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OntoPortal Documentation
  1. Contributing to OntoPortal (and BioPortal)
    1. Code of Conduct
    2. I don’t want to read this whole thing, I just have a question!
    3. What should I know before I get started?
      1. Don’t try to install from GitHub source
      2. BioPortal/OntoPortal repositories
    4. How Can I Contribute?
      1. Reporting Bugs
        1. Before Submitting A Bug Report
        2. How Do I Submit A (Good) Bug Report?
      2. Requesting Features / Suggesting Enhancements
        1. How Do I Submit A (Good) Enhancement Suggestion?
      3. Pull Requests

Contributing to OntoPortal (and BioPortal)

First off, thanks for taking the time to contribute! 👍

The following is a set of guidelines for contributing to BioPortal/OntoPortal software, which is hosted in the NCBO project on GitHub. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.

Code of Conduct

This project and everyone participating in it is governed by the Terms of Service. By participating, you are expected to uphold this code.

I don’t want to read this whole thing, I just have a question!

Note: Please don’t file an issue to ask a question. You’ll get faster results by using the resources below.

We have an official message board where the community chimes in with helpful advice if you have questions.

What should I know before I get started?

Don’t try to install from GitHub source

We encourage anyone wanting to start developing with BioPortal/OntoPortal software to get a copy of the Virtual Appliance, then submit changes to our repositories based on changes to that code base. Read the Repositories section below for better understanding of our rationale, but basically, we have a lot of installation steps that are a bit one-off.

BioPortal/OntoPortal repositories

The GitHub ncbo project contains many repositories that are not critical to BioPortal operations. Conversely, there are one or two critical repositories that you do not have access to.

You do have to install several different code bases (repositories) as well as some back-end services. Please contact us for more information via the support list.

How Can I Contribute?

Reporting Bugs

Before creating bug reports, you can check our issue board as you might find out that you don’t need to create one. When you are creating a bug report, please include as many details as possible. You can submit it via the support list, or via a ticket in the appropriate ncbo repository, or via the bioportal-project repository.

Note: If you find a Closed issue that seems like it is the same thing that you’re experiencing, open a new issue and include a link to the original issue in the body of your new one.

Before Submitting A Bug Report

  • Perform a cursory search of the issue repository and/or the support archive to see if the problem has already been reported. If it has and the issue is still open, add a comment to the existing issue instead of opening a new one.

How Do I Submit A (Good) Bug Report?

Bugs are tracked as GitHub issues. If you’ve determined which repository your bug is related to, create an issue on that repository and provide the following information:

  • Use a clear and descriptive title for the issue to identify the problem.
  • If you can describe exactly what time the issue occurred, we can more confidently review our logs to look for reports related to your issue.
  • Describe the exact steps which reproduce the problem in as many details as possible.
  • Provide specific examples to demonstrate the steps. Include links to your ontology, the BioPortal page(s) you were visiting, and/or copy/pasteable snippets using Markdown code blocks.
  • Describe the behavior you observed and point out what exactly is the problem with that behavior.
  • Explain which behavior you expected to see instead and why.
  • What’s the name and version of the browser you’re using?
  • Are you running BioPortal in a virtual machine? If so, which VM software and which operating systems and versions are used for the host and the guest?

Requesting Features / Suggesting Enhancements

For simple requests/suggestions, an email to our support list is the simplest route. We will attempt to respond to your email and document your suggestion.

If you want to document a request in more detail, you may use our ticket system as described above for reporting bugs.

How Do I Submit A (Good) Enhancement Suggestion?

Enhancement suggestions are tracked as GitHub issues. Create an issue on the appropriate repository and provide the following information:

  • Use a clear and descriptive title for the issue to identify the suggestion.
  • Provide a step-by-step description of the suggested enhancement in as many details as possible.
  • Describe the current behavior and explain which behavior you expected to see instead and why.
  • Include screenshots and animated GIFs which help you demonstrate the steps or point out the part of OntoPortal the suggestion is related to.
  • Explain why this enhancement would be useful to most OntoPortal users.
  • Specify which version of OntoPortal you’re using.

Pull Requests

Please follow these steps to have your contribution considered by the maintainers:

  1. Test your code before submitting a pull request.
  2. [Optional] Contact us to discuss your pull request, to be sure we will be able to use it.
  3. Follow the existing style in the software you are modifying.
  4. After you submit your pull request, verify that all status checks are passing.

While the prerequisites above must be satisfied prior to having your pull request reviewed, the reviewer(s) may ask you to complete additional design work, tests, or other changes before your pull request can be ultimately accepted.