Instructions for GitHub for GO: Difference between revisions

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[[Category: GO Consortium]]  
[[Category:GOC Overview]]


==GitHub account==
=Main repositories and their scope=
* '''[https://github.com/geneontology/helpdesk Helpdesk]'''. For general questions about GO, or if you are unsure which repo to submit a ticket to. 


==Main repositories and their scope==
* '''[https://github.com/geneontology/go-ontology Ontology]''' - Source files for the Gene Ontology.  
   


===[https://github.com/geneontology/helpdesk Helpdesk]===
* '''[https://github.com/geneontology/go-annotation Annotation]''' - Annotation queries/issues, disputes, including PAINT disputes.
The Gene Ontology Helpdesk.


===[https://github.com/geneontology/go-ontology Ontology]===
* '''[https://github.com/geneontology/go-site GO-site]''' - A collection of metadata, tools, and files associated with the Gene Ontology public web presence.  
Source ontology files for the Gene Ontology.


===[https://github.com/geneontology/go-annotation Annotation]===
* '''[https://github.com/geneontology/amigo AmiGO]''' bugs and feature requests for the AmiGO GO browser.
Annotation queries/issues, disputes, including PAINT disputes.


===[https://github.com/geneontology/go-site GO-site]===
* '''[https://github.com/geneontology/geneontology.github.io GO website]''' - The GO public presence, '''[http://geneontology.org/ geneontology.org]'''.
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.  


===[https://github.com/geneontology/amigo AmiGO]===
* '''GO-CAM models and Noctua'''
AmiGO bugs and feature requests.
** '''[https://github.com/geneontology/noctua-models noctua-models]''' - GO-CAM models repository.
 
** '''[https://github.com/geneontology/noctua noctua]''' - Repo for bug reports and feature requests for the Noctua Graph Editor workbench.
===[https://github.com/geneontology/geneontology.github.io GO website]===
** '''[https://github.com/geneontology/simple-annoton-editor simple-annoton-editor]''' - Repo for bug reports and feature requests for the Noctua Simple Annotation Editor workbench.
 
** '''[https://github.com/geneontology/neo neo] - Repo for bug reports and feature requests for the Noctua entity ontology.
===GO-CAM models and Noctua===
 
 
===GO-CAM models repository===
noctua-models
 
===Noctua stack===
Bugs/feature requests: noctua
 
 
===Noctua Simple Annotation Editor workbench===
Bugs/feature requests: simple-annoton-editor
 
===Noctua entity ontology===
neo
 
===Reasoner (?)===
noctua-reasoner = minerva
 
 
 
===PAINT bugs and feature requests for PAINT===
paint (Huaiyu?)


==Repo coordinators==
==Repo coordinators==
Each repo has a coordinator. The responsibilities of the coordinator are to:  
Each repo has a coordinator. The responsibilities of the coordinator are to:  
* Add assignee(s) to each issue
* Add assignee(s) to each issue.
* Add labels as appropriate
* Add labels as appropriate.
* Follow up
* Follow up.
* Propose prioritization for tickets (shared responsibility with product owner, technical lead, PIs, managers, creator of ticket, etc)
* Propose prioritization for tickets (shared responsibility with product owner, technical lead, PIs, managers, creator of ticket, etc).


==Procedure for using the GitHub repositories==


==Procedure for using the GitHub repositories==
* Create issue in the appropriate tracker.
* Create issue in the appropriate tracker
* If you want, add label for your group.
* If you want, add label for your group
* Other labels are added by the repo coordinator.
* Other labels are added by the repo coordinator


For operating on resource metadata on go-site, we have started a more specialized guide
[https://github.com/geneontology/go-site/blob/master/documentation/how-do-i-edit-metadata.md here].


