New member onboarding: Difference between revisions

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[[Category: GO Consortium]]
[[Category:GOC Overview]]
'''Welcome to the GO Consortium!'''
'''Welcome to the GO Consortium!'''


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=Project organization=
=Project organization=
The Gene Ontology project is a consortium made up of different groups and people associated with the project to various degree. We welcome contributions from anyone.  
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 (see also sidebar 'GOC Project' menu). Note that members of the different groups may overlap.
There are different groups within the project (see also sidebar 'GOC Project' menu). Note that members of the different groups may overlap.
* '''[[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_Project|phylogenetic annotation]]''', annotation inferences across evolutionary related proteins based on known function of proteins within '''[http://www.pantherdb.org/ PANTHER phylogenetic family trees]''' (annotations can be view with the [http://www.pantree.org/ Pantree] browser).  
* '''[[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_Project|phylogenetic annotation]]''', annotation inferences across evolutionary related proteins based on known function of proteins within '''[http://www.pantherdb.org/ PANTHER phylogenetic family trees]''' (annotations can be view with the [http://www.pantree.org/ Pantree] browser).  
* '''[[Ontology Development|Ontology]]:''' This group is responsible for maintaining the ontology itself, and related products such as links to other resources.  
* '''[[Ontology Development|Ontology]]:''' This group is responsible for maintaining the ontology itself, and related products such as links to other resources.  
* '''[[QC/QA_Group|Quality Control]]:''' Ensures the integrity of the ontology and the annotations.  
* '''[[Quality Control|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.
* '''[[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 ([http://noctua.berkeleybop.org/ Noctua]), and view annotations ([http://amigo.geneontology.org/amigo AmiGO]).  
* '''[[Software and Utilities]]''': Develops and implement the software required to build the ontology, generate annotations ([http://noctua.berkeleybop.org/ Noctua]), and view annotations ([http://amigo.geneontology.org/amigo AmiGO]).  
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==Communication==
==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 '''[https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar]'''. Follow the steps in the '''[[Documentation_for_New_Members#New_members:_joining_the_GO_project |New members: joining the GO project]]''' section of this document.  
*'''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 '''[https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar]'''. Follow the steps in the checklist of the '''[[New_Member_Onboarding#All_new_members:_joining_the_GO_project |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 <code>go-consortium mailing list</code>.
*'''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 <code>[https://mailman.stanford.edu/mailman/listinfo/go-consortium go-consortium mailing list]</code>.


==Project management: GitHub==
==Project management: GitHub==
* The GO consortium uses '''[https://github.com/geneontology/ 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.
* The GO consortium uses '''[https://github.com/geneontology/ 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 '''[[Instructions_for_GitHub_for_GO#GO_projects |GO projects]]''' for details.
* Within GitHub, group of related tasks are organized into 'projects'. See '''[[Instructions_for_GitHub_for_GO#GO_Projects |GO projects]]''' for details.


