Publishing calculations into Browse

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Calculations uploaded into the Create module are only accessible to registered ioChem-BD users, this will usually be comprised of a small group of individuals that conform the research group/center. Their calculations will not be accessible until they are published in the Browse module, the public module of ioChem-BD.
Before moving to the publication mechanism, it is interesting to read again the section about the organizational elements that conform each module: ioChem-BD organizative elements
So published projects become Collections and published calculations become items on the Browse module, it is a mere grammatical change to align with DSpace software naming convention. Once published, both elements are linkable, searchable and viewable publicly.

Publication requirements

To perform calculation publication, users must meet the following requirements:

  • Publishing user must have defined (on Browse module) a community where to publish.
  • Publishing user must have administrator rights to publish on such community, so he/she will has to be able to create collections and publish items.

The steps required to create a community and assign its administrator falls upon ioChem-BD's system administator and are described on publishing endpoints definition page.

Publication steps

Select the elements to publish

On Create we will first navigate to the project where the calculations that we wish to publish reside, we can select an individual calculation by clicking on it, or multiselect with Ctrl + Click, Alt + Click. Another way to select calculations is to display parent project context menu with right click and choose the option Select child elements

Note: You must select the project and its inner calculations prior publishing. If you only select the project element and not its content you will publish the project but empty of contents.

Once our projects/calculations are selected, we will right click on the current selection to display its options menu. We will select Publish option.

Calculation selection

A dialog box will appear asking for our account password:

Credential validation

If an error message appears at this point, please read the FAQ entry about no publishing community defined.
A new form will be presented, showing all end points available on the Browse module.

Selected elements form

In the publication process, a project hierarchy will be replaced for a collection element with all its subprojects concatenated as a Unix path.

Note: If they exist, we can select the endpoint where to publish by using drag and drop. Already published elements (the ones with a green tick) cannot be moved because their path has been already set. We can change published calculation and project names by clicking the element name.

Publication steps

Publication options

On right side of the publication form there is a group of option tabs that allow to define published element metadata and its relation to journal articles.

Step 1: Titles and description

This tab allog to configure information related to published calculation:

  • Calculation naming convention : We can choose to prepend full parent projects name into calculation name or set only calculation name
  • Description field: If checked, calculation description field will be added as a metadata field and will be publicly accessible on Browse module.
Titles and description tab

Step 2: Publication details

The next tab has two options:

  • Generate DOI for top projects: will request a DOI identifier that points to the published collection
  • Embargo published elements: if marked, all published elements will be embargoed.

DOI determination can take some minutes to resolver because it requires to contact third party services (CrossRef). Once DOI has been assigned, you will receive an email with the DOI for the published collection.
The second option will allow you to embargo (restrict) the access to your published content.You can read more about the embargo feature on this page.


Step 3: Dataset type

This tab allows to add extra manuscript information in the case that the dataset is part of the supporting information of a paper.
You can define the manuscript title, DOI and Journal. In the situation that the paper doesn't have a valid DOI yet, you can check the checkbox Not yet published, will provide it later.


Step 4: Additional fields

The last step is used to define other authors and institutions related to the dataset. There is also a listbox with chemical terms to enrich the published elements, such terms will be later indexed by Browse module to ease data search.
Once all the step forms have been filled, we will click the Publish button.

Additional fields tab

After the publication process has ended, a resume window will display the link to edit published elements on Browse module and, only if you checked the embargo option, another link to review embargoed elements.


Published elements manipulation

In the navigation frame, published elements will display a green tick on the right side.
Published projects and subprojects will also have an additional black tick that points to the Browse Collection edit page.


This page allows to:

  • Change published collection name
  • Set related article information
  • Lift embargo (read more here)
  • Copy reviewers link
This first section allows to change Title, subtitle and description of the published collection
The next section allows set publisher metadata and embargo options

View published elements from Create

The projects and calculations published have a handle and a green tick on its right side. Clicking on the handle link will navigate to the published Browse content.

Publication handle
List of published Collections

Each collection can hold multiple Items (calculations) inside.

Published Collection items

Each published item displays the uploaded input file, an output converted CML file, additional files and its metadata.

Published item detail