==Tracking issues==
==Tracking issues==
 
When you are added as a member of the GO GitHub project, you automatically follow a number of repositories (different ones, depending on your role). By default, emails will be sent for all new and updated tickets. You can reduce this by going to the individual repo, and clicking on the 'eye' icon at the top right of the screen. Options are:
* '''Not watching: Be notified only when participating (ie when you comment on a ticket or manually watch it) or @mentioned.''' This is the optimal option to get relevant information.
* Releases only: Be notified of new releases, and when participating or @mentioned.
* Watching: Be notified of all notifications
* Ignoring: Never be notified


===Daily Emails to go-consortium===
===Daily Emails to go-consortium===
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* Github Annotation Tracker Update
* Github Annotation Tracker Update
Make sure to look at these emails and comment on tickets that may impact your work as appropriate.
Make sure to look at these emails and comment on tickets that may impact your work as appropriate.
=GO Projects=
* Within GitHub, group of related tasks are organized into '''Projects'''. 
* Projects may be associated with the '''[https://github.com/orgs/geneontology/projects top-level repository]''' or with '''individual repositories''' (see the 'Projects' tab within each repo, for example [https://github.com/geneontology/go-ontology/projects Ontology Projects]).
* Projects may represent a task with a specific goal (for example, the conversion of Reactome data into GO-CAM models), or an ongoing project (such as ontology development). In this case, projects are used to keep track of progress from one milestone to the next.
* '''Milestones''' usually correspond to GO Consortium meetings.
==Product Owner and Technical lead==
Each ongoing project has two key participants: the Product Owner and Technical lead.
* The '''Product Owner''' is responsible to provide user specifications for the project, and approve work done for public deployment.
* The '''Technical lead''' is responsible to propose technical solutions to implement the specifications, and to supervise the technical tasks.
* The Product Owner and Technical lead work together to agree on the scope of a project.
== Review Status ==
Last reviewed: April 11, 2019

Revision as of 19:30, 8 May 2019


Main repositories and their scope

  • Helpdesk. For general questions about GO, or if you are unsure which repo to submit a ticket to.
  • Ontology - Source files for the Gene Ontology.
  • Annotation - Annotation queries/issues, disputes, including PAINT disputes.
  • GO-site - A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
  • AmiGO bugs and feature requests for the AmiGO GO browser.
  • GO-CAM models and Noctua
    • noctua-models - GO-CAM models repository.
    • noctua - Repo for bug reports and feature requests for the Noctua Graph Editor workbench.
    • simple-annoton-editor - Repo for bug reports and feature requests for the Noctua Simple Annotation Editor workbench.
    • neo - Repo for bug reports and feature requests for the Noctua entity ontology.

Repo coordinators

Each repo has a coordinator. The responsibilities of the coordinator are to:

  • Add assignee(s) to each issue.
  • Add labels as appropriate.
  • Follow up.
  • Propose prioritization for tickets (shared responsibility with product owner, technical lead, PIs, managers, creator of ticket, etc).

Procedure for using the GitHub repositories

  • Create issue in the appropriate tracker.
  • If you want, add label for your group.
  • Other labels are added by the repo coordinator.

For operating on resource metadata on go-site, we have started a more specialized guide here.

Tracking issues

When you are added as a member of the GO GitHub project, you automatically follow a number of repositories (different ones, depending on your role). By default, emails will be sent for all new and updated tickets. You can reduce this by going to the individual repo, and clicking on the 'eye' icon at the top right of the screen. Options are:

  • Not watching: Be notified only when participating (ie when you comment on a ticket or manually watch it) or @mentioned. This is the optimal option to get relevant information.
  • Releases only: Be notified of new releases, and when participating or @mentioned.
  • Watching: Be notified of all notifications
  • Ignoring: Never be notified

Daily Emails to go-consortium

Automatic emails are sent daily to the go-consortium mailing list with a list of the new and updated tickets for these two trackers:

  • Github Ontology Tracker Update
  • Github Annotation Tracker Update

Make sure to look at these emails and comment on tickets that may impact your work as appropriate.

GO Projects

  • Within GitHub, group of related tasks are organized into Projects.
  • Projects may be associated with the top-level repository or with individual repositories (see the 'Projects' tab within each repo, for example Ontology Projects).
  • Projects may represent a task with a specific goal (for example, the conversion of Reactome data into GO-CAM models), or an ongoing project (such as ontology development). In this case, projects are used to keep track of progress from one milestone to the next.
  • Milestones usually correspond to GO Consortium meetings.

Product Owner and Technical lead

Each ongoing project has two key participants: the Product Owner and Technical lead.

  • The Product Owner is responsible to provide user specifications for the project, and approve work done for public deployment.
  • The Technical lead is responsible to propose technical solutions to implement the specifications, and to supervise the technical tasks.
  • The Product Owner and Technical lead work together to agree on the scope of a project.

Review Status

Last reviewed: April 11, 2019