=New members: joining the GO project=
=All new members: joining the GO project=
* Go over the '''[[Background reading on Ontologies, the Gene Ontology and Annotation]]'''
* Go over the '''[[Background reading on Ontologies, the Gene Ontology and Annotation]].'''
* Register to the project at '''[https://github.com/geneontology/helpdesk/issues/new?assignees=&labels=&template=new-member-onboarding.md&title=New+User+Onboarding New User Onboarding]'''
==Checklist for all Gene Ontology Consortium Members and Contributors==
==Checklist for all Gene Ontology Consortium Members and Contributors==
#'''[http://wiki.geneontology.org/index.php/Special:CreateAccount Create a GO wiki account]'''
#'''[http://wiki.geneontology.org/index.php/Special:CreateAccount Create a GO wiki account]'''
#'''Create a GitHub account''' at [http://github.com GitHub]
#'''Create a GitHub account''' at [http://github.com GitHub]
#* Check your mail (including spam), and accept the invitation when you receive it.
#* Check your mail (including spam), and accept the invitation when you receive it.
#'''Get an ORCID''' at [https://orcid.org/signin ORCID]
#'''Create a ticket in the Gene Ontology's GitHub [https://github.com/geneontology/helpdesk/issues Helpdesk repository] to request to''' (please copy the following list in the ticket):  
#'''Create a ticket in the [https://github.com/geneontology/helpdesk/issues Helpdesk repo] to request to''' (please copy the following list in the ticket):  
#*'''Be invited to the Gene Ontology Project''': Please mention your role: Biocurator, software developer or domain expert.  
#*'''Be invited to the Gene Ontology Project''': Please mention your role: Biocurator, software developer or domain expert.  
#*'''Get access to GO google drive:''' Please provide the email account you want to use
#*'''Get access to GO google drive:''' Please provide the email account you want to use
#*'''Be added to the [https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar],''' so you can view conference call information
#*'''Be added to the [https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar],''' so you can view conference call information
#*'''Be added to [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv Group contacts]:''' Please provide your expertise (1-3 keywords)  
#*'''Be added to [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv Group contacts]:''' Please provide your expertise (1-3 keywords)  
#*'''Be added to [https://github.com/geneontology/go-site/blob/master/metadata/users.yaml Users]:''' Please provide your ORCID, the name of your organization, and [https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml group].
#*'''Be added to [https://github.com/geneontology/go-site/blob/master/metadata/users.yaml Users]:''' Please provide your ORCID (can be obtained at [https://orcid.org/signin ORCID]), the name of your organization, and [https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml group].
#'''Sign up to the [https://mailman.stanford.edu/mailman/listinfo/go-consortium GO-consortium mailing list]'''.  This also gives you emails to go-friends and go-discuss.
#'''Sign up to the [https://mailman.stanford.edu/mailman/listinfo/go-consortium GO-consortium mailing list]'''.  This will automatically also send you emails from the <code>[https://mailman.stanford.edu/mailman/listinfo/go-friends go-friends]</code> list.


==Checklist for new Biocurators==
==Checklist for new Biocurators==
* Annotation documentation: '''[[Annotation]]''', including '''[[Noctua |Noctua documentation]].'''
* [[Annotation|Annotation documentation]], including [[Noctua |Noctua documentation]].
* Communication:
* Communication:
** Attend '''[[Annotation#Annotation_Conference_Calls |Annotation]]''' and '''[[Annotation#GO-CAM_and_Noctua_Calls |GO-CAM conference calls]]''' (on Tuesdays; see the '''[https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar]''' for details).
** Attend [[Annotation#Annotation_Conference_Calls |Annotation]] and [[Annotation#GO-CAM_and_Noctua_Calls |GO-CAM conference calls]] on Tuesdays; see the [https://calendar.google.com/calendar?cid=Z2VuZW9udG9sb2d5QGdtYWlsLmNvbQ GO Google calendar] for details.
** GitHub: Biocurators should be following the '''[https://github.com/geneontology/go-ontology/issues ontology]''' and '''[https://github.com/geneontology/go-annotation/issues annotation]''' GitHub repositories.  
** GitHub: Biocurators should be following the [https://github.com/geneontology/go-ontology/issues ontology] and [https://github.com/geneontology/go-annotation/issues annotation] GitHub repositories.  
*** For queries or feedback on specific tools, see the list of our '''[[Instructions_for_GitHub_for_GO#Main_repositories_and_their_scope |Main repositories and their scope]]'''.  
*** For queries or feedback on specific tools, see the list of our [[Instructions_for_GitHub_for_GO#Main_repositories_and_their_scope |Main repositories and their scope]].
** '''[https://gitter.im/geneontology/go-annotation go-annotation Gitter]''': Live chat with other GO curators.
** [https://geneontologyworkspace.slack.com/home GO Slack]
** Slack: '''[https://alliance-project.slack.com/ Genome Alliance Function Group Slack]'''.  
** [https://alliance-project.slack.com/ Genome Alliance Function Group Slack].  
<!---(Note: If you have an @wormbase.org, @flybase.org, @uoregon.edu, @zfin.org, @stanford.edu, @morgan.harvard.edu, @berkeleybop.org, @lbl.gov, @jax.org, @mcw.edu, or @cam.ac.uk email address, you can create an account, can others create an account?)
<!---(Note: If you have an @wormbase.org, @flybase.org, @uoregon.edu, @zfin.org, @stanford.edu, @morgan.harvard.edu, @berkeleybop.org, @lbl.gov, @jax.org, @mcw.edu, or @cam.ac.uk email address, you can create an account, can others create an account?)
--->
--->
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* Relevant orgs: http://github.com/geneontology/
* Relevant orgs: http://github.com/geneontology/
** See all pinned repos
** See all pinned repos
* [http://github.com/berkeleybop/ Javascript libs]
* [http://github.com/owlcollab/ OWLTools]
* [http://github.com/biolink/ APIs, python]
* [http://github.com/biolink/ APIs, python]
* [http://ontobio.readthedocs.org ontobio documentation (Python)]
* [http://ontobio.readthedocs.org ontobio documentation (Python)]
* [https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Stack technical docs]
* [https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Stack technical docs]
* For continuous Integration, we use Travis for per-repo checks
* For continuous Integration, we use GitHUb Actions for per-repo checks
** http://build.berkeleybop.org
* For data pipeline, we use Jenkins https://build.geneontology.org/ (GO pipeline)
** https://build.geneontology.org/  
* Communication:
* Communication:
** https://groups.io/g/godev-internal/
** https://groups.io/g/godev-internal/
** Slack: function group on alliance slack
** [https://geneontologyworkspace.slack.com/home GO Slack]: Informal group chats
** [https://gitter.im/geneontology/noctua Gitter (for developers)]


