them to your Node.&#x20;

##


# Update Your Node

Make changes • Version Control • Delete

## Nodes are versionable

Knowledge is dynamic. That's why Nodes are [versionable](/technical-background/persistent-identifiers-101). This allows you to publish-as-you-go, and to make any changes (from fixing typos or adding additional petabytes of datasets) post publishing.

{% hint style="info" %}
Any edits that are made post publication of a Node will require you to [publish a new version](/create-and-publish/publish/update-your-node/publish-a-new-version-of-your-research-node) of this Node before those edits are publicly visible.&#x20;

**Note that older versions of your Nodes will remain accessible to the public through your Nodes version history.**
{% endhint %}

Updating your Nodes is simple. All changes -- creating new components, changing metadata tags, and deleting components -- work exactly the way you would implement them in an unpublished Node. As such, refer to the rest of the user guide for guidance.&#x20;

## Dynamic knowledge: Edit post publication

{% content-ref url="/pages/bl5c709ZzAPq4lkHXiRH" %}
[Editing a published Node](/create-and-publish/publish/update-your-node/editing-a-published-node)
{% endcontent-ref %}

{% content-ref url="/pages/vCBkJD63yWh7c0daTzBh" %}
[Delete Components After Publication](/create-and-publish/publish/update-your-node/delete-components-after-publication)
{% endcontent-ref %}

{% content-ref url="/pages/KWddu59xdZTtn6TIjCno" %}
[Delete Published Node - Cannot](/create-and-publish/publish/update-your-node/delete-published-node-cannot)
{% endcontent-ref %}

{% content-ref url="/pages/hc5skvKFUxwj8BfTz9Vk" %}
[Publish a new version of your Research Node](/create-and-publish/publish/update-your-node/publish-a-new-version-of-your-research-node)
{% endcontent-ref %}


# Editing a published Node

Edit • Collection • Version Control

Knowledge is dynamic, and your Nodes should reflect that. You can always make changes to your Nodes, even once they are published. This works exactly like creating a Node from scratch.&#x20;

From your [General user overview](/general-user-overview#collection), select the published Node you want to update. As the creator, your Nodes will always open up in edit mode for you (unless you log out and open it via a public share link).

From here, open up the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) by clicking <img src="/files/UoRuQl5zORaACttG8b4P" alt="" data-size="line"> in the top left corner or use the [Information Panel](/general-user-overview/node-workspace/information-panel) <img src="/files/ATNiJYmmOues7Sr0VCS7" alt="Screenshot 2024-02-02 at 00.10.02.jpg" data-size="line"> in the upper right corner to make adjustments to your Node. Now you can [add components](/create-and-publish/create-a-node/add-components), [change component titles](/create-and-publish/create-a-node/organise-access-and-present/component-presentation/renaming-components), and [annotate your Node](/create-and-publish/create-a-node/add-information/add-comments).


# Publish a new version of your Research Node

Edit • Publish • Version Control

## Versionability

Part of the versatility of DeSci Nodes is the ability to update publications, and yet have a continuous track record of versions. For any publications, previous versions are shown and accessible. These versions can be found in the top navigation bar, after 'Home'. The version number will be visible as 'vX', and this is clickable - rolling out a menu of previous versions. Here you can choose the version you would like to explore. As you publish a new version of your work, this number will increase and earlier versions will be available in the version menu.

## Publish the new version

Publishing a new version of your Node works exactly like [publishing for the first time](/create-and-publish/publish).&#x20;


# Delete Components After Publication

Edit • Workspace • Delete

{% hint style="danger" %}
Components **deleted after publishing a Node will remain publicly available** in previous versions of the Node. The new version will not contain the component any more, but viewers can still find them by checking the old Node versions or the original dPID path.
{% endhint %}

You can delete Node components from your [Node Workspace](/general-user-overview/node-workspace) the same way after publication as [**before**](/create-and-publish/create-a-node/delete-before-publication/delete-unpublished-components). *The only difference is that components/files deleted before publication will not be visible, whereas those deleted after will remain online in older versions of your Node.*&#x20;

To delete a component you've previously uploaded to your Node, open up the [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel) panel by clicking the hamburger icon <img src="/files/UoRuQl5zORaACttG8b4P" alt="" data-size="line"> in the top left corner.&#x20;

In the **Drive** tab, hover over the component or folder you wish to delete, and click on the three dots that appear next to the component or folder name.&#x20;

<figure><img src="/files/IiGAU7gMlfO0letpZ3iD" alt="" width="151"><figcaption></figcaption></figure>

From the mini-list that pops up, click on Delete at the bottom. <img src="/files/stbevI1JPt3S35QIy4AU" alt="Screenshot 2024-01-30 at 12.28.35.jpg" data-size="line">

<figure><img src="/files/C3QcT8HHvAV0DP6NPjPG" alt="" width="141"><figcaption></figcaption></figure>

A pop-up window will ask you if you want to delete the component/folder:

<figure><img src="/files/89uwODAZadJruL3cRrdh" alt="" width="375"><figcaption></figcaption></figure>

To confirm this step, hit OK in the pop-up window. *This will delete your component/folder.*&#x20;

NB: It might take a refresh for the change to show.&#x20;

<figure><img src="/files/JQoZbuz8WMhzPHR850Ze" alt=""><figcaption></figcaption></figure>


# Delete Published Node - Cannot

Edit • Workspace • Delete

{% hint style="warning" %}
**Published Nodes can never be deleted.**
{% endhint %}

Makes sure you have all your copyrights etc. in order before publishing. This is super important, as a Node cannot be deleted.

You may delete an Unpublished Node.

We repeat: ***Published*****&#x20;Nodes can NEVER be deleted.**


# Submit for Curation

## Attestations

Attestations are verifiable claims about a publication. The DeSci Nodes ecosystem uses Attestations as a coordination mechanism for collective work on the scientific record. Authors claim Attestations to [invite validation](/create-and-publish/submit-for-curation) and discussion about explicit aspects and attributes of their work, like "Open Data". Community members conduct [atomic validation](/community/community-curation) of Nodes by verifying individual claimed Attestations. Communities use Attestations as [Curation Criteria](/community/community-curation#curation-criteria) for their [Curated Nodes](/community/community-home#curated-nodes) feed.

## Submission in a Bottom-Up Curation System

In [bottom-up community curation](/community/community-curation), submission means that an author claims to meet the explicit curation criteria defined by a community, denominated in a set of Attestations. So instead of sending your research to each community you are interested in being curated by, you claim the set of Attestations that you believe describe the important attributes of your Node. Multiple communities may have overlapping curation criteria, meaning that claiming all Attestations relevant for submission to community A may also lead to automatically submitting to community B.&#x20;

This is a deliberate design choice made for an open, transparent, pluralistic system optimized for scientific discourse around explicit quality criteria. It also allows you as an author to discover communities that align with your values when you realize that the Attestations you deem as important overlap with those representing a community's curation criteria.

Once you submit (claim all required Attestations), your Node will appear on the community's [Radar](/community/community-home#radar-find-nodes-to-validate) where community members can find, review and curate it.

## Submitting via Attestation Tab

After publishing your Node, you can open the Attestation tab in the upper left corner of your Node. From here, you are able to claim any Attestation you deem relevant to your Node. The Attestations are grouped by curating community: All Attestations selected by one community as curation criteria will be listed below this community. Note that since communities' curation criteria may overlap, some Attestations may appear multiple times in this list, under each community that has selected it. From this list, you can Claim individual attestations, or, in order to submit to a community, select Claim all.

As explained [above](#submission-in-a-bottom-up-curation-system), submitting to a community means claiming all Attestations selected as curation criteria by the community. Once submitted, your Node will appear on the community's [Radar](/community/community-home#radar-find-nodes-to-validate) where community members can find, review and curate it.

## Submitting via Community Home

When [visiting a community](/community/community-home), you are able to directly submit your Node for curation via the Submit button in the top right corner. This will open a list of your published Nodes, allowing you to select one or more Nodes to submit for review and curation by the community you are viewing. As explained [above](#submission-in-a-bottom-up-curation-system), submitting to a community means claiming all Attestations selected as curation criteria by the community. Once submitted, your Node will appear on the community's [Radar](/community/community-home#radar-find-nodes-to-validate) where community members can find, review and curate it.


# Share

Share  •  Cite  •  Re-Use

You can share your Nodes with others in four ways:&#x20;

* via [bibliographical citation](#share-via-bibliographical-citation),&#x20;
* [via share link](#share-via-private-share-link),&#x20;
* [via persistent identifier](#share-via-persistent-identifier),&#x20;
* [via content identifier](/create-and-publish/share/content-identifier-cid), and&#x20;
* [via CID](#share-and-re-use-via-cid).

{% hint style="info" %}
Gateways to browse and surface published Research Nodes are coming soon.
{% endhint %}

## Share via Bibliographical Citation

You can share your Nodes document, data or code in your bibliography through classic citation methods and styles. You can generate and copy the citation in a number of different styles, to suit your choice of citation programme.&#x20;

See further information and options under [Cite](/create-and-publish/share/cite).

## \[update] Share via Persistent Identifier

When you publish your Node, it will automatically receive a [decentralized persistent identifier (dPID)](/technical-background/persistent-identifiers-101). You can share your work with others by forwarding this permanent link to your work. Others can cite your work using this PID.&#x20;

dPID feel and function like [simple filepaths](/technical-background/open-state-repository/pid). This makes it super simple to share and granularly cite individual components.&#x20;

You can access your Node's dPID from [General user overview](/general-user-overview#node-drive). Click on **Cite** for whichever component you want to share and simply copy the dPID. The root dPID always looks like this: `dpid.org/{some number}`. This root dPID always points to the latest version of the full Node. But with dPID, you can get specific: Want to share a CSV from Dataset 5 from Version 2 of your Node? Sure. Just select the component in [General user overview](/general-user-overview#node-drive) and copy its dPID -- or type out the dPID yourself. It's always `dpid.org / {Your Node's root PID} / {version number} /{component type}/ {component name}`.&#x20;

[Learn more about the dPID Schema.](/technical-background/open-state-repository/pid)

<figure><img src="/files/HoWrBoFLI1WNkocJQDcU" alt=""><figcaption><p>Grab component dPID from Node Drive</p></figcaption></figure>

## \[update] Share via Share Link

You can share published Nodes with peers by sending them a share-link. You can even direct them to specific components of your Node by sending them a public link to that specific component. Simply click on the ![](/files/caRGjX3YOsGV1PTpFLGL) share icon in the top right corner. This will open a window with public share links to your entire Node as well as each individual component. Copy the one you need and send it to your peers! Sharing research is that easy.

{% hint style="warning" %}
Share Links are traditional URLs. They may be subject to reference rot. **Do not use these links for in-manuscript citations.**
{% endhint %}

<figure><img src="/files/apqxL3kIesSLeSqpZkQF" alt=""><figcaption><p>Grab private share links for each component</p></figcaption></figure>

## \[update] Share and Re-Use via CID

Nodes are optimized for re-usability and interoperability. Each component published with DeSci Nodes has its unique [content identifier (CID)](/technical-background/persistent-identifiers-101#solving-content-drift). This identifier is, as the name says, based on the component's content -- and therefore unique to this component (and its exact duplicates). You can use CIDs to access your components through other applications connected to the IPFS network, like compute over data with [Bacalhau](https://www.bacalhau.org/).

Grab any component's CID via [General user overview](/general-user-overview#node-drive). Navigate to the component of interest and hit <img src="/files/dcVwdc4Fm4xCWm2cdpw2" alt="" data-size="line">. Click on **Copy Link** to save the CID to your clipboard.

<figure><img src="/files/3g1Y96PmmA0I7uTOhhrr" alt=""><figcaption></figcaption></figure>


# Cite

Cite • Publish • Re-Usability

Simply credit others' Nodes. Readers of a Node are able to get a [fine-grained](/technical-background/open-state-repository/pid), formatted citation to any component of that Node. Export formats currently include: BibTex; DataCite; APA; and MLA.

<figure><img src="/files/NZFn0t14mhpLXjFD76QD" alt="" width="133"><figcaption></figcaption></figure>

## Access Formatted Citation

In your [Node Workspace](/general-user-overview/node-workspace), navigate to the component you wish to cite. Access the right hand navigation panel - if it's not open, click on the little <img src="/files/eCuLqAsp6ERcSjbN6KyA" alt="Screenshot 2024-01-19 at 11.29.52.jpg" data-size="line"> icon at the top right hand corner to open it. You will see a tab with **Cite** at the top left of this panel, <img src="/files/4DsGUY0ErwPN3GQEcgep" alt="Screenshot 2024-01-19 at 11.30.09.jpg" data-size="line">. Click here to open up the citation creator.&#x20;

{% file src="/files/8r1deNBHm63wpvuPRFF9" %}

You can select your preferred citation format and simply copy the pre-formatted text snippet by clicking on the <img src="/files/SpXNcLGgIotNwmmFIjia" alt="Screenshot 2024-01-19 at 11.30.09.jpg" data-size="line">. Paste anywhere you need it, including your reference manager.

{% hint style="info" %}
**Support for BibTex citations is available**. Your citations will be formatted and ready to be pasted into your reference list just the way you are already familiar with from other research tools.&#x20;
{% endhint %}

<figure><img src="/files/fKl3fTmrsqmaaegVNGvO" alt=""><figcaption><p>Let DeSci Nodes create granular citations for you</p></figcaption></figure>

In the right hand panel, you are also able to access your component root's [dPID](/technical-background/open-state-repository/pid) path (as a URL in the citation), CID, and see its current size under Properties.&#x20;

<figure><img src="/files/nVuZ17u4utIrLBQNvoFq" alt="" width="274"><figcaption></figcaption></figure>


# Share Link

{% hint style="warning" %}
These pages relate to our Beta version and the features are under redevelopment.
{% endhint %}

## Share via Share Link

You can share published Nodes with peers by sending them a share-link. You can even direct them to specific components of your Node by sending them a public link to that specific component. Simply click on the ![](/files/caRGjX3YOsGV1PTpFLGL) share icon in the top right corner. This will open a window with public share links to your entire Node as well as each individual component. Copy the one you need and send it to your peers! Sharing research is that easy.

