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How to contribute to FBBI

Contributing to the ontology by opening tickets

The easiest way to contribute to the Biological Imaging Methods Ontology is by opening tickets on our issue tracker to requests new terms or amendments to existing terms.

This does not require you to be familiar with ontology editing procedures, as your request will be handled by someone in the Biological Imaging Methods Ontology editorial team, who will do the actual editing.

To help the editorial team to process your request(s), please consider the following recommendations:

  • Does the term already exist? Before submitting a new term request (NTR), check whether the term you need already exists, either as a primary term or a synonym term. You can search using an online ontology browser such as OLS.

  • Write a detailed request. A request that simply says “please add a new term for ‘foo‘” or “please fix the definition of ‘bar’” is unlikely to be acted upon. Do not assume that the editorial team will know what “foo” is (or what meaning you give to that term), or what is wrong with the current definition of “bar”. Please be specific and include as many details as necessary.

  • Include suggestions. You may include suggestions for the precise label, definition, and optional synonyms that you think the new term you are requesting should use. If you are familiar with the structure of the ontology, you may also suggest a position for the new term within the existing hierarchy.

  • Provide references. Whenever possible, please include PMIDs, DOIs, or other references to source the definition of new or updated terms.

Contributing to the ontology by editing it directly

If you know how to edit a OWL ontology, then you may also contribute more directly by editing it yourself, and submitting your proposed changes to the editorial team in a pull request (PR).

If you want to do so, please consider the following recommendations:

  • Open a ticket prior to submitting a PR. Even if you plan to make the changes yourself, you should still start by opening a ticket explaining what you think the problem is. You may then mention in the ticket that you plan to fix the issue yourself in an upcoming PR.

  • Request an ID range. If you plan to submit PRs in which you will add new terms, please request (through a dedicated ticket) that an ID range be assigned to you.

  • Do not edit fbbi-edit.owl manually. Please use a specialized ontology editor such as Protégé for all your changes.

If you really want to implement your changes using a non-OWL-aware program, please make sure to “re-serialize” the fbbi-edit.owl file before committing your changes.

  • Finding help. The Biological Imaging Methods Ontology is maintained using the Ontology Development Kit and overall follows (or attempts to follow) the editing guidelines of the OBO Foundry. You can find more informations about both the ODK and the OBO Foundry practices in the OBO Semantic Engineering Training website (commonly known as “the OBOOK”), and you can also find people to help you in the OBO Community Slack workspace.

On behalf of the Biological imaging methods ontology editorial team, Thanks!