New member onboarding

Welcome to the GO Consortium!

This page explains how to join and contribute to the Gene Ontology project, either as a biocurator, a software developer, or to provide feedback on the ontology or the annotations.

Project organization

The Gene Ontology project is a consortium of different groups and individuals associated with the project to various degrees. We welcome contributions from anyone.

There are different groups within the project. Note that members of the different groups may overlap.

• GO Managers oversee and prioritize projects.
• Annotation: Responsible for developing annotation guidelines, as well as training and guiding biocurators in applying GO terms correctly to gene products. This group also includes phylogenetic annotation, annotation inferences across evolutionary related proteins based on known function of proteins within PANTHER phylogenetic family trees (annotations can be view with the Pantree browser).
• Ontology: This group is responsible for maintaining the ontology itself, and related products such as links to other resources.
• Quality Control: Ensures the integrity of the ontology and the annotations.
• Outreach: Responsible for the GO public presence and communication with the general research community, via the GO website, Twitter, the GO helpdesk, etc.
• Software and Utilities: Develops and implement the software required to build the ontology, generate annotations (Noctua), and view annotations (AmiGO).

Communication

• Phone conferences. The different groups meet on a regular basis via phone conferencing (zoom). Meetings are announced by email on one of the mailing lists, and are listed in the GO Google calendar. Follow the steps in the checklist of the New Member Onboarding: joining the GO project section of this document below.

• GOC consortium meetings. The GO consortium meets twice a year, alternating between American and European locations. Information about meetings can be found here: Consortium_Meetings_and_Workshops. Meetings are also announced on the go-consortium mailing list.

Project management: GitHub

• The GO consortium uses GitHub to track tasks for the various aspects of the project: software development, ontology maintenance, annotation issues, etc. See Instructions for GitHub for GO for details.
• Within GitHub, group of related tasks are organized into 'projects'. See GO projects for details.

All new members: joining the GO project

• Go over the Background reading on Ontologies, the Gene Ontology and Annotation.
• Register to the project at New User Onboarding

Checklist for all Gene Ontology Consortium Members and Contributors

1. Create a GitHub account at GitHub
2. * Check your mail (including spam), and accept the invitation when you receive it.
3. Create a ticket in the Gene Ontology's GitHub Helpdesk repository to request to (please copy the following list in the ticket):
4. * Be invited to the Gene Ontology Project: Please mention your role: Biocurator, software developer or domain expert.
5. * Get access to GO google drive: Please provide the email account you want to use
   If you are a consortium member, your permissions are handled by being added to the "go-consortium" Google Group
   If you are not a consortium member, your permissions are handled by being added to the "go-guest" Google Group
6. * Be added to the GO Google calendar, so you can view conference call information
7. * Be added to Group contacts: Please provide your expertise (1-3 keywords)
8. * Be added to users.yaml: Please provide your ORCID (can be obtained at ORCID), the name of your organization, and group.
9. Sign up to the GO-consortium mailing list. This will automatically also send you emails from the go-friends list.
10. Create a GO wiki account (optional)

Checklist for new Biocurators

• Annotation documentation, including Noctua documentation.
• Communication:
  • Attend Annotation and GO-CAM conference calls on Tuesdays; see the GO Google calendar for details.
  • GitHub: Biocurators should be following the ontology and annotation GitHub repositories.
    • For queries or feedback on specific tools, see the list of our Main repositories and their scope.
  • used regularly for smaller discussions, specific technical channels: GO Slack
  • less active: Genome Alliance Function Group Slack.

Checklist for new Software Developers

• Relevant orgs: http://github.com/geneontology/
  • See all pinned repos
• APIs, python
• ontobio documentation (Python)
• Noctua Stack technical docs
• For continuous Integration, we use GitHUb Actions for per-repo checks
• For data pipeline, we use Jenkins https://build.geneontology.org/ (GO pipeline)
• Communication:
  • https://groups.io/g/godev-internal/
  • GO Slack: Informal group chats

Checklist for new Ontology Editors

• Read the Ontology Editors manual:  Ontology Development documentation.
• Subscribe to the go-ontology email list.
• Follow the Ontology GitHub repository.
• Get an id range in go-idranges.owl.
• Do the GO Protege/OWL tutorial.

Checklist for new GO Managers, Product Owners, Technical Leads

• Subscribe to the go-managers email list.
• Attend weekly calls: Projects progress calls.

Useful links

• GO Google calendar
• GO GitHub Project
• GO website
• AmiGO
• Noctua
• GO wiki

Key contacts

Role	Name	GitHub handle	email
Project management & Ontology development	Pascale Gaudet	@pgaudet	pascalegaudet-at-swib.swiss
Technical Lead	Seth Carbon	@kltm	sjcarbon-at-lbl.gov
Annotation	Kimberly VanAuken	@vanaukenk	vanauken-at-caltech.edu
GO-CAM modeling	David Hill	@ukemi	david.hill-at-jax.org
Phylogenetic Annotation	Huaiyu Mi	@huaiyumi	huaiyumi-at-usc.edu
Outreach and User Support	Suzi Aleksander	@suzialeksander	suzia-at-stanford.edu

Review Status

Last reviewed: February 28, 2022