{% hint style="warning" %}
Share Links are traditional URLs. They may be subject to reference rot. **Do not use these links for in-manuscript citations.**
{% endhint %}

<figure><img src="/files/v4C6eje0u4OZfsjQXmZk" alt=""><figcaption></figcaption></figure>


# Persistent Identifier (dPID)

{% hint style="warning" %}
These pages relate to our Beta version and the features are under redevelopment.
{% endhint %}

Another product from DeSci Labs is our dPID layer - . DeSci Nodes is built around the dPIDs which are persistent identifiers that stick to the root of the Nodes in a sustainable manner.&#x20;

\
You can get the link to the dPID of the Node, to share but also for your own reference, as follows.

## Share via Persistent Identifier

When you publish your Node, it will automatically receive a [decentralized persistent identifier (dPID)](/technical-background/persistent-identifiers-101). You can share your work with others by forwarding this permanent link to your work. Others can cite your work using this PID.&#x20;

dPID feel and function like [simple filepaths](/technical-background/open-state-repository/pid). This makes it super simple to share and granularly cite individual components.&#x20;

You can access your Node's dPID from [General user overview](/general-user-overview#node-drive). Click on **Cite** for whichever component you want to share and simply copy the dPID. The root dPID always looks like this: `dpid.org/{some number}`. This root dPID always points to the latest version of the full Node. But with dPID, you can get specific: Want to share a CSV from Dataset 5 from Version 2 of your Node? Sure. Just select the component in [General user overview](/general-user-overview#node-drive) and copy its dPID -- or type out the dPID yourself. It's always `dpid.org / {Your Node's root PID} / {version number} /{component type}/ {component name}`.&#x20;

[Learn more about the dPID Schema.](/technical-background/open-state-repository/pid)

<figure><img src="/files/Bc8jvCbMlrJX3P7iD7TU" alt=""><figcaption><p>Grab component dPID from Node Drive</p></figcaption></figure>


# Content Identifier (CID)

{% hint style="warning" %}
These pages relate to our Beta version and the features are under redevelopment.
{% endhint %}

## Share and Re-Use via CID

Nodes are optimized for re-usability and interoperability. Each component published with DeSci Nodes has its unique [content identifier (CID)](/technical-background/persistent-identifiers-101#solving-content-drift). This identifier is, as the name says, based on the component's content -- and therefore unique to this component (and its exact duplicates). You can use CIDs to access your components through other applications connected to the IPFS network, like compute over data with [Bacalhau](https://www.bacalhau.org/).

Grab any component's CID via [General user overview](/general-user-overview#node-drive). Navigate to the component of interest and hit <img src="/files/dcVwdc4Fm4xCWm2cdpw2" alt="" data-size="line">. Click on **Copy Link** to save the CID to your clipboard.

<figure><img src="/files/3g1Y96PmmA0I7uTOhhrr" alt=""><figcaption><p>Grab private share links for each component</p></figcaption></figure>


# Social Media

{% hint style="warning" %}
In progress: we are working on creating an easy link to your social media.
{% endhint %}

We are working on making your Nodes and Node components easy to share on social media.&#x20;

You can already share associated social media posts on your Node through the [URL integration](/create-and-publish/create-a-node/add-components/external-links) function.&#x20;


# Interact & Reuse

Explore • Download • Compute • Annotate • Attest

The 'Explore'  button <img src="/files/gvdibc3IqOtDSIKa1P4C" alt="ExplorerButton.jpg" data-size="line"> in the left side-menu brings you to a page with - the newest/curated - published Nodes.&#x20;

You can browse through Nodes published by others here, checking out their publications, data, code, etc. This includes the ability to [**download data for re-use**](/create-and-publish/interact-and-reuse/download), and, *in the near future*, [**compute scripts**](/create-and-publish/interact-and-reuse/compute)**,** and leave [**comments**](/create-and-publish/interact-and-reuse/support/tbd-comment) or [**attestations**](/create-and-publish/interact-and-reuse/communities) on components of published works.&#x20;

*Nodes aims to be communal in its re-use, feedback and support for and from the global research community. These interact features are part of what inspires Nodes to exist.*&#x20;


# Browse

Find published Nodes (both your own and others) in Explore, <img src="/files/gvdibc3IqOtDSIKa1P4C" alt="ExplorerButton.jpg" data-size="line"> in the left hand navigation panel. Click on the titles you are interested in; to have a look at their contents, [Download](/create-and-publish/interact-and-reuse/download) available data, [Compute](/create-and-publish/interact-and-reuse/compute) codes, etc.&#x20;

{% hint style="warning" %}
*NB as some Nodes are large, they might take a little while to load the first time around. Please be patient!*
{% endhint %}

<figure><img src="/files/JmzJsanqTFTohvcJBDsU" alt=""><figcaption></figcaption></figure>

You can Browse through Nodes Explore in several different ways:&#x20;

* **Browse All:** browse through general Nodes published recently. Either by going through All Nodes chronologically from the most recent, or going through an initial automated selection.&#x20;
* **Browse by** [**Community**](/create-and-publish/interact-and-reuse/communities)**:** go through Nodes selected and curated by different communities. We are currently working with a few front-runner groups to set up these curation opportunities, including the DeSci Foundation, MoonDAO, Longevist and GridCoin.

**Future:**

We are working on implementing a section that incorporates [**Attestations**](/create-and-publish/interact-and-reuse/communities) - a badging and community quality indexing system. A selection of most highly reviewed and/or most popular articles will be visible here.&#x20;

You will also be able to add your own reactions to the articles, if you have an account with us.&#x20;


# Download

Reuse  •  Acknowledge

Downloading data presented on Nodes is relatively straightforward. However, for using large datasets we recommend you use compute options that process the data without having to download it. For these see the [Compute](/create-and-publish/interact-and-reuse/compute) section.&#x20;

To download data, access the Node you are interested in using the data of. Find their data, which should be clearly marked, in the Drive panel on the left ( [Node Drive Panel](/general-user-overview/node-workspace/node-drive-panel)) or in the main viewer window of the Node when opening, as a pinned component ( \[link to pinned components] this is up to those publishing a Node, but a recommended way of presenting Node components).&#x20;

When you have found the data files you want to download, you can either:

1. Go into the triple dot menu on the right of the filename in the **Drive** panel, click on **Download**, or,
2. In the viewer window, click on the **Download** option.

<figure><img src="/files/bbLiI55YjzTqlw2uiMV3" alt=""><figcaption><p>File download options</p></figcaption></figure>

Example video for data download options:

<figure><img src="/files/v0YuZGwe6dHvzJojamBp" alt=""><figcaption></figcaption></figure>

{% hint style="info" %}
When you reuse data published by others, please acknowledge it. You can use several options for this:&#x20;

* Text citations for reference managers, as found here [Cite](/create-and-publish/share/cite)
* Direct links to the dPID of the data, including in comments, as found here [\[TBD\] Comment](/create-and-publish/interact-and-reuse/support/tbd-comment)
  {% endhint %}


# Support

{% hint style="warning" %}
In progress: Support features are under rapid development. You may find features that are not yet mentioned here, or features mentioned here might not be available yet.&#x20;
{% endhint %}

There are several different ways to give feedback and provide support on Nodes created by others:

* [Comment](/create-and-publish/interact-and-reuse/support/tbd-comment) - provide comments on Node components, similar to how you can comment on your own Nodes.&#x20;
* [Attest](/create-and-publish/interact-and-reuse/support/tbd-attest) - verify whether the Node (component) has the quality claimed from a set selection of standards.&#x20;


# \[TBD] Comment

Annotation • Manuscript • Workspace

{% hint style="warning" %}
Comment functions are under development.&#x20;
{% endhint %}

Annotate published manuscripts to suggest additional context or hyperlinks to other work and components.&#x20;

####


# \[TBD] Attest

Attest  •  Verify  •  Badge

{% hint style="warning" %}
Attestation functions are under development.&#x20;
{% endhint %}

You can interact with other Nodes by Attesting to them fulfilling specific criteria, as set out by Attestation Badges. Attestation Badges are either singular ones for important, overarching qualities, e.g. such as FAIR data, or set by Communities to select Nodes for curated presentation.&#x20;

See more on attesting, curation and communities here: [Validate and Curate](/community/community-curation)

<figure><img src="/files/1PBkJWADELl2qR5vup0T" alt=""><figcaption></figcaption></figure>


# Compute

Compute  •  Read  •  Reproduce

{% hint style="warning" %}
**Compute methods are under development.**&#x20;
{% endhint %}

DeSci Nodes will provide three ways in which you can interact with someone else's research by running their computational workflows. Running compute on a Node is key to enhanced reproducibility and we are working hard to make sure you are able to use the tools and workflows you are already used to.&#x20;

Providing the ability to use compute on your Node makes your work interoperable and is part of making your research FAIR.

## Computation Methods

<table data-view="cards"><thead><tr><th></th><th data-hidden data-card-cover data-type="files"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><strong>Node IDE</strong></td><td><a href="/files/ijfTWaBrA2CxOnqVQ3KD">/files/ijfTWaBrA2CxOnqVQ3KD</a></td><td><a href="/pages/CmXIR2JRx58flpIorB7n">/pages/CmXIR2JRx58flpIorB7n</a></td></tr><tr><td><strong>Send data to programs</strong></td><td><a href="/files/wT03K0k59OdLVkAXk3ur">/files/wT03K0k59OdLVkAXk3ur</a></td><td><a href="/pages/xWm2bPJVog5947vJPWhN">/pages/xWm2bPJVog5947vJPWhN</a></td></tr><tr><td><strong>Send programs to data</strong></td><td><a href="/files/8zJppiS3mPDvWEsLWHAI">/files/8zJppiS3mPDvWEsLWHAI</a></td><td><a href="/pages/3Tpp4u83Dm5LJKDxINX5">/pages/3Tpp4u83Dm5LJKDxINX5</a></td></tr></tbody></table>

{% hint style="info" %}
If you are re-using someone's data or code in your own work, make sure to [cite them](/create-and-publish/share/cite).
{% endhint %}


# \[TBD] Node IDE

Learn how to use the Node IDE

{% hint style="warning" %}
**Node IDE Compute is currently disabled.**&#x20;

Compute is in testing phase with trusted users.&#x20;
{% endhint %}

To use in-browser compute, simply click on the code component in your Node. This will activate the Node IDE, which is being built from the popular [open-source VScode platform](https://code.visualstudio.com/).&#x20;

In-browser IDE is ideal for running [Jupyter notebooks](https://docs.jupyter.org/en/latest/). You can learn more about running Jupyter notebooks in the IDE extension of our node [here](https://code.visualstudio.com/docs/datascience/jupyter-notebooks).&#x20;

{% hint style="info" %}
**In-browser Node IDE.**

To run code in the Node IDE, you must ensure that the **source data** is in your Github repo.&#x20;

Alternatively, you can update your Github repo to use your Node's [dPIDs](/create-and-publish/interact-and-reuse/compute/tbd-data-to-compute) as data sources (highly experimental, limited support for data types).&#x20;

IDE compute comes from our cloud servers, and is presently offered for free for testing purposes. Please use respectfully as this feature is under active development.&#x20;
{% endhint %}

<figure><img src="/files/2D8qewmNFk1lJj8BOtpE" alt=""><figcaption><p>Click on the code component in the right menu to access the Node IDE. </p></figcaption></figure>


# \[TBD] Compute to data

Learn how to use edge computing with Nodes

{% hint style="warning" %}
**Compute to Data is currently disabled.**&#x20;

Compute is in testing phase with trusted users.&#x20;
{% endhint %}

With Nodes, you can send programs over to the data. This is known as [edge computing](https://en.wikipedia.org/wiki/Edge_computing) and is especially powerful for data-intensive research. Nodes use [Bacalhau](https://docs.bacalhau.org/), an architecture for fast, cost efficient, and secure computation to run jobs where the data is generated and stored. A major advantage is that you don't need to rewrite your code - you can simply send it over to the data into an arbitrary docker container and WebAssembly (wasm) images as task.

### **Getting started with Edge computing**&#x20;

First step is to install Bacalhau:&#x20;

`$ curl -sL https://get.bacalhau.org/install.sh | bash`

Next step is to [head over to their documentation](https://docs.bacalhau.org/getting-started/installation).&#x20;

### **Using Edge computing with Nodes**&#x20;

Navigate to Node drive, and click on the ![](/files/W8I4dRdnb2dwclVxXu1A) "use" icon. From there, copy the CID of the data object you wish to run your compute job on. You can use this CID in Bacalhau. Follow the [Bacalhau documentation](https://docs.bacalhau.org/getting-started/installation) for edge computing on your data.

\[update video below]

<figure><img src="/files/hjjcCeROFgGC7hVBMAlI" alt=""><figcaption><p>Fetching the CID of the Digital Object for Edge Computing</p></figcaption></figure>


# \[TBD] Data to compute

Import code and data locally into your IDE

{% hint style="warning" %}
**Data to Compute is currently disabled.**&#x20;

Compute is in testing phase with trusted users.&#x20;
{% endhint %}

## Basic dPid Fetch usage (WIP)

You can find the dPid Fetch repository here <https://github.com/desci-labs/desci-fetch>

**Quick start guide**

1. Clone the dpid fetch repository <https://github.com/desci-labs/desci-fetch>
2. Open up the file 'example-run.py', take note of the dpid being passed in, and the mapping of files to variables (WIP - EXAMPLE BEING UPDATED FOR LATEST RESOLVER).
3. Run the example in your IDE using `'python3 example-run.py'`

**Syntax Guide**

`import desci.fetch as dpid`

`with dpid.fetch([('hello.py', 'imported')], dpid="3/v1/1"):`&#x20;

`import imported`

`print(str.upper(imported.hello()) + " world!")`

Given the above example, the parameters passed in are as such;

`dpid.fetch(`<mark style="color:blue;">`[`</mark><mark style="color:purple;">`(`</mark><mark style="color:orange;">`'hello.py'`</mark>`,`` `<mark style="color:yellow;">`'imported'`</mark><mark style="color:purple;">`)`</mark><mark style="color:blue;">`]`</mark>`, dpid="3/v1/1")`

The first parameter is an <mark style="color:blue;">array</mark> of <mark style="color:purple;">tuples</mark> that accepts a <mark style="color:orange;">valid string path to a python file</mark> within the imported code repository, and a <mark style="color:yellow;">variable name</mark> that the imported code should be assigned to, e.g. in this instance, <mark style="color:orange;">'hello.py'</mark> will be assigned to variable <mark style="color:yellow;">'imported'</mark>.