==Checklist for new Ontology Editors==
==Checklist for new Ontology Editors==
* Read the Ontology Editors manual: '''[[Ontology Development| Ontology Development documentation]].'''
* Read the Ontology Editors manual: '''[[Ontology Development| Ontology Development documentation]].'''
* Subscribe to the <code>[https://mailman.stanford.edu/mailman/listinfo/go-ontology go-ontology email list]</code>.
* Subscribe to the <code>[https://mailman.stanford.edu/mailman/listinfo/go-ontology go-ontology email list]</code>.
* Be sure to follow the '''[https://github.com/geneontology/go-ontology/issues Ontology GitHub repository]'''.
* Follow the '''[https://github.com/geneontology/go-ontology/issues Ontology GitHub repository]'''.
* Get an id range in go-idranges.owl.
* Get an id range in go-idranges.owl.
* Do the '''[http://go-protege-tutorial.readthedocs.io/en/latest/ GO Protege/OWL tutorial]'''.
* Do the '''[http://go-protege-tutorial.readthedocs.io/en/latest/ GO Protege/OWL tutorial]'''.


==Checklist for new GO Managers==
==Checklist for new GO Managers, Product Owners, Technical Leads==
* Subscribe to the [https://mailman.stanford.edu/mailman/listinfo/go-managers go-managers email list].
* Subscribe to the <code>[https://mailman.stanford.edu/mailman/listinfo/go-managers go-managers email list]</code>.
* Attend weekly calls: [[GO_Managers_conference_call_minutes_and_rota |GO Managers calls agendas and minutes]]
* Attend weekly calls: '''[[Projects_progress |Projects progress calls]]'''.


==Useful links==
==Useful links==
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* '''[https://github.com/geneontology/ GO GitHub Project]'''
* '''[https://github.com/geneontology/ GO GitHub Project]'''
* '''[http://geneontology.org/ GO website]'''
* '''[http://geneontology.org/ GO website]'''
* '''[http://amigo.geneontology.org/amigo AmiGO]'''  
* '''[http://amigo.geneontology.org AmiGO]'''  
* '''[http://noctua.berkeleybop.org/ Noctua]'''
* '''[http://noctua.geneontology.org/ Noctua]'''
* '''[http://wiki.geneontology.org GO wiki]'''
* '''[http://wiki.geneontology.org GO wiki]'''


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! email
! email
|-
|-
|Project management
|Project management & Ontology development
|Pascale Gaudet
|Pascale Gaudet
|@pgaudet
|@pgaudet
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|@kltm
|@kltm
|sjcarbon-at-lbl.gov
|sjcarbon-at-lbl.gov
|-
|Bioinformatics Outreach
|Laurent-Philippe Albou
|@lpalbou
|albou-at-usc.edu
|-
|-
|Annotation
|Annotation
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|vanauken-at-caltech.edu
|vanauken-at-caltech.edu
|-
|-
|Ontology
|GO-CAM modeling
|David Hill
|David Hill
|@ukemi   
|@ukemi   
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|huaiyumi-at-usc.edu
|huaiyumi-at-usc.edu
|-
|-
|User Support
|Outreach and User Support
|Suzi Alexander
|Suzi Aleksander
|@suzialeksander  
|@suzialeksander  
|suzia-at-stanford.edu
|suzia-at-stanford.edu
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== Review Status ==
== Review Status ==