How to Contribute

In order to create a Health Atlas account, you have to click the Register button in the top right corner of the Health Atlas web page.
It will take you to a screen where you need provide

• A Login name (can be your real name, or another appropriate name)
• An email address
• A password for your account

As well as:

• First Name
• Last Name
• Your email address, which should be automatically populated from the previous screen.
• ORCID ID – if you do not have an ORCID you will need to register for one here http://orcid.org/

Information that is required is indicated with a red star.

After you have registered the rest of your information, in most installations of SEEK, you will need to activate your account. You will receive an email in the email account you have provided.

When you have completed the registration you will be asked to request a new project or join an existing one. This process is show in the image below. You are only allowed to contribute content to the Health Atlas, if you are a member of at least one project.

To register a publication in the Health Atlas you need to log into your Health Atlas account.

The Create button should be visible in the navigation bar. Go to Create > Publication

It will take you to a screen where you can choose between registration with PubMed-ID (PMID), manual entry or file import.

Registration by PubMed-ID

This is the default way. You need to provide:

• Publication type
• PubMed-ID
• Associated Project

After clicking the Fetch button, the Health Atlas will retrieve the information from PubMed.

Now click the button Register and your publication will be registered.

The next screen leads you to the editing of the dependencies of the publications. (read more in section 3)

Manually registration of a Publication

The second way to register a publication is the manually one.

You need to provide:

• a project
• title
• list of authors
• abstract
• maybe journal or other publication platform
• maybe citation
• published Date

By filling in a DOI number you can fetch the related data by clicking on the button Crossref. It will automatically fill in the fetched data.

Authors are added by tipping the first letters of the author’s last name.
In the appearing List you can pick an already known author or a registered person.
A known author is an author how is already related to other publications but not registered in the Health Atlas as a person.

If the author is not in the list fill in the name in publication style and click on the name under New Author.

Registered authors will be linked to their author profiles.

After filling in all your related information click the button Create.

The next screen leads you to the editing of the dependencies of the publications. (read more in section 3)

Import by file

The third and last way to register a publication is by uploading a bibtex-file.

The bibtex should contain one or many entries of publications related to one project.
So it would be neccessary that you provide one bib-tex file for every project containing your publications.

After clicking the button Import first, the first entry will be imported and the editing screen will show up. (read more in section 3)

By clicking the button Import all, all entries will be imported and no editing screen will be shown.
If you want to edit the publications, go to My items in your account in the right corner of the screen.

There you can pick the item you want to edit from the list.

To get to the editing mode select the button Manage Publication under the Administration drop down menu.

The next Screen leads you to the editing of the dependencies of the publications. (read more in section 3)

By entering the edit mode of a specific publication (as described in the previous sections) you can manage the meta data of the publication.

• Under Project you can add some more projects or remove existing relations.
• Associate Authors is a list of all the authors related to the publication. The portal is suggesting the author based on existing, registered authors in the database. If there is a wrong or missing suggestion, pick the correct one by writing first letters of the last name from the list.

• Under Summary you can write a short summary of the main facts of this publication.
• Reference specifies a HTML link if there is no DOI or PubMed entry.
• Human Diseases related to a publication can be assigned by selecting the HDO phrase of the list or by typing the first Letters.

Events, Investigations, Studies, Assays, Data files, Models, Presentations and Documents can also be associated to the publications. These entities must be created before being referenced.

What you have to provided to contribute a model?

There are two ways to contribute models:

1. Upload the model as archive.
2. Provide a link to a preferably public repository (e.g., on GitHub or BitBucket).

If you choose the first option please include the following in the archive:

• the actual source code of the model
• a LICENSE file
• a descriptive README.md or README.txt file
• a META.json or META.yml file, which contains information about requirements and dependencies to use the model (see below for an example META.json file)

Embedding a live demo

You can upload the source code of your model to our GitLab in order to build an automated Continuous Integration and Continuous Delivery (CI/CD) pipeline.
All models, which are processed with this pipeline will be deployed automatically to https://apps.health-atlas.de/<app-name>.
More information can be found in our example Shiny App (currently only accessible from the subnet of the University of Leipzig).

View example Shiny App

If there are live demos or deployed apps for this model, you can add links to this demos into the section “Tool References”.

The links will be shown as buttons next to the description of the model.

If your demo is public and you want to embed it into the Health Atlas portal (the demo will be visible on the model page), add the link to the “App URL” field and enable the checkbox “embeddable”. This feature is best suited for Shiny Apps.

Selecting a proper license

In the “License” field you can select a license and the link below the field will automatically update and point to an external web page, where the license is described.

https://choosealicense.com could be of help to choose the most appropriate license. https://opensource.guide/legal/ contains even more information about legal implications of open source.

Example META.json file

{

  “name”: “My Test Model”,

  “version”: “1.0.0”,

  “author”: “Random Dude”,

  “summary”: “Can be used to calculate fancy stuff.”,

  “license”: “Apache-2.0”,

  “source”: “https://example.com/source”,

  “project_page”: “https://example.com/project”,

  “issues_url”: “https://example.com/issues”,

  “dependencies”: [

    {

      “name”: “dependency 1”,

      “version_requirement”: “>= 4.13.1 < 5.0.0”

    }

  ],

  “operatingsystem_support”: [

    {

      “operatingsystem”: “Debian”,

      “operatingsystemrelease”: [ “5”, “6”, “7” ]

    }

  ],

  “description”: “A more detailed description of this awesome model can be added here.”

}

In order to contribute a data file please got to +Create → Data file

What you have to provided to contribute a data file?

There are two ways to contribute data files:

1. Upload the data file.
2. Provide a link to a preferably public repository (e.g., Gene Expression Omnibus).

Adding additional information about the data file

Most of the fields for providing metadata of a data file are identical to those of models. Please refer to section “4. Contributing Models” for detailed information.