`dpid.fetch([('hello.py', 'imported')], dpid="`<mark style="color:purple;">`3`</mark>`/`<mark style="color:orange;">`v1`</mark>`/`<mark style="color:yellow;">`1`</mark>`")`

The second parameter is a string that accepts a dpid query that points to a code file, as a reminder the syntax for dPIDs is as follows; <mark style="color:purple;">{dpid}</mark>/<mark style="color:orange;">{version}</mark>/<mark style="color:yellow;">{component Index}</mark>

<mark style="color:purple;">dpid</mark>: The identifier assigned for a published node.

<mark style="color:orange;">version</mark>: A number that's zero indexed, or a version with a 'v' prefix. e.g. for the first version specify "0" or "v1", for the second version specify "1" or "v2"

<mark style="color:yellow;">component index</mark>: The index number of the component as specified in the manifest file, which you could access by appending ?raw to the dpid link as such: "<https://beta.dpid.org/2/v1?raw>"


# Communities

Attest  •  Verify  •  Badge

Communities can set up their own environments that support and highlight different aspects of research, according to their own interests. You can become part of a community, or submit your work to them to get it verified according to their choice of attestations.&#x20;

You will be able to check out and subscribe to certain Nodes curation communities, that will present a selection of their favourite nodes, curated according to their own principles.&#x20;

For example: Nodes that use particularly FAIR data, high quality Node publications in a particular field, or Node publications that have particularly interesting new ideas that challenge the status-quo, or a combination of these.&#x20;

These will be shown on the Explore page - giving you the option to browse Explore according to your interests.<br>

More on this is found in the [Validate and Curate](/community/community-curation) section of the guidebook.

<figure><img src="/files/I6FlnNV5KU2ilobLxnu9" alt=""><figcaption><p>Find the Browse by Community tab in the Explore page.</p></figcaption></figure>

Nodes together with communities will develop the opportunity for communities, businesses and individuals to set up their own curated collections of Node publications - similar to a journal or other format.&#x20;

{% embed url="<https://www.loom.com/share/ec63bb8e6af44fa59424f1017d002843?sid=dd8b39e7-637d-4815-b902-7805b1815d13>" %}
Communities and community attestations
{% endembed %}

<figure><img src="/files/1PBkJWADELl2qR5vup0T" alt=""><figcaption><p>Example of a community page</p></figcaption></figure>

{% hint style="info" %}
NB: This part of our remit is under development. Please get in touch with us at <help@desci.com> if you want to know more.
{% endhint %}


# \[TBD] Apply for Comms Curation

{% hint style="warning" %}
In progress: Curation features are under rapid development. You may find features that are not yet mentioned here, or features mentioned here might not be available yet. \
\
Please contact us directly if you are interested in Community Curation.&#x20;
{% endhint %}


# \[TBD] Apply for Comms Attestations

{% hint style="warning" %}
In progress: Curation & Attestation features are under rapid development. You may find features that are not yet mentioned here, or features mentioned here might not be available yet. \
\
Please contact us directly if you are interested in Community Attesting.&#x20;
{% endhint %}


# \[TBD] Become a Comms Member

{% hint style="warning" %}
In progress: Curation & Attestation features are under rapid development. You may find features that are not yet mentioned here, or features mentioned here might not be available yet. \
\
Please contact us directly if you are interested in Community Membership.&#x20;
{% endhint %}


# Community Curation

In bottom-up community curation, curation communities (journals, scientific societies, etc.) define explicit curation criteria, and any piece of work that meets those criteria is automatically curated: There's no final bottleneck decision-maker. This allows for more explicit quality standards, and implies that communities may also benefit from validation signal generated by actors outside of the community: For example, a community may define Open Data as a necessary curation criterion, benefit from the validation services of other communities by curating any Node with the according verified Attestation.

You can [apply to join the Community MVP](< https://airtable.com/appgLeZk1veURa9gS/pagAGXjuFmxrpqCZL/form>) now to create your own curation community on DeSci Nodes.

## View Curated Nodes

To view Nodes curated by communities on DeSci Nodes, check the Browse page and make sure you've selected Browse by Community. You can filter curated Nodes by selecting a community. Once selected, the Feed will update to show only Nodes that have been curated by this community. You will also see a short description and some keywords per community, making it easier to know which Feeds to pay attention to, based on your own interests. You can also view a community's Curated Nodes list from their [Community Home](/community/community-home#curated-nodes).

## Curation Criteria

Each curation community on DeSci Nodes selects a set of Attestations as their curation criteria. This means that any Node claiming this set of Attestations will appear as a submission on the community's [Radar](/community/community-home#radar). From here, members can review the Node and choose to verify the claimed attestations based on the content of the claiming Node. Once every Attestation within the curation criteria has been validated by at least one person, the Node is automatically curated into the Curated Nodes list.

{% hint style="info" %}

#### Current Limitations of the Curation Functionality

In order to keep things simple, communities right now are able to select which Attestations need to be verified in order for a Node to be curated into their feed. Communities are currently not able to define whose verification signal to count, meaning that verifications from actors outside of the community may lead to a Node getting curated by the community. This may be beneficial, as the community gets to benefit from work done by others, but it may also lead to unwanted curations as well as fake verifications with malicious intent. This is a limitation we are aware of and will address in the future releases of this feature.

Communities are currently also not able to create their own Attestations. They will be able to do so very soon with our upcoming Attestation Manager.

#### Visions Around Curation

Our vision for scientific curation is one with the broadest design space possible, in order to allow for communities to create the quality standards and mechanisms that best represent and advance their values and purpose. This means that communities will not only be able to define their own Attestations, but also granularly set curation thresholds for each of them. They will be able to decide how many verifications any attestation needs in order for the Node to be eligible for curation, and set explicit rules for whose verificaiton signal to count in the first place. For some Attestations the public signal may be informative, while for others you may trust only a small set of people's opinions. Communities can also use OR conditions to define the set of Attestations in the curation criteria.
{% endhint %}


# Community Home

Each community on DeSci Nodes has their own Home page. This is where your community gets to define itself, and organize scientific discourse according to its values.

## Community Bio

This section introduces the community at hand, including their topics of interest and mission/purpose. Authors can [**submit their research**](/create-and-publish/submit-for-curation) for curation via the Submit button.

## Curated Nodes

Here is where visitors can browse the Nodes that have been curated and showcased by the community. The quality standards and interests of the community are expressed in the [Curation Criteria](/community/community-curation#curation-criteria). This is a list of Attestations that the community has selected need to be claimed and verified in order for a Node to be curated. Once each Attestation has been verified, the Node gets curated via the [bottom-up curation mechanism](/community/community-curation). Curated Nodes remain in the list unless the Attestations are unclaimed by the author or unverified by a validator.

Below each Node you will see this Node's Engagement Signal, composed of all social activity around Attestations on a Node, including verifications, reactions, and comments. This creates additional information for readers to actively direct their attention beyond just the Node title and authors. Next to this, you will see the Curation Signal, showing you how many verifications have been provided over all Attestations on this Node.

## Radar

Community members can find Nodes submitted for curation on the Radar. Members can [contribute to the scientific discourse by validating these Nodes](/community/validate-and-curate). The Community Radar surfaces all Nodes that claim the set of Attestations selected as [Curation Criteria](/community/community-curation#curation-criteria) by the community. As soon as a Node claims all of these Attestations, it is considered submitted for curation and requires review by the community.&#x20;

### Radar Feed Elements

Since community-based validation may be granular, meaning that members get to specialize in terms of which kind of validation they perform, the Radar Feed shows a diverse range of activities around the submitted Nodes: Submitted Nodes, claimed Attestations, and Comments on claimed Attestations. This way, members looking to contribute via validations can find the right Nodes and/or Attestations to review. Each entry comes with Curation and Engagement Signal, telling you how many verifications, comments, and/or reactions have been left on the corresponding Node or Attestation.

### Curation Signal

The Curation Signal on a Node allows you to understand, at a glance, whether a Node has received sufficient verifications to be curated or if it still needs your attention. Those Nodes and/or Attestations that are missing verifications show up at the top of the feed to make sure the community doesn't miss these. To curate these Nodes into your community's feed, click on the Node/Attestation and [start validating](/community/validate-and-curate).


# Validate and Curate

{% hint style="info" %}
We believe that [a vibrant scientific information sphere values diverse perspectives](https://descilabs.notion.site/Community-Validations-MVP-Q1-2024-032eb18bbfd24c0488096f1299e07c27?pvs=74). All social features in DeSci Nodes are created with this hypothesis in mind. And while we recognize that privacy and anonymity are valuable in some contexts, the first, and most natural iteration of the DeSci Nodes social system is as open and transparent as possible. This means that all users are able to verify, react to, or comment on Attestations claimed by authors, contributing to the meaning-making process around scientific publications. Eventually, authors and/or communities may restrict who gets to verify which Attestations, and/or whether the information generated in the process is made publicly visible.
{% endhint %}

## Attestations Guide Validation

Attestations are verifiable claims about a publication. The DeSci Nodes ecosystem uses Attestations as a coordination mechanism for collective work on the scientific record. Authors claim Attestations to [invite validation](/create-and-publish/submit-for-curation) and discussion about explicit aspects and attributes of their work, like "Open Data". Community members conduct [atomic validation](/community/community-curation) of Nodes by verifying individual claimed Attestations. Communities use Attestations as [Curation Criteria](/community/community-curation#curation-criteria) for their [Curated Nodes](/community/community-home#curated-nodes) feed.

When viewing a Node, you may want to contribute to its validation, either to help the author gain recognition, contribute to your community's [curated feed](/community/community-home#curated-nodes-browse-validated-nodes), or to boost your own reputation as a good actor in the scientific ecosystem. Scientific validation in the DeSci Nodes ecosystem is guided by [attestations claimed by authors](/create-and-publish/create-a-node/add-information/claim-attestations). This means that rather than writing general review reports, reviewers verify individual claims made by authors about their work in the form of Claimed Attestations.

By granularizing the validation activity around a publication, we hope to enable specialization and increased efficiency of the scientific validaiton process.

### Attestation Overview

On every Node's Title Page, you will find a list of all Attestations that the author has claimed on this Node. This can help you guide your attention to the relevant aspects of a Node that need independent validation. For example, unless a Node claims the Open Code Attestation, there is limited use in checking if the Code used to create the key findings reported in the paper is provided as part of the Node. (Though this may be relevant info for you, and you may suggest the Author claims that Attestation if the code is indeed present via a comment).

You can get a full overview of all Attestations claimed on a Node by visiting the Attestations tab. This is also where all corresponding validation activity happens. Note that validation on a Node is scoped to one Attestation at a time, meaning that there's no general comment section or similar general validation mechanism. This allows you to pay attention to the types of Attestations that are within your area of expertise (or interest): If you are a master of programming, you may want to check for Open Code and/or Basic Reproducibility. If you are not, maybe don't bother. Instead, you may want to focus on the Commercializable or Big If True Attestation.

### Verify an Attestation

To verify an Attestation, click on it to open it in Detail View. From here, you can check the explicit verification requirements stated in the description. Based on this, you may need to browse the Node further, either by following any links to components stated in the Attestation comments by the author, or via the [Node Drive](/general-user-overview/node-workspace/node-drive-panel).&#x20;

#### Verify

Before verifying an attestation, make sure you've checked all requirements detailed in the Attestation description are met. Once you've made up your mind, you can verify the Attestation for this Node by clicking the Verify button. This will lead to you being listed as a reviewer for this Node, allowing you to accrue credit as a reviewer.

#### Comment

Leave comments below an Attestation to share your questions and/or feedback around the topic of the Attestation with the Author. Comments are scoped to Attestations in order to prompt discussions around specific aspects of the Node as decided by the author. Down the line, certain Attestations may require reviewers to leave a comment before being able to verify, in order to invite more qualitative signals from reviewers.

Note that authors may claim the AMA Attestation, inviting open commentary on all topics, but may also choose to restrict comments to a certain set of attributes of their Node, represented by claimed Attestations.&#x20;

#### React

You can leave a quick emoji reaction on any claimed Attestation to signal your opinion. Leave a heart to signal support, or a skeptical face to express doubts. Reactions are recorded as engagement, but have nothing to do with the actual verification of an Attestation and, in turn, the curation of a Node.

## Curate a Node

DeSci Nodes use a [bottom-up community curation model](/community/community-curation). This means that rather than an editor deciding which submission to curate (in a top-down fashion), curation happens as an emergent property of the community-organized validation process.&#x20;

In short, once each Attestation selected as [curation criteria](/community/community-curation#curation-criteria) has been verified by at least one reviewer, the Node is automatically curated into the community's feed.&#x20;

[Read more about bottom-up curation here.](/community/community-curation)


# FAQ

FAQ • Help

Browse the most frequently asked questions about DeSci Nodes here.

