Submitting Term Suggestions to GO

There are a number of ways to submit requests for new ontology terms for GO. Here we outline information on how to submit a request using each option. A helpful guide to deciding which avenue for requests best fits your needs is available on the page 'Contributing to the Ontology'.

1. TermGenie

TermGenie (J Biomed Sem, 5(1), 48) is a web-based tool that automates the creation of new ontology class with the use of templates. Using a TermGenie template, curators may quickly verify and create a new class with its corresponding metadata and permanent identifier. This pattern-based approach reduces the amount of time required for GO editors to review and process term requests.

There are many TermGenie templates including those to create terms for 'regulation of [biological process X]', 'regulation of [molecular function Y]', and '[chemical Z] metabolic process'. Users may also create terms that refer to external ontologies such as the Cell Ontology (CL), Plant Ontology (PO) and Chemicals of Biological Interest (ChEBI).

Learn more about how to obtain a user name and password, explore examples on the use of TermGenie templates on the TermGenie Documentation Page.

2. GOC GitHub Tracker

The GOC GitHub tracker also captures suggestions for changes to the ontologies, from suggestions to new terms to correcting typos in the documentation. By signing up for GitHub account, users are able to track their submissions online and via email. This tracker also opens the discussion to include the wider community.

 

2.1 Set up a GitHub account

  1. On the Github website press the 'Sign up for GitHub button and follow instructions.
  2. Once registered, sign in using button in the upper right-hand corner.
 

2.2 Submit a suggestion to GO via GitHub

Visit the GO ontology requests tracker. A list with all recently submitted requests is visible on the landing page. Clicking on any summary will bring up detailed information about that request. All requests whether completed ('Closed') or still in progress ('Open') remain in GitHub indefinitely; by default only 'Open' suggestions are displayed in this page.

More details about contributing to the ontology are available in the 'GitHub Guidelines for Contributing Ontology tickets'. A brief description is included below.

 

Steps to enter a suggestion or a term request:

  1. Click on the green 'New Issue' button.
  2. Enter the subject of your request in the 'Title' field, which will be your queue to find the issue from the list of requests.
  3. Enter details of your request in the 'Leave a Comment' box. When requesting a new term for the ontology, please include the following details to the best of your ability:
    • New term name
    • Suggested definition
    • Suggestion about where it should appear in the GO hierarchy
    • Pertinent literature references (PMID:xxxx, ISBN:xxxx, DOI:xxxx)
    • Any possible synonyms of the new term
  4. You may submit a separate request for each new term to track them separately.
  5. Alternatively, you may upload a file with multiple requests in the same issue using the 'Add Attachments' button at the bottom of the page.
  6. When you are satisfied with your request, press the 'Submit new issue' button at the bottom of the box.
 

Keep track of your requests

  • You may receive specific emails about a single request by choosing to 'Watch' an issue using the button with the 'eye' icon, found at the upper right corner of the issue page. Users may choose to watch, not watch, or ignore a GitHub issue by pressing this button. If you choose to 'Watch' an issue, an email will be sent every time comments are added to the issue, or its status changes.
  • To find your request again in the GOC tracker, while on the page listing all submitted issues, use the 'Filters' box and drop-down menu to restrict the types of request you may display.