<table data-view="cards"><thead><tr><th></th><th data-hidden data-card-cover data-type="files"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><strong>FUNDAMENTALS</strong></td><td></td><td><a href="/pages/ZWrdejTvFxmaeXIZWCMq">/pages/ZWrdejTvFxmaeXIZWCMq</a></td></tr><tr><td><strong>USING NODES</strong></td><td></td><td><a href="/pages/9wRGNLfkOwFegxhShMNh">/pages/9wRGNLfkOwFegxhShMNh</a></td></tr><tr><td><strong>NODES &#x26; JOURNALS</strong></td><td></td><td><a href="/pages/bHibnfsbNEfV0BoyMFUP">/pages/bHibnfsbNEfV0BoyMFUP</a></td></tr><tr><td><strong>FAIR</strong></td><td></td><td><a href="/pages/DhZTAXo9z8dAw23JcX2X">/pages/DhZTAXo9z8dAw23JcX2X</a></td></tr><tr><td><strong>WHY USE NODES</strong></td><td></td><td><a href="/pages/YeGhAJ42QX4Vmo72iaSN">/pages/YeGhAJ42QX4Vmo72iaSN</a></td></tr><tr><td><strong>YOUR IDENTITY</strong></td><td></td><td><a href="/pages/svkybOuTOvcKkWgvGNvq">/pages/svkybOuTOvcKkWgvGNvq</a></td></tr><tr><td><strong>METRICS, CITATIONS, PID</strong></td><td></td><td><a href="/pages/VSundFYTBuCtoCM9bhOg">/pages/VSundFYTBuCtoCM9bhOg</a></td></tr><tr><td><strong>GOVERNANCE</strong></td><td></td><td><a href="/pages/Nf2tCTbIuDLZTiT3J7Yf">/pages/Nf2tCTbIuDLZTiT3J7Yf</a></td></tr></tbody></table>


# Fundamentals

Definitions • Concepts • Review

### What is a DeSci Node?

<details>

<summary>A Node is an interoperable research object stored on an open state repository.</summary>

Nodes have permanent identifiers that protect against [link rot](https://en.wikipedia.org/wiki/Link_rot) and [content drift](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167475), and are [compute-enabled](/technical-background/open-state-repository/methods). You can conveniently [import data into your workflow](/technical-background/open-state-repository/methods). In the future, it will also be possible to send [programs over to the data](/technical-background/open-state-repository/methods).&#x20;

Nodes are a next-generation open-science solution that enables you to immediately publish every relevant aspect of your research project in one convenient place, share it with others, get credit and citations for it and interact with Node content directly (e.g. computation, citations as function calls). &#x20;

Nodes make it easy for researchers to establish and follow best scientific practices. Nodes are [FAIR](https://www.go-fair.org/fair-principles/)-enabling by design, helping you to make every relevant part of your research findable, accessible, interoperable, and reusable. This unleashes the full utility of your work to others and raises the bar by making it easier for your future self and others to trace your steps and to check the reproducibility of your work.&#x20;

Nodes also help you to communicate your research in novel ways. For example, you can embed code and data into your figures to allow others to reproduce your results easily and to re-use your artifacts.&#x20;

Nodes are capable of storing massive amounts of scientific data, making it globally accessible, and allowing you and others to perform compute functions on those data, directly where the data lives. Instead of having to rely on your own or your institutions computational facilities, Nodes enable you to conduct analyses and reproducibility runs without the need to download data or to move it around (data egress/ingress) – a feature that gets increasingly important with data size, and also offers environmental benefits. For small data objects, Nodes also enable “citations as function calls”, enabling you to pull data or code from any Node into your local environment easily and at a high level of granularity (e.g. pull a specific code file or a specific dataset file).&#x20;

Nodes secures your data against content drift with cryptographically-secured identifiers, and provides protection against link rot by storing multiple redundant copies across a distributed network of storage and compute providers, all while enabling granular version control.

By using Nodes, you help to contribute to a digital future of the scientific record that will be open and accessible to all humans and machines. Most people have only very limited access to the scientific record at the moment, although science is an essential public good that is largely financed by tax-payer money. By removing content paywalls and adding machine-readable actionable resolution, Nodes will enable machines to “make sense” of science in new ways, enabling AIs to navigate and make sense of the scientific record

</details>

### What is a research object?

<details>

<summary>A research object is a digital collection of information about a research project “under one roof”.</summary>

This could be different versions of the manuscript, supplementary information, data, videos, computational pipelines, images, interviews, or any other type of data that researchers find useful and that they want to store and work with.&#x20;

Traditional publications of manuscripts are static. In contrast, a research object is dynamic and evolves over time, allowing users to add and to update content. It also allows viewers to access all of that content and to browse through its history.&#x20;

The [research object framework](https://en.wikipedia.org/wiki/Research_Object) provides a mechanism to associate related resources about a scientific investigation so that they can be shared using a single identifier. As such, research objects are an advanced form of enhanced scientific publication.

</details>

### What is an Open State repository?

<details>

<summary>An open state repository is a novel type of repository that relies on distributed, content-addressed, machine-actionable storage and indexing systems.</summary>

It is “open state” because access to the information it contains cannot be revoked by any central entity. The Open State repository's architecture has been designed as a response to the call to action set forth by[ Leiden declaration](https://www.fdo2022.org/programme/leiden-declaration-fdo), of which DeSci Labs is a signatory. [Learn how it works](/technical-background/open-state-repository).&#x20;

</details>

### Are Nodes peer-reviewed?

<details>

<summary>Nodes may or may not contain peer-reviewed content.</summary>

It is the Node creator’s responsibility to indicate the peer-reviewed status of any manuscripts contained within a Node via inclusion of the publisher’s DOI.&#x20;

**Readers should be aware that Nodes may contain unfinished or preliminary work, contain errors or misleading claims, or contain information that has not yet been accepted or endorsed in any way by the scientific community. We urge journalists and other individuals who report on research to the general public to consider this when discussing work that appears on Nodes.**

Nodes currently do not have systematic content moderation, content selection, or “peer review” processes in place yet. The responsibility for the shared content lies entirely with the authors. Please see our Terms of Service for additional information.&#x20;

To provide additional context: Before formal publication in a scholarly journal, scientific articles are traditionally certified by “peer review.” In this process, the journal’s editors take advice from various experts—called “referees”—who have assessed the paper and may identify weaknesses in its assumptions, methods, and conclusions. Typically, a journal will only publish an article once the editors are satisfied that the authors have addressed referees’ concerns and that the data presented support the conclusions drawn in the paper.

Because this process can be lengthy, authors often make their manuscripts available as “preprints” before certification by peer review, allowing other scientists to see, discuss, and comment on the findings immediately. We encourage scientists to use Nodes for this purpose.&#x20;

Furthermore, traditional academic journals typically do not have the infrastructure to store, evaluate, and share anything else than a manuscript. As a result, important parts of the scientific process such as data, images, videos, voice recording, or code are typically not evaluated during peer-review. Worse, these integral parts of the scientific record are often not accessible at all. Nodes provide a convenient solution to this problem. By doing so, Nodes provide additional information and resources that enhance and complement the existing scientific journal system. For example, authors can post their “pre-print” on Nodes and archive their data and code in the process. Once their manuscript is submitted to a journal, editors and referees can access the additional information available in a Node to guide their feedback to authors during the peer-review process, creating additional transparency and increasing the odds that authors will get their work accepted in the scientific journal of their choice.&#x20;

The dynamic nature of research objects also implies that they serve a different function than traditional journal publications: Research objects can grow and evolve over time, providing a track record of the entire research project from the first ideas, intermediary products such as data, code, preliminary drafts of the main manuscript, a version of the manuscript that is equivalent in content to the published version, as well as updates and additions that occur after the main manuscript has been published. In this sense, Nodes also serves as a [Green Open Access](https://en.wikipedia.org/wiki/Open_access) solution for authors to deposit their peer-reviewed work.&#x20;

</details>

### Are submissions reviewed before posting?

<details>

<summary>No. Nodes are, however, randomly reviewed for violations of our Terms of Service. </summary>

Posting copy-right protected, privacy violating, fraudulent, harmful, obscene, or non-scientific content is prohibited. DeSci Labs maintains the right to filter out inappropriate content that is in violation of our Terms of Service. Filtering will delete content from DeSci Labs’ servers and affect the findability of inappropriate content. Please see our Terms of Service for additional information.

</details>


# Using Nodes

Charges • Computation • Guidelines

### Is there a charge for Nodes?

<details>

<summary>There is no charge associated with publishing or accessing a Node.</summary>

The read functions of Nodes and access to their content are architecturally designed to always remain free for humans and machines.&#x20;

There may be charges in the future associated with large data preservation and premium features such as multiplayer node creation and computing functions from DeSci Labs Node gateway. Other gateways are free to implement their own policies.&#x20;

</details>

### What type of content can be posted on Nodes?

<details>

<summary>Nodes allows authors to post manuscripts, data, code or other research artifacts.</summary>

It is not allowed to post illegal or non-scientific content. For additional information, please read the Terms of Service.&#x20;

</details>

### What computational methods are provided?

<details>

<summary>We provide three types of computational methods to interact with data contained in a Node.</summary>

Note that each of these methods are under active development and experimental at this stage. Learn more about [methods](/technical-background/open-state-repository/methods).&#x20;

* Send compute to data: Send a containerized version of your program over to where the data lives and return the results.&#x20;
* Send data to compute: Import Node components such as datasets and code into your local computer or high performance computing environment directly with Node PIDs.
* Nodes in-browser compute: A web-based integrated development environment to run compute jobs directly in a convenient web-browser interface.&#x20;

</details>

### Can I post manuscripts that are not in English?

<details>

<summary>We recommend you publish in english. </summary>

We strongly encourage all users to post content on DeSci Lab's Node Gateway in standard academic English. You are free to publish non-English manuscripts and content, but please be aware that this may limit the accessibility and usefulness of your work.

</details>

### How long does it take for posted content to appear on Nodes?

<details>

<summary>Clicking the “publish” button in the applications means that the content is made available to be viewed and read by the public. </summary>

Any content added after a node has been published will not be available publicly until the new version of the node is published.&#x20;

</details>

### Who holds the copyrights for materials posted on Nodes?

<details>

<summary>Nodes allow authors to choose from a diverse set of <a href="https://creativecommons.org/licenses/?lang=en">Creative Commons</a> licenses to publish their work.</summary>

For code components, we automatically pull the software licensing agreement from your Github repository.

Under these licenses, authors retain the copyright of their work, while allowing others to access and make use of it (at least non-commercially). A Creative Commons license has many advantages, including the possibility to publish articles elsewhere, improving the reproducibility of scientific research, and making valuable scientific products such as data and code reusable by other scientists.&#x20;

</details>

### Can I remove materials that have already been published on Nodes?

<details>

<summary>It’s complicated. For now, you should act as though the answer is "no"</summary>

Once the content is published, the data is mirrored on a distributed repository over three continents and five countries.&#x20;

</details>

### Can I revise or update materials posted on Nodes?

<details>

<summary>Yes. It's one of the core features.</summary>

One of the big advantages of using Nodes is that they support version control at the level of the data model and persistent identifier. Publishing new versions of a document will not overwrite the old version. The revisions or additions will simply be added to the research object. Even older versions of a paper can be specifically addressed and cited. Through this functionality, users can also browse through the version history of any material that is part of a Node and transparently track its evolution.&#x20;

</details>

### Can I post medical research on Nodes?

<details>

<summary>Yes, as long as you as the author ensure that the work you are posting complies with all relevant legal and ethical guidelines.</summary>

Note that the responsibility for compliance with legal and ethical guidelines lies entirely with the authors. For additional information, please refer to our Terms of Service and read “Can I post human subject data on Nodes”.

</details>

### Can I post a hypothesis or study protocol on Nodes?

<details>

<summary>Yes.</summary>

We offer support for [pre-registered reports](https://en.wikipedia.org/wiki/Preregistration_\(science\)) and [pre-registered analysis plans](https://en.wikipedia.org/wiki/Preregistration_\(science\)). We encourage authors to treat their Nodes as dynamic objects that evolve with time.

</details>

### Can I comment on content posted on Nodes?

<details>

<summary>Not yet. </summary>

While we plan to implement a social layer in the future, we do not support commenting within individual Nodes at this time unless you are the Node's author.&#x20;

</details>

### Can I post human subject data on Nodes?

<details>

<summary>Data archived in Nodes are publicly available.</summary>

Any human subject’s data must be properly anonymized and prepared under applicable legal and ethical guidelines to be posted on Nodes. **Be aware that authors are fully responsible for doing so**. Please see our Terms of Service for additional information.&#x20;

[Dryad](https://datadryad.org/docs/HumanSubjectsData.pdf), the [NIH](https://grants.nih.gov/policy/humansubjects/research.htm), and the [European Commission](https://ec.europa.eu/info/funding-tenders/opportunities/docs/2021-2027/horizon/guidance/ethics-and-data-protection_he_en.pdf) provide highly recommended guidelines on sharing human subject data. If your study has made use of human subject data, consider creating a restricted access data component. Restricted access data components could either contain the path to accessing this data as well the metadata in accordance with the [FAIR principles](https://www.go-fair.org/fair-principles/). Alternatively, consider sharing your data in encrypted form, containing clear and complete instructions about how and under which circumstances users can obtain a decryption key. Note that encrypted data also need to comply fully with all applicable legal and ethical guidelines.&#x20;

</details>

### How can people find my Node?

<details>

<summary>The best way to ensure the discoverability of your Node is to include a standard academic manuscript that will be indexed by Google Scholar. </summary>

To ensure Google Scholar indexes your manuscript, ensure that it contains:&#x20;

* The full text of your paper needs to be a a PDF file that ends with ".pdf",
* The title of the paper appears in a large font on top of the first page,
* The authors of the paper are listed right below the title on a separate line,&#x20;
* Bibliography section titled, e.g., "References" or "Bibliography" at the end.

Google Scholar will then ensure that your Node is findable by others and track citations of your Nodes. In the future, Nodes will also be indexed by other indexing services.

Furthermore, we plan to develop the following:&#x20;

* Node-to-Preprint platform: You can implant a QR code with a clickable PID link directly into your manuscript that securely redirects to your Node. You can then freely publish or update the current version of your manuscript on the preprint platform that matters to you community. This feature is under active development. &#x20;
* Node-to-Publisher platform: We are in discussion with members of the publishing community to allow PID link / HTML widget embedding following the CrossMark model. Similar to funders, incentives are aligned, but we expect that it will take some time.
* DeSci Gateways: Gateways will surface curated Nodes and handle permissions for users on behalf of organisations. &#x20;

</details>

### Can I include images of individuals in my Node?

<details>

<summary>Unless you have specific permission from the person(s) being displayed, you cannot share images of individuals publicly.</summary>

The responsibility for the shared content lies entirely with the authors. Please see our Terms of Service for additional information.&#x20;

</details>

### Can I publish a Node when I am not an original author of the work?

<details>

<summary>Yes, you can. But please make sure you are not violating any license agreements.</summary>

When you publish a Node, you can declare that you are not one of the original authors. However, it is important to check the license agreements for all components you are publishing and make sure these are permissive enough for a re-publication.

Best practice for publishing a Node that is not your original work is to notify the original authors about this. We are currently developing a workflow for authors to claim authorship over Nodes that have been created on their behalf.

</details>


# Nodes and Journals

Impact factor • Preprint policy • Linking postprints

### Do Nodes have an impact factor?

<details>

<summary>No. Nodes are infrastructure, not a scientific journal.</summary>

Authors can use Nodes as a repository and archival solution for their research and publish their manuscripts in the scientific journals that are most relevant for them.&#x20;

</details>

### Which journals allow posting of preprints and research materials prior to submission?

<details>

<summary>Most scientific journals will consider manuscripts that were posted on Nodes or preprint servers or open repositories prior to submission.</summary>

A list of journal policies can be found on [Wikipedia](https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy), as maintained by individual publishers, and [SHERPA/RoMEO](http://www.sherpa.ac.uk/romeo/journalbrowse.php?la=en\&fIDnum=%7C\&mode=simple). Authors should consult these lists and other sources of information before posting on Nodes.&#x20;

</details>

### Can the content contained in my Nodes also be posted elsewhere?

<details>

<summary>Yes, provided that the licensing agreements of the places you previously posted or published your content on (or plan to do so) allow this.</summary>

The responsibility for the shared content lies entirely with the authors. Please see our Terms of Service for additional information.

</details>

### Can I post an article on Nodes that I have submitted to a journal?

<details>

<summary>Yes. The only thing to note is whether posting your work on an open-state repository like Nodes is accepted by the respective publisher.</summary>

Certain journals require you to inform the editor about this. A list of journal policies can be found on [Wikipedia](https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy), as maintained by individual publishers, and [SHERPA/RoMEO](http://www.sherpa.ac.uk/romeo/journalbrowse.php?la=en\&fIDnum=%7C\&mode=simple). Make sure to check first. The responsibility for the shared content lies entirely with the authors. Please see our Terms of Service for additional information.

</details>

### How can my materials on Nodes be linked to the journal version when it is published?

<details>

<summary>We are working on this.</summary>

In the near future, content from a Node can be linked to the published version of the manuscript via the Node’s PID embedded into the PDF version of the manuscript and the publisher’s HTML, provided the publisher agrees. Authors can already post the [green open access](https://en.wikipedia.org/wiki/Open_access) version of their manuscript on Nodes, which will be linked to the publisher’s server via its DOI.

</details>


# FAIR

Community • Funders • Self

### What is FAIR&#x20;

<details>

<summary>FAIR stands for Findability, Accessible, Interoperable, and Reusable research outputs.</summary>

You can read more about FAIR [here](https://www.go-fair.org/fair-principles/). FAIR research outputs are an important building block of a healthy, future-proof scientific record. At the moment, FAIR research outputs are still the exception rather than the rule in most fields of science. This is partially due to infrastructural limitations, but also due to current scientific practices and incentives. The lack of FAIR scientific data creates [enormous costs and slows down scientific progress](https://op.europa.eu/en/publication-detail/-/publication/d375368c-1a0a-11e9-8d04-01aa75ed71a1).&#x20;

Nodes are being developed to be FAIR-enabling by design, making it easy for authors to create FAIR digital research objects.&#x20;

</details>

### What makes Nodes a FAIR-enabling technology?

<details>

<summary>Nodes provide persistent identifiers (PIDs), data, metadata, and methods for every digital object contained in a Node. </summary>

Node PIDs are based on [cryptographic hash functions](https://en.wikipedia.org/wiki/Cryptographic_hash_function) that protect data integrity and that provide consistent resolution to human- and machine-actionable content.&#x20;

</details>

### Will my Node automatically be FAIR?

<details>

<summary>No</summary>

It is the responsibility of the Node author(s) to provide quality metadata, ideally based on machine-actionable ontologies that are widely used and agreed upon in the respective scientific community. While DeSci Labs is expanding R\&D efforts [to leverage embeddings and LMM's to generate machine-actionable metadata for you](/technical-background/open-state-repository/metadata), there remains significant hurdles to overcome, and while extremely promising, these methods should be considered experimental for the time being. &#x20;

</details>


# Benefits of using Nodes

Community • Funders • Self

### How does posting my research on Nodes benefit the scientific community?

<details>

<summary><a href="https://www.cos.io/">Open science</a>, reproducible research, and <a href="https://www.go-fair.org/">FAIR digital research objects</a> serve the scientific community...</summary>

... and the world at large by contributing to an accessible, transparent and trustworthy scientific record. The implementation of FAIR principles also has the potential for [substantial time and cost savings](https://op.europa.eu/s/xzUo), and to accelerate scientific research. Our goal is to make it easy for your community to re-use your work by providing powerful computational methods to operate with your code, data, and other resources.&#x20;

</details>

### Will my funders or employer care if I use Nodes?

<details>

<summary>Funders care about FAIR data (e.g. <a href="https://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/data-management_en.htm">European Commission</a>) and open science (e.g. <a href="https://www.whitehouse.gov/wp-content/uploads/2022/08/08-2022-OSTP-Public-Access-Memo.pdf">White House OSTP Memo</a>).</summary>

While Nodes is still in early stage development,the incentives are aligned. Nodes are built to make it easy and rewarding for scientists to follow open science and FAIR mandates.

</details>

### How does posting my work on Nodes benefit me?

<details>

<summary>Nodes are your personal research archive. You and your colleagues can access your code, data, manuscripts etc., all in one place.</summary>

Nodes also help you to comply with your data management plan and funding mandates for open science (e.g. the [White House OSTP Memo](https://www.whitehouse.gov/wp-content/uploads/2022/08/08-2022-OSTP-Public-Access-Memo.pdf)). Preprint platforms took off because they created incentive alignment by accelerating the pace of citation accrual. Our hypothesis is that by enabling FAIR digital research objects combined with powerful computational methods, researchers will accrue citations sooner and at a higher rate because of ease of re-useability. Last but not least, we encourage you to use Nodes in support of journal article submissions. You can earn trust from journal editors and referees by making your data, code, and other research artifacts accessible from the beginning, helping you to publish your work in the journals that matter most to you.&#x20;

</details>


# Your identity

Securing my identity • Anonymity • Loss of key

### How can I secure my identity?

<details>

<summary>You will soon be able to verify your identity</summary>

We are implementing an identity verification procedure that relies on [ORCID](https://orcid.org/), verification of your institutional email, and request of a community-bound identity verification token.&#x20;

Publishing a Node requires you to employ a cryptographic key that we will link to your ORCID profile. As the controller of the key, only you can publish updates to the Node you created. There are a variety of wallet providers to choose from. We recommend [Torus](https://tor.us/).&#x20;

We take researcher identity security seriously and it is presently an unsolved problem. While we are a member organization of [ORCID](https://orcid.org/) and are aware of steps taken to improve their security model, work remains to be done in this regard. Promising new approaches include [verifiable credentials](https://en.wikipedia.org/wiki/Verifiable_credentials) and community-bound access tokens. We are working on implementing both.&#x20;

</details>

### Will I need to verify my identity to publish a Node?

<details>

<summary>It won't be mandatory for the beta.</summary>

There are inevitable tradeoffs between security and accessibility. We currently opt for accessibility and will adjust our policy as we scale.&#x20;

</details>

### Can I publish my work anonymously?

<details>

<summary>Don't do it. It's too early. </summary>

In the future, you will be able to switch your identity to anonymous with [ZK-proofs](https://en.wikipedia.org/wiki/Zero-knowledge_proof). ZK-proofs will allow you to prove you have certain credentials without revealing your identity. For this function, real identity is a requisite. This combines the best of both world, while minimising the threats of identity spoofing and trolls.&#x20;

</details>

### What if I lose access to my key?

<details>

<summary>We can rotate your Node access tokens to another key on the dPID registry.</summary>

This will require an identity verification procedure and is quite cumbersome for the time being. Our custodianship is a temporary measure as we implement new solutions that will enable your community or institution to act as your social recovery mechanism.&#x20;

</details>


# Metrics, citations and PIDs

PIDs • Citing Nodes • Citation fragmentation

### What are persistent identifiers (PIDs) and dPIDs?

<details>

<summary>A <a href="https://en.wikipedia.org/wiki/Persistent_identifier">persistent identifier</a> (PID) is a long-lasting reference to a document, file, web page, or other object.</summary>

PIDs are a core requirement for [FAIR](https://www.go-fair.org/fair-principles/) digital research objects and for the integrity of the scientific record. DeSci Labs built the decentralized PID ([dPID](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/open-state-repository)) system, which creates unique, persistent identifiers for each Node and each component of a Node, enabling version and history control, as well as very fine-grained citations and new methods to interact with research objects.

Unfortunately, commonly used [URLs](https://en.wikipedia.org/wiki/URL) and [URIs](https://en.wikipedia.org/wiki/Uniform_Resource_Identifier) do not fulfill this requirement. They point to a server where content is stored. But if that content changes, this is typically not reflected in the URL or URI, leading to [content drift](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167475). Furthermore, if a file is moved to a different location or deleted, URLs and URIs, leading to [link rot](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115253). The [DOI system](https://en.wikipedia.org/wiki/Digital_object_identifier) has been established to deal with this fundamental problem of the current Internet infrastructure. However, [DOIs resolve inconsistently](https://arxiv.org/abs/2004.03011) and they require manual updates from publishers, making this system brittle, expensive and error-prone. [Learn more about the history and problems with the DOI system](/technical-background/persistent-identifiers-101).&#x20;

Nodes solve this problem by using [content addressed storage](https://en.wikipedia.org/wiki/Content-addressable_storage), based on the [IPFS protocol](https://ipfs.tech/). Content addressed storage secures content against content drift. Using a cryptographic hash function, each uploaded component of Node gets a unique hash that allows users to verify the content. DeSci Labs has built the [dPID system](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/open-state-repository) on top of that, which allows creating short, human-friendly URLs that address each Node and each component within a Node, enabling version and history control. Learn more about identifiers in our [documentation](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/technical-and-product-explainers/about-dpid).

</details>

### Do Nodes provide metrics?

<details>

<summary>Nodes that contain a standard scientific manuscript will be indexed by Google Scholar.</summary>

To ensure that happens, your node needs at least on document with the following properties:&#x20;

* The full text of your paper needs to be a a PDF file that ends with ".pdf",
* The title of the paper appears in a large font on top of the first page,
* The authors of the paper are listed right below the title on a separate line,&#x20;
* The bibliography section titled, e.g., "References" or "Bibliography" at the end.

Google Scholar will then ensure that your DeSci Node is findable by others and track citations of your Nodes.In the future, Nodes will also be indexed by other services and scientific databases, but this will take time.&#x20;

DeSci Labs is also planning to offer a variety of complementary attestations for research objects, such as badges similar to the [OSF](https://www.cos.io/initiatives/badges) and [ACM](https://www.acm.org/publications/policies/artifact-review-and-badging-current) around the availability of code, data, and supplementary materials.&#x20;

</details>

### Will Nodes lead to citation fragmentation?

<details>

<summary>Google and other indexers of science resolve fragmentation via disambiguation systems.</summary>

Google Scholar also offers users the option to combine various entries of the same content into one entry to consolidate citation counts. We plan to interface with all major indexers and provide open API endpoints to make it as seamless as possible for their IT teams to index your research.&#x20;

</details>

### Can I get a DOI for my Node?

<details>

<summary>Not yet.</summary>

Our goal is to make our Node PID system backward compatible with the DOI system, but this will take time. Note that DOIs are not [persistent identifiers](https://doi.org/10.1007/978-3-030-54956-5_8). Learn more about DOIs in our [documentation](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/technical-and-product-explainers/about-dpid).&#x20;

</details>

### How should Nodes be cited?&#x20;

<details>

<summary>Any component of a Node can be cited, just like a regular article.</summary>

Every node component, such as manuscript, data, code, and more, have a “cite” button. You can access this button from the Node Drive. You can then copy the citation in the format of your choice. We support APA, Bibtex and more. Learn more about citing nodes in [our documentation](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/quick-start/citing-a-node/~/comments/QAXwyknEOnzRA7DjxuC5?node=ec09665de67b4ab280b4d511f93af011).&#x20;

</details>


# Governance

Governance • Open Source • Storage

**How will the Open State repository be governed?**&#x20;

<details>

<summary>In our design, all research objects are controlled by the individuals who published them. Edits and deletions are solely managed by the works' original authors.</summary>

There are certain things like protocol updates, platform development, and data migrations which currently are controlled and managed by DeSci Labs and could affect future data availability and author eligibility into scientometric calculations used by funders.\
\
We at DeSci Labs believe no single entity should be solely in charge of long-term data availability and grant eligibility metrics. We believe with proper technical design, we can eliminate almost all forms of "vendor lock-in" or similar problems. We pledge to minimize if not completely eliminate our ability to maintain influence over the protocol in the long term. If any influence over the protocol, its data or users continues to be maintained, our plan is to transfer control and governance over any influential mechanisms to the [DeSci Foundation](https://descifoundation.org/), a non-profit in Geneva, Switzerland. \
\
The DeSci Foundation's mission is to make science better using emerging technologies, and thus should represent all major stakeholders in the scientific record, with a particular emphasis on metascientists to guide the protocol forward. Our goal is to create credible neutrality for the protocol.

</details>

#### Is the software Open Source?

<details>

<summary>Yes! We believe Open Science is built on Open Source. You can find our releases <a href="https://github.com/desci-labs">in our GitHub</a></summary>

</details>

**Where is data being stored?**

<details>

<summary>Prior to publication, your data is privately stored on DeSci Labs cloud infrastructure, which is hosted by various cloud providers depending on market conditions such as storage costs.</summary>

Once published, your [data](/find-help/faq/fair) and [metadata](/technical-background/open-state-repository/metadata) are transferred and stored in the [open state repository](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/open-state-repository). Our goal is to provide the most secure, open, long term, transparent, and platform-independent storage solution for research outputs possible.&#x20;

Traditional repository architecture binds the perennity of the data and metadata to the sustainability and continued existence of the operator and its legal entity.&#x20;

In contrast, we are building a so-called open state repository which relies on open, peer-to-peer storage and decentralized indexing of your research object. Technically, Nodes are [IPLD](https://ipld.io/docs/)-compliant [JSON-LD](https://json-ld.org/) structures that form a [Merkle DAG](https://docs.ipfs.tech/concepts/merkle-dag/). We index the root hash of this Merkle object on a decentralized registry that provides a version-invariant PID and ties versioning rights to the creator’s digital signature.&#x20;

Nodes store all content on this open state repository powered by the [IPFS network](https://docs.ipfs.tech/) and its associated [incentive-layer](https://docs.filecoin.io/reference/reference/overview/), with at least 5 archival copies across 3 continents plus 1 “hot” copy, provided by several different storage providers which are incentivized to preserve an unaltered copy of your data and operate competitively on an open market for storage deals. This data redundancy greatly reduces the chance of valuable data getting lost and creates independence from specific storage providers.

Our vision involves decoupling the “data layer” from the “application layer” - Nodes is an interface to access this open state repository architecture. As such, Nodes inherits the fault tolerance of the underlying networks on which it is built. While Nodes and their PIDs are completely secured against content drift, malicious or unintentional, they are only immune to link rot to the extent that its underlying networks continue to operate.&#x20;

In accordance with the FAIR principles, we treat metadata with redundancy of caution by storing an additional backup copy. All metadata is licensed under [CC0](https://creativecommons.org/share-your-work/public-domain/cc0/)

You can learn more about the Open State repository [here](https://app.gitbook.com/o/fEWLZQfJ8rfwwOXOWc6z/s/MYxRLCpbB6u9NiTwuU16/explainers/open-state-repository/~/comments/QAXwyknEOnzRA7DjxuC5).&#x20;

</details>


# Community Support

Support • Feature Requests • Community

For assistance, contact us via email at <help@desci.com>.

If you wish to join our Discord community and ask a question, use this [invite link](https://discord.gg/A5P9fgB5Cf) and [create your profile](https://support.discord.com/hc/en-us/articles/360033931551-Getting-Started).

{% hint style="info" %}
If you find any bugs in the software, please submit these via the <img src="/files/SYbw4Syv3TFQdwUL8XBw" alt="" data-size="original"> button in the lower right corner of the app.
{% endhint %}


# Feedback & Contact

Support • Bugs • Feedback

## Report Bugs or Submit Feedback

This is a first version: DeSci Nodes is currently still under heavy development. This means two things.

1. We would love and appreciate your feedback;
2. You may experience bugs in the software.

### Feedback

DeSci Nodes is being built for researchers. That's why your voice really matters. Please help us build the best scientific publishing software out there by sharing your feedback with us. If you run into any issues, don't know where to find something, or are missing a key feature, please do let us know via the <img src="/files/SYbw4Syv3TFQdwUL8XBw" alt="" data-size="original"> button in the bottom right corner. If there's no specific bug you are describing, feel free to ignore the pre-filled format and just let us know what you think.

We will ask for your contact details so that we can inform you that we received your feedback, the status of handling it, and can get back to you in case there's any questions about it.

<figure><img src="/files/87S31zcna4W9OawpsO2N" alt=""><figcaption></figcaption></figure>

### Bug Reports

If you do happen to run into bugs, please make use of the <img src="/files/SYbw4Syv3TFQdwUL8XBw" alt="" data-size="original"> button in the bottom right corner.&#x20;

<img src="/files/SYbw4Syv3TFQdwUL8XBw" alt="" data-size="original"> automatically takes a screenshot for you to help our dev team understand which part of the app you were in while you experienced the bug. Please follow the pre-filled format of the bug report.&#x20;

**Steps to reproduce:** Please describe as precisely as you can, what exactly you were doing right before the bug occured.

**Actual result:** What happened after you did what you did?

**Expected result:** What should have happenened instead?

We will ask you for your contact info so we can get back to you if there are any questions about your feedback.

## Request Hands-On Support

For any larger issues, or in case something really unexpected happened, please do not hesitate to contact our support team via the dedicated [Support Channel](https://discord.gg/PagG3CnBxq) on our [Discord Community](https://discord.gg/H83eVwkxK6).

If you do not use Discord, feel free to send us and email at <help@desci.com>. Please try to describe your issue in as much detail as possible, and provide screenshots if helpful.


# Persistent Identifiers 101

Persistent Identifiers • DOI • dPID

## **Persistent Identifiers**

A [Persistent Identifier](https://en.wikipedia.org/wiki/Persistent_identifier) or PID, is a unique identifier for a specific object - much like a driver's license or social security number. These identifiers act as a long-lasting reference to an object. The vast majority of entries into the scientific record are accompanied by a PID, typically a Digital Object Identifier ([DOI](https://en.wikipedia.org/wiki/Digital_object_identifier)). A DOI is a PID that resolves to the page of the publisher that contains the specific resource in question. &#x20;

### Brief history of the DOI system

The [history of the DOI system is fascinating](https://quod.lib.umich.edu/j/jep/3336451.0003.204?view=text;rgn=main). Digital object identifiers (DOIs) have emerged as a response to the need for cataloguing and interoperability between scientific publishers. This fulfilled important business priorities:&#x20;

* Cataloguing ownership of copyright
* Metadata for digital distribution management and content repurposing&#x20;
* Maintaining control over accessing the data (e.g. through paywalls)
* Preserve stable URLs when content is transferred following an acquisition to a new IT infrastructure owned by a different entity

These business constraints came with substantial tradeoffs - DOIs are based on a social contract between the maintainer of the registry's lookup table, and the registrant's promise to maintain the URL to their proprietary server. DOIs are not 'persistent' nor securely mapped to their underlying content, and [inconsistent resolution](https://arxiv.org/abs/2004.03011) is a tremendous obstacle that stands in the way of the goals set by the [FAIR principles](https://www.go-fair.org/fair-principles/).&#x20;

**Though one of the best solutions at the time, shortcomings of the DOI system include:**

* **Not persistent**: content can change, either intentionally or not. There is no versioning schema for DOIs. DOIs need to be crawled for broken links and are expensive to maintain.&#x20;
* **Fragmented**: DOIs lack support for [Linked Data](https://en.wikipedia.org/wiki/Linked_data) - leading to the need to mint a PID for every digital object. This is not efficient and causes fragmentation of our knowledge graphs.&#x20;
* **Inconsistent resolution**: [DOIs rarely resolve to their content](https://arxiv.org/abs/2004.03011). This makes machine-readability extremely arduous.

### **Now**

**Fast forward twenty years, the DOI is used almost universally and is the de-facto primary key of the scientific record.**&#x20;

In the meantime, the content monetisation strategy of the industry and the needs of primary research content consumers have radically shifted. We live in the era of open access, and the release of the [OSTP Nelson memo](https://www.whitehouse.gov/wp-content/uploads/2022/08/08-2022-OSTP-Public-Access-Memo.pdf) and [Plan S](https://www.coalition-s.org/) have called into question the business imperatives of gating content access.&#x20;

Simultaneously, there is an increasing demand for the accessibility of interactive research files such as models, datasets and notebooks. As this demand often comes from analysts interested in reusing the information, access formats that easily facilitate reuse, for example through convenient web apps or [via APIs](https://huggingface.co/) calls integrated into the researcher's computational workflow, are popular.&#x20;

**This has an effect on the incentives of publishers**: Why pay for proprietary storage infrastructure when access cannot be monetised? Why incur high maintenance costs on data cataloguing? &#x20;

Transitioning to [digital content has been prohibitively expensive for small publishers](https://scholarlykitchen.sspnet.org/2016/11/08/why-technology-will-not-get-cheaper/), largely driven by labour costs associated with the personalised IT infrastructure to organise content and gate content access.&#x20;

New requirements on the horizon - such as FAIR data storage, high-quality metadata, machine resolution of PIDs, and cloud computing - are certain to lead to soaring IT costs, which will aggravate the industry's ownership consolidation by favouring large players over small and medium operations. These costs will inevitably be passed onto researchers and funders through rising [APC costs](https://en.wikipedia.org/wiki/Article_processing_charge).&#x20;

### A new PID system

With these large systemic changes in mind, there is a window of opportunity to fix the primary key of the scientific record and rethink architectural requirements from first principles. DeSci Lab is building PID system which lies at the heart of our vision for a truly Open and Decentralized repository for knowledge, and aims to solve four main challenges:&#x20;

* **Providing value to research communities**: PIDs that are designed to be [interoperable and compute-enabled](/technical-background/open-state-repository/methods). Send programs over to the data, or import the content of PIDs directly into your workflows such as code, data, and [inference APIs](https://huggingface.co/inference-api).&#x20;
* **Solving for data security**: PIDs linked to [content-identifiers](https://docs.ipfs.tech/concepts/content-addressing/) (CID) that preserve their underlying data and metadata on a [decentralized, content-addressed storage network](https://docs.ipfs.tech/). These PIDs do not rely on a social contract, rather, they are permanently registered on a distributed ledger.&#x20;
* **Solving for artefact fragmentation**: PIDs specifically designed for [linked data](/technical-background/open-state-repository/pid). A single PID can secure an entire linked data graph, and resolve securely to any [linked digital object](https://en.wikipedia.org/wiki/Linked_data).&#x20;
* **Solving for inconsistent resolution**: PIDs that resolve to a distributed, open, and [credibly neutral repository architecture](/technical-background/open-state-repository) in a predictable and machine-actionable way.&#x20;

You can learn more about our PID system and the Open State Repository [here](/technical-background/open-state-repository).&#x20;

### An upgrade - not a new standard

We can preserve the DOI system as the topmost overlay on this new PID system, essentially augmenting the DOI system without changing it fundamentally. Compatibility is important because we want to prevent the proliferation of standards, preserve familiarity, and lower adoption costs.


# FAIR Data

FAIR Data • Machine Actionability • Compliance

The FAIR movement in academia is an initiative aimed at making research data machine actionable through improving the Findable, Accessible, Interoperable, and Reusable in scientific information. These four principles provide a framework for ensuring that scientific data and related metadata are well-described, well-organized, and widely available for reuse. This movement was launched in response to the growing realization that a significant portion of scientific data is lost, forgotten, or simply inaccessible to other researchers due to poor data management practices. By following the FAIR principles, researchers can increase the value and impact of their research by making it more discoverable, accessible, and reusable by others in the scientific community.


# All About FAIR


# The FAIR Principles


# GoFAIR Criteria


# Red and Blue Principles


# FAIR Digital Object Framework (FDOF)


# The FAIR Hourglass


# The Internet of FAIR Data and Services (IFDS)


# FAIR Compliance

FIPs • FAIR Assessment Tools

The FAIR ecosystem is still in its early phases. Current compliance with FAIR mandates is assessed in several ways. The FAIR Implementation Profile for DeSci Nodes is a statement of the FAIR enabling resources used by the Nodes application to satisfy the individual FAIR principles. Standardized Assessments are also used to assess the FAIRness of data, but often rely on hard coded workflows targeted at legacy systems. Reasoning for non-compliance is listed in the standardized assessments page. &#x20;


# DeSci Nodes FIP

FAIR Implementation Profile for DeSci Nodes

The full DeSci Nodes FIP can be found at the [FIP Wizard.](https://fip-wizard.ds-wizard.org/projects/b4b039a7-d194-4c3c-b67d-0caf6d987c5f) The content from the FIP Wizard which comprise the FIP for DeSci Nodes can be found below:

<table><thead><tr><th width="186.33333333333331">Question</th><th>RDF Comment</th></tr></thead><tbody><tr><td>F1 MD: What globally unique, persistent, resolvable identifiers do you use for metadata records?</td><td>DeSci Nodes has built the dPID resolver which enables the creation of versionable, secure, decentralized, and human readable GUPRIs. dPIDs uses blockchain to allow for the resolution of an unsigned 256 bit integer and a prefix to a content addressed manifest file which contains versioned CIDs for individual components. The identifiers residing in the manifest file for each component in a research object can be considered the ultimate GUPRI for individual components, resolved by the IPFS network for content addressed storage.<br><br>Comment #2: While DOIs are not technically persistent, they are used to resolve to dPIDs for backwards compatibility to legacy systems. </td></tr><tr><td>F1 D: What globally unique, persistent, resolvable identifiers do you use for datasets?</td><td>DeSci Nodes has built the dPID resolver which enables the creation of versionable, secure, decentralized, and human readable GUPRIs. dPIDs allow the resolution of an unsigned 256 bit integer and a prefix to a content addressed manifest file which contains versioned CIDs for individual components. The identifiers residing in the manifest file for each component in a research object can be considered the ultimate GUPRI for individual components, resolved by the IPFS network for content addressed storage.</td></tr><tr><td>F2: Which metadata schemas do you use for findability?</td><td>DeSci Nodes uses JSON-LD through an IPLD-compliant version of RO-Crate. </td></tr><tr><td>F3: What is the technology that links the persistent identifiers of your data to the metadata description?</td><td>Directed Acyclic Graphs and IPLD have been retrofitted with JSON-LD to allow for machine actionable linkages between metadata in manifest files and the CIDs referencing data.</td></tr><tr><td>F4 MD: In which search engines are your metadata records indexed?</td><td>Metadata record are indexed and searchable through the dPID Indexer service. Blockchain functions as a permanent record on which metadata is indexed. It functions in a BC/DR capability for the scientific record. Attaching DOIs to Nodes allow for metadata to be indexed through DataCite in legacy systems.</td></tr><tr><td>F4 D: In which search engines are your datasets indexed?</td><td>Datasets are indexed and searchable through the dPID Indexer service. Blockchain functions as a permanent record on which metadata is indexed. It functions in a BC/DR capability for the scientific record. Attaching DOIs to Nodes allow for metadata to be indexed through DataCite in legacy systems.</td></tr><tr><td>A1.1 MD: Which standardized communication protocol do you use for metadata records?</td><td>Metadata is transferred primarily through IPFS but allows HTTP-based clients to access content stored on the IPFS network through an HTTP API.</td></tr><tr><td>A1.1 D: Which standardized communication protocol do you use for datasets?</td><td>Data is transferred primarily through IPFS but allows HTTP-based clients to access content stored on the IPFS network through an HTTP API.</td></tr><tr><td>A1.2 MD: Which authentication &#x26; authorisation technique do you use for metadata records?</td><td>Write access on Metadata records is provisioned through ownership of a Node's underlying ERC-721 token. The standard for read authorization on metadata is public and open.</td></tr><tr><td>A1.2 D: Which authentication &#x26; authorisation technique do you use for datasets?</td><td>Both read and write access on datasets is provisioned through ownership of a Node's underlying ERC-721 token.</td></tr><tr><td>A2: Which metadata longevity plan do you use?</td><td><a href="https://beta.dpid.org/36/v1">Link to Metadata Preservation Policy Draft Document</a></td></tr><tr><td>I1 MD: Which knowledge representation languages (allowing machine interoperation) do you use for metadata records?</td><td>DeSci nodes uses JSON-LD to allow machine interoperability in metadata records</td></tr><tr><td>I1 D: Which knowledge representation languages (allowing machine interoperation) do you use for datasets?</td><td>DeSci nodes uses JSON-LD to allow machine interoperability in metadata records</td></tr><tr><td>I2 MD: Which structured vocabularies do you use to annotate your metadata records?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate. RO-Crate context information for types can be found at https://w3id.org/ro/crate/1.1/context</td></tr><tr><td>I2 D: Which structured vocabularies do you use to encode your datasets?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate. RO-Crate context information for types can be found at https://w3id.org/ro/crate/1.1/context</td></tr><tr><td>I3 MD: Which models, schema(s) do you use for your metadata records?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate.</td></tr><tr><td>I3 D: Which models, schema(s) do you use for your datasets?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate.</td></tr><tr><td>R1.1 MD: Which usage license do you use for your metadata records?</td><td>Metadata for DeSci Nodes is always under a CC0 License</td></tr><tr><td>R1.1 D: Which usage license do you use for your datasets?</td><td>DeSci Nodes allows users to enter a variety of licenses on different component types. The options for pdfs include a variety of CC licenses such as CC0 and CC BY. The options for code and datasets include (but are not limited to) MIT, GPL, and CC0.</td></tr><tr><td>R1.2 MD: Which metadata schemas do you use for describing the provenance of your metadata records?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate. RO-Crate versioning information can be found through https://w3id.org/ro/crate/1.1/context</td></tr><tr><td>R1.2 D: Which metadata schemas do you use for describing the provenance of your datasets?</td><td>DeSci nodes uses an IPLD compliant implementation of RO-Crate. RO-Crate versioning information can be found through https://w3id.org/ro/crate/1.1/context</td></tr></tbody></table>


# Standardized Assessments

FAIR Assessments

In their current format, most FAIR assessment tools are not yet capable of handling / assessing decentralized web technologies. Their workflows have been (understandably) designed with assessing the FAIRness of legacy systems in mind.&#x20;

A few examples of this disconnect in practice:

* In legacy systems, PIDs resolve to a journal's website instead of resolving straight to their intended resource (i.e. the pdf). This introduces an extra step for machines actionability which relies on a social contract with a 3rd party (journals need to maintain consistency and standardization in their website). Introducing this extra step to machine actionability undermines persistence. As such, DeSci Nodes avoids this step and resolves straight to the CID being referenced (i.e. pdf, code, etc). Since the nodes architecture prioritizes persistence and simplicity in machine actionability instead of adhering to legacy workflows, we regularly fail (and will purposefully continue to fail) this particular check.&#x20;
* Assessment tooling checks for machine actionable navigation instructions using legacy methods (i.e. signposting). We use IPLD and DAGs to provide machines with more comprehensive navigation instructions. While this new method of navigation is more comprehensive and persistent, it does not fall within the standard workflow and fails the subsequent assessment checks.&#x20;
* Many assessment tools are built on a sequential workflow targeted at the legacy system. If you fail F3 (for example the tool only checks for signposting), the tool is not able to check requirements for F4 and subsequently fails the FAIR enabling resource for all following requirements (F4, A1.1, A1.2, A2, I1, I2, I3, R1.1 and R1.2). This results in artificially deflated scores for tooling that does not adhere to the legacy system.&#x20;

We practice a strict adherence to persistence, decentralization and security. FAIR Assessment tooling is still in early stage and is improving daily. We hope that this tooling will generalizable across architectures in the future. Decentralized web technology is the gold standard of red principle implementation, and we are excited to work with the community to build understanding and implementation around this. We understand that this technology is new and are happy to help where we can.&#x20;


# FAIR Metadata Publishing

FDPs • APIs • Metadata Publishing


# Open State Repository

Open State Repository • Infrastructure • Zooko's Triangle

Nodes are published on an "open state" repository. The open state repository's core architecture has been designed in line with the principles set forth by the [Leiden declaration](https://www.fdo2022.org/programme/leiden-declaration-fdo) on digital infrastructure. This is the first step towards an [Internet of FAIR digital objects](https://www.go-fair.org/resources/internet-fair-data-services/) where access is guaranteed to all humans and machines.&#x20;

**The open state repository irrevocably separates control over the data layer from control over the application layer. This not only guarantees accessibility to all research outputs, but also protects against the formation of vendor lock-in.**&#x20;

The open state repository achieves this separation through a distributed and open peer-to-peer architecture based on [content-addressed storage](https://en.wikipedia.org/wiki/Content-addressable_storage) and ledger-based anchoring of secure data structures on an open state PID registry. For an example of a similar architecture, [see Microsoft's Sidetree protocol](https://identity.foundation/sidetree/spec/).&#x20;

The open state registry PID namespace combines all three properties of [Zooko's triangle](https://en.wikipedia.org/wiki/Zooko%27s_triangle): secure, decentralized, and human-meaningful. This is a solution that is famously [owed to Aaron Schwartz](http://www.aaronsw.com/weblog/squarezooko), the open internet activist. Every digital object on the repository is secured in a tamper-proof data structure and is versionable at will by its creators across all access points (Gateways) to the open state repository. DeSci Nodes is the first access point or Gateway to the open-state repository. It is a prototype interface to build research objects and to broadcast them on the network.&#x20;

Our end goal is to usher a future where the scientific record is **FAIR** and **OPEN**.&#x20;

{% hint style="info" %}
**Core properties of the Open State Repository**

**FAIR:** [PID](/technical-background/open-state-repository/pid) + [Data](broken://spaces/qoc26HB22iW0xirA1o4c) + [Metadata](/technical-background/open-state-repository/metadata) + [Methods](/technical-background/open-state-repository/methods) for every digital object in a research object

**OPEN**: Open read & writes on a decentralized registry with data retrieval on a content-addressed storage network.&#x20;
{% endhint %}

## **What happens when you publish a Node on the open state repository**

When a Node is published, it is broadcasted from your private staging area hosted on our cloud infrastructure to the open state repository. Publishing triggers the repository’s registry to mint a single, version-invariant PID (called [dPID](https://www.dpid.org/put)). This PID serves as an anchoring point for the current version of your Node, which is structured into an efficient and secure data structure known as a [Merkle DAG](https://proto.school/merkle-dags). The individual branches of this Merkle DAG are [CIDs](https://docs.ipfs.tech/concepts/content-addressing/), serialized as an [IPLD-compliant](https://ipld.io/docs/), [JSON-LD](https://json-ld.org/) object. The root of this Merkle object is a cryptographic hash, and this hash is anchored to the Node’s PID on the open state registry contracts.&#x20;

Every time you publish a new version of your Node, a new root hash is anchored to your Node’s PID. This means that version history is preserved, and every event is logged with traceability: *who, what, and when.*&#x20;

## **Secure PIDs for linked digital objects**

Every Node has a single version invariant PID. From this PID, it is efficient to traverse the Merkle DAG and address any component of your node independently and uniquely. This is as simple as addressing a file path, something that everyone is familiar with. This means that every component of your Node has a provably unique path to every digital object contained, and therefore a unique PID. Because these PIDs are based on cryptographic hashes encoding the fingerprint of their content, they are architecturally guaranteed to secure data integrity.&#x20;

## **Permissions over the Node PID**

The Node creator can version the PID. As we upgrade the registry system, we will add permission delegation and a community recovery system to expand the flexibility and fault tolerance of the permission configuration.

## **Node PID permission recovery**

For the time being, DeSci Labs has admin rights over the open state repository registry contracts, which are upgradable via [proxy delegate](https://docs.openzeppelin.com/upgrades-plugins/1.x/proxies). This means that in the event of lost keys, we can re-assign your permissions to a new key. This is a necessary measure for the duration of the development process.&#x20;

## **Good UX for humans and machines**

Our goal is to make PIDs as useful to humans and machines as possible. For convenience, they are resolvable over HTTP as short, secured and human-friendly URLs via the DNS gateway [dpid.org](https://www.dpid.org/). You can learn more about the dPID schema [here](/technical-background/open-state-repository/pid).&#x20;

## **DeSci PID properties**

You can compare below the properties of Node dPIDs with [DOIs](https://www.doi.org/) (which are based on the [HANDLE system](https://en.wikipedia.org/wiki/Handle_System)) and [content-identifiers](https://docs.ipfs.tech/concepts/content-addressing/) (CID).&#x20;

<table><thead><tr><th>Properties</th><th width="144">DOI</th><th width="177">CID</th><th>dPID</th></tr></thead><tbody><tr><td>Does not depend on a central authority</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Consistent resolution to their content</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Protects against content drift</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Linked Data support</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Method to compute over the data</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Native support for versioning</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Method to resolve to metadata</td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr><tr><td>Enables Short URLs</td><td><mark style="color:blue;">TRUE</mark></td><td><mark style="color:red;">FALSE</mark></td><td><mark style="color:blue;">TRUE</mark></td></tr></tbody></table>


# PID

dPID • Persistent Identifiers • Content Adressing

The dPID system for research objects allows resolution to the underlying components in a consistent and granular way over HTTP and the IPFS network. You can learn more about the schema, syntax and variants below. Note that the system is under active development, and the specification is subject to change.

CID refers to Content Identifier according to the [Multiformats CID Specification](https://github.com/multiformats/cid)

## **dPID anatomy**

`HTTP URL = {Resolver}/{PID}/{version identifier OR CID}/{Component index}/{Component suffix}`

<table><thead><tr><th width="230">Component</th><th>Component Description</th></tr></thead><tbody><tr><td>Resolver</td><td>The <a href="https://en.wikipedia.org/wiki/Domain_Name_System">DNS</a> resolver, currently beta.dpid.org</td></tr><tr><td>PID</td><td>The registry's unique and version-invariant PID</td></tr><tr><td>Version identifier or CID</td><td>The version identifier (e.g. "v1" or "0") mapped to the CID of the manifest file or the manifest CID</td></tr><tr><td>Component index</td><td>The index of the component in the research object's data model, or the component ID</td></tr><tr><td>Component suffix</td><td><a href="https://github.com/json-path/JsonPath">JSONPath</a> to manifest component. Encoded with slashes and compact format for URL friendliness.</td></tr></tbody></table>

**Example dPID Links for Data Access**

<table><thead><tr><th width="184">Type</th><th>Link</th></tr></thead><tbody><tr><td>Web</td><td><a href="https://beta.dpid.org/46">https://beta.dpid.org/46</a></td></tr><tr><td>Metadata</td><td><a href="https://beta.dpid.org/46?jsonld">https://beta.dpid.org/46?jsonld</a> and <a href="https://beta.dpid.org/46?raw">https://beta.dpid.org/46?raw</a></td></tr><tr><td>Past Metadata</td><td><a href="https://beta.dpid.org/46?raw">https://beta.dpid.org/46/v1?raw</a></td></tr><tr><td>Code</td><td><a href="https://beta.dpid.org/46/3/root/exploring-lupus/casa/J15430131-3409153_cont.py?raw">https://beta.dpid.org/46/3/root/exploring-lupus/casa/J15430131-3409153_cont.py?raw</a></td></tr><tr><td>Data</td><td><a href="https://beta.dpid.org/46/v4/root/exploring-lupus/output/data_lup.txt?raw">https://beta.dpid.org/46/v4/root/exploring-lupus/output/data_lup.txt?raw</a></td></tr></tbody></table>

**Note:** Excluding `?raw` results in resolving the human-accessible data in the Nodes App or another configured resolver application.

**API for Research Objects**

<table><thead><tr><th>Route</th><th>Behavior</th></tr></thead><tbody><tr><td>GET https://beta.dpid.org/api/v1/dpid</td><td><p>List all registered research objects</p><p></p><p>Query Params</p><p><code>page: number = 1 // first page</code></p><p><code>size: number = 100 // 100 items</code></p><p><code>sort: "asc" | "desc" = "desc" // sort descending</code></p><h4>Response</h4><pre class="language-json" data-overflow="wrap"><code class="lang-json">{
    "dpid": "54",
    "id": "0x0...",
    "recentCid": "bafkre...",
    "researchObject": {
        "id": "0x0...",
        "versions": [
            {
                "id": "0x0...",
                "time": 1685098464,
                "cid": "bafkre...",
            },
            {
                "id": "0x0...",
                "time": 1685098776,
                "cid": "bafkre...",
            }
        ]
    }
}
</code></pre></td></tr><tr><td>GET https://beta.dpid.org/46/v1?raw</td><td>Get metadata for specific version of specific research object (application format)<br><br>Response Typescript specification: <a href="https://github.com/desci-labs/nodes/blob/develop/desci-models/src/ResearchObject.ts">https://github.com/desci-labs/nodes/blob/develop/desci-models/src/ResearchObject.ts</a></td></tr><tr><td>GET https://beta.dpid.org/46/v1?jsonld</td><td>Get metadata for specific version of specific research object (semantic format)<br><br>Returns in <a href="https://www.researchobject.org/ro-crate/1.1/">RO-Crate 1.1 format</a><br><br>Response Typescript specification: <br><a href="https://github.com/desci-labs/nodes/blob/develop/desci-models/src/RoCrate.ts">https://github.com/desci-labs/nodes/blob/develop/desci-models/src/RoCrate.ts</a></td></tr></tbody></table>

**Navigating Data via dPID API**

| Route                                                                                                                                                                                                                                                                                                                   | Behavior                                                                                                                                                                                                      |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| <p>GET <a href="https://beta.dpid.org/46/root?raw"><https://beta.dpid.org/46/root?raw></a><br>GET <a href="https://beta.dpid.org/46/v1/root?raw"><https://beta.dpid.org/46/v1/root?raw></a><br><br><code>deprecated</code><br>GET <https://beta.dpid.org/46/data?raw><br>GET <https://beta.dpid.org/46/v1/data?raw></p> | These all do the same thing. Get the [DAG-JSON](https://ipld.io/docs/codecs/known/dag-json/) encoded content of the root data folder. If version specified, uses that version, otherwise uses latest version. |
| GET <https://beta.dpid.org/46/root/exploring-lupus-report.pdf?raw>                                                                                                                                                                                                                                                      | Download the specific file specified, if not a file, but a folder, the DAG-JSON encoded content is shown                                                                                                      |

**Valid PID syntax and variants**

There are three different and valid variants of the PIDs that can be resolved over HTTP. These variants offer different levels of friendliness for humans.&#x20;

<table><thead><tr><th width="107.33333333333331">Variant types</th><th width="318">Variant syntax (human)</th><th>Variant syntax (machine)</th></tr></thead><tbody><tr><td>Short form URL variant <br>(<strong>recommended</strong>)</td><td><a href="https://beta.dpid.org/46/v4/root/exploring-lupus/output/data_lup.txt">https://beta.dpid.org/46/v4/root/exploring-lupus/output/data_lup.txt</a></td><td><a href="https://beta.dpid.org/46/v4/data/exploring-lupus/output/data_lup.txt?raw">https://beta.dpid.org/46/v4/data/exploring-lupus/output/data_lup.txt?raw</a></td></tr><tr><td>Short form URL variant 0-index<span data-gb-custom-inline data-tag="emoji" data-code="26a0">⚠️</span><br><code>deprecated</code></td><td><a href="https://beta.dpid.org/46/3/data/exploring-lupus/output/data_lup.txt"><em><mark style="color:blue;">https://beta.dpid.org/46/3/data/exploring-lupus/output/data_lup.txt</mark></em></a></td><td><a href="https://beta.dpid.org/46/3/data/exploring-lupus/output/data_lup.txt?raw">https://beta.dpid.org/46/3/data/exploring-lupus/output/data_lup.txt?raw</a></td></tr><tr><td>Long form URL <span data-gb-custom-inline data-tag="emoji" data-code="26a0">⚠️</span> <strong>coming soon</strong></td><td><em><mark style="color:blue;">dpid.org/42/bafybeigdyrzt5sfp7udm7hu76uh7y26nf3efuylqabf3oclgtqy55fbzdi/1/measurements.csv</mark></em></td><td><em><mark style="color:blue;">dpid.org/42/bafybeigdyrzt5sfp7udm7hu76uh7y26nf3efuylqabf3oclgtqy55fbzdi/1/measurements.csv?raw</mark></em></td></tr></tbody></table>


# Data

Staging area • OSR storage • Big Data storage

## **Node Private Drive**

The Node Private Drive is a private staging area for your draft Nodes. It is hosted on our secure cloud infrastructure. In the staging area, you can build your research object and share with with your co-authors and collaborators privately.&#x20;

The storage capacity is on a **per-user basis**. Publishing your Node clears your personal storage space.&#x20;

<table><thead><tr><th width="184">Products</th><th>Free storage (per user)</th></tr></thead><tbody><tr><td>Nodes Capybara</td><td>100 gigabytes</td></tr><tr><td>Google drive</td><td><a href="https://one.google.com/faq/storage">15 gigabytes</a></td></tr><tr><td>Dropbox</td><td><a href="https://www.dropbox.com/basic">2 gigabytes</a></td></tr></tbody></table>

## **Open state repository storage**

Once you click "Publish" and sign the transaction, your data is mirrored to the open state repository and progressively cleared from our cloud infrastructure. By publishing your Node, you clear storage space in your private staging area.

Multiple copies keep things safe: **your data is mirrored in 5 countries across 3 continents.**&#x20;

The five copies are in an archival state in the form of [CAR files](https://ipld.io/specs/transport/car/carv2/). One additional "hot" copy is made accessible over the network at a high degree of availability, for a total of six copies. You can learn more about distributed archival storage [here](https://estuary.tech/).&#x20;

{% hint style="info" %}
**Contact us to store massive amounts of data efficiently and securely**

We are building our big data onboarding process. For datasets of >50TB, you can apply for sponsored storage via the [DeSci Foundation funding program](https://descifoundation.org/funding). We will help you onboard your data, link it to your node, and make it easily re-useable and creditable.
{% endhint %}


# Metadata

RDF graphs • Embeddings •  Traceability

## Machine Actionable Metadata

DeSci Labs aims to build machine actionable metadata in line with the FAIR principles. Our intent is to be the gold standard of Red Principle implementation while satisfying Blue Principles through widely used, standardized vocabularies. This is achieved through a combination of two methods of machine actionability.&#x20;

#### RDF graphs through the semantic web

Research Objects are invaluable for machine-generated metadata regarding semantic types. Nodes are [RDF graphs](https://en.wikipedia.org/wiki/Resource_Description_Framework) at their core. The Node RDF graph maps connections between digital objects that are not inferable by machine-generated metadata because in most cases, there is [little to no mutual information](https://en.wikipedia.org/wiki/Mutual_information) between the embeddings derived from these components in the absence of user-inputed metadata records.&#x20;

For example, there is no way to know that a particular .csv dataset file is linked to a given research paper in the absence of a human-generated metadata annotating .csv file indicating to the machine that "this is the data of paper X". By adding components with their semantic types to your Node, we create such a relational mapping:&#x20;

`Data.csv -> isOpenDataComponentOf -> ResearchReport.pdf.`&#x20;

#### Embeddings as supplementary metadata&#x20;

In order to enhance Machine Actionability during FAIR's uptake phase, DeSci Labs automatically [generates embeddings using OpenAI's API](https://platform.openai.com/docs/guides/embeddings/what-are-embeddings) for all text based components (manuscripts, preprints, presentations, code repositories, etc) in a research object. These embeddings are stored into a [vector database](https://en.wikipedia.org/wiki/Distributional%E2%80%93relational_database) for efficient retrieval and updates, and mapped to the PIDs of the digital objects. For manuscripts, we generate multiple runs of embeddings on the sections of the research report extracted from the PDFs.&#x20;

{% hint style="info" %}
At a high level, Node Metadata is:&#x20;

* Base metadata for components as provided in RO-Crate through Schema.org
* RDF graph of functional types, contributors (ORCID) and funders (ROR)
* Content embeddings over text based digital objects
* Traceability of change (who, what, when)
  {% endhint %}

#### **Example:**

Once we have the RDF graph of a Node and embeddings over its digital objects, we can query the the vector database to return all Nodes related to COVID19. And because we know the relationships between Node components, we can run more advanced queries, for instance - returning all open datasets or code repositories related to COVID19.&#x20;

## **Metadata Model**

Our base metadata model can be seen in our [open source code on Github](https://github.com/desci-labs/nodes/). We use an RO-Crate implementation which has been modified to allow for IPLD and CIDs. The manifest files underpinning individual dPIDs can be seen through the following link structures:

`https://[prefix].dpid.org/[#]?jsonld`

`https://[prefix].dpid.org/[#]?raw`

### Metadata Collected

The metadata we collect can generally be split along three criteria (level of generation, user vs machine generation, required vs optional field) which are visualized in the table below. It should be noted that this data model is still undergoing revisions (specifically the JSON -> RO-Crate Transformer).&#x20;

| Metadata                         | Level           | User vs Machine | Required vs Optional |
| -------------------------------- | --------------- | --------------- | -------------------- |
| Author(s) Name                   | Application     | User            | Optional             |
| Author(s) ORCID                  | Application     | User            | Optional             |
| Author(s) Google Scholar Profile | Application     | User            | Optional             |
| Node Title                       | Node            | User            | Required             |
| Field of Science                 | Node            | User            | Required             |
| License Type (Default)           | Node            | User            | Required             |
| Version Number                   | Version         | Machine         | Required             |
| Publishing Timestamp             | Version         | Machine         | Required             |
| Semantic Type                    | All Components  | Machine         | Required             |
| Functional Type                  | All Components  | User            | Required             |
| License Type (Component)         | All Components  | User            | Optional             |
| Keywords                         | All Components  | User            | Optional             |
| Descriptions                     | All Components  | User            | Optional             |
| Vectorized Embeddings            | Text Components | Machine         | Required             |

### **User Entered, Required Metadata**

While we try our best to minimize the workload on a scientist to FAIRify their work, two metadata fields (license and functional type) require user entry on a component-by-component level. At scale this can be quite time consuming. In both cases, we use a combination of interfaces and inheritance to optimize the data publishing experience for users.&#x20;

* **License agreement:** The absence of a clearly defined licensing agreement de-facto blocks the re-use of the digital objects. Hence, it is enforced. When you create a Node, you can choose a **default license agreement** that will apply to all components of your Node by default unless it is overridden by a license agreement that you manually modified or in conflict with the license agreement retrieved from an API call (e.g., if you select CC BY, and your code on Github is under MIT, then MIT will override CC BY for your code component). All Node metadata is **licensed under** [**CC0**](https://creativecommons.org/share-your-work/public-domain/cc0/), and the metadata remains available even if the underlying data has been deleted, intentionally or not. &#x20;
* **Functional type**: the functional type refers to the nature of the digital object. For instance, a "research report" or "code repository" are functional types. We use the functional types to create the [RDF graph](https://en.wikipedia.org/wiki/Resource_Description_Framework) of your Node. In the future, it should be possible to infer the functional types based on content embeddings.&#x20;

## FIP and Metadata Permanence Plan

DeSci Labs is working hand in hand with the GoFAIR Foundation to create a machine-actionable FIP. The current [FIP Draft can be seen on FAIRConnect](https://fairconnect.pro/eriks-index/content-desci-nodes-fair-implementation-profile).&#x20;

## **Future Metadata Efforts**

#### **Enhanced embeddings**&#x20;

For all digital objects in a research object, we [generate embeddings using OpenAI's API](https://platform.openai.com/docs/guides/embeddings/what-are-embeddings). These embeddings are stored into a [vector database](https://en.wikipedia.org/wiki/Distributional%E2%80%93relational_database) for efficient retrieval and updates, and mapped to the PIDs of the digital objects. For manuscripts, we generate multiple runs of embeddings on the sections of the research report extracted from the PDFs.&#x20;

#### **Machine-extracted metadata**

We would like to extract authors, affiliations and grant funding information from research reports to expedite the process of adding co-authors to a Node. This means automating the matching of [ORCID IDs](https://orcid.org/) and [ROR PIDs](https://ror.org/registry/). Time permitting, we may look into the concept of keyword and semantic extraction.

#### **Community defined vocabulary integration**

Tools like [CEDAR workbench](https://metadatacenter.org/) provide scientists with workflows to create machine actionable metadata through the semantic web. We will be evaluating CEDAR and similar tools in the future with the possibility of integration in mind.&#x20;

#### Publishing RDF metadata in addition to JSON and JSON-LD

It's very possible that RDF will become a mandate in the FAIR ecosystem. Nodes currently publish through JSON-LD (as RO-Crate uses Schema.org). Conversion between JSON-LD and RDF is easy to do but difficult to do well. It is our opinion that bad metadata is worse than no metadata. When effective, resourced/maintained, and community accepted means of converting from JSON-LD to RDF become available, we will investigate means of integration.&#x20;


# Methods

Compute Methods • Compute over Data • Local Compute • Web-Based Compute

## Compute methods

We provide three types of computational methods to interact with data contained in a Node. Note that each of these methods are in prototype stage.&#x20;

### **Send Compute to Data (Edge computing)**

With Nodes, you will be able to send programs over to the data. This is known as [edge computing](https://en.wikipedia.org/wiki/Edge_computing) and is especially powerful for data-intensive research. Nodes use [Bacalhau](https://docs.bacalhau.org/), an architecture for fast, cost efficient, and secure computation to run jobs where the is generated and stored. A major advantage is that you don't need to rewrite your code - you can simply send it over to the data into an arbitrary docker container and WebAssembly (wasm) images as task.

### **Send Data to Compute**&#x20;

Import Node components such as (small) datasets and code into your local computer or high performance computing environment directly with Node PIDs. You can use the [python](https://www.python.org/) library [desci\_fetch](https://github.com/desci-labs/desci-fetch) for this purpose. With it, you can import code and datasets from HTTP into your IDE. Please note that the library is under active development, feedback and contributors are welcome.

### **In-Browser Compute**

Run code directly from your web browser in your Nodes [General user overview](/general-user-overview#ide). Ideal for running results reproducibility checks or executing [Jupyter notebooks](https://jupyter.org/).&#x20;

## **Access Methods**

#### **Human Access over HTTP**

To access content published on Nodes, refer to our [PID schema](/technical-background/open-state-repository/pid). Nodes are resolved via the DNS resolver [dpid.org](https://www.dpid.org/).&#x20;

#### **Machine Access over HTTP**

{% hint style="info" %}
**Open Beta Note**

Please note that machine access over HTTP is currently under development.

We will soon be providing a syntax to enable machine resolution of the Node PID schema. This will allow consistent resolution to the machine-actionable manifest file of the Node.&#x20;
{% endhint %}


# Roadmap

Next Up on Nodes

## Immediate priorities (Q1-Q2 2023)

* Finalise [ROR](https://ror.org/registry/) and [ORCID](https://orcid.org/) integration and source edit to add collaborators and affiliations based on PID registries
* Invite flow to collaborate privately with your co-authors in your workflow area
* Finalise support for citation formats (BIBTEX)
* Fix support for hosted jupyter notebooks
* Node PID implants into preprints/postprints for portability across platforms
* Fix annotation tools

## On the Horizon

### **Methods**

**Node IDE**

* Redesign IDE backend to work from IPFS
* Use Node IDE as default data preview engine

**Compute to data**

* Store and manage CID-based compute outputs and their metadata in Nodes

**Node PID-based import**&#x20;

* Support PID-based import of datasets&#x20;
* Support PID-based import of inference APIs from [huggingface](https://huggingface.co/) and [replicate](https://replicate.com/)&#x20;

### **Machine actionability**

* Implement dPID resolution to the machine-actionable, self-describing JSON LD data model.
* Embedding-based approach for Node components and vector database
* Machine extraction of authors, affiliations, and grant information with PID matching

### Mobile experience

* Minimum mobile experience: Research Object component aggregator.&#x20;

### More In-browser support for interactive research artefacts

* Add support for rendering images and video components

### **Node Drive API-based data retrieval integrations**

* Integrate from [Dropbox](https://www.dropbox.com/home), [Google Drive](https://en.wikipedia.org/wiki/Google_Drive), [Gitlab](https://about.gitlab.com/), and others

### **Permission and identity management**&#x20;

* Simplify identity management and identity verification
* Enable community recovery of Node versioning right token
* Implement delegation of versioning rights

### **Verifiable attestation and plural curation**

* Implement Git primitives in Nodes (e.g. fork request)
* Implement badging system
  * Add support for [OSF](https://www.cos.io/initiatives/badges), [ACM](https://www.acm.org/publications/policies/artifact-review-and-badging-current), DeSci Foundation badges, and custom badges

### **Gateways for publishers, funders, organisations and libraries**

* Custom portals for Nodes with whitelisted users, tools for content curation and discovery (e.g. browse and search, featuring specific Nodes on the landing page), and advanced features for organizations (e.g. analytics, integration with other software systems such as [CRIS](https://en.wikipedia.org/wiki/Current_research_information_system))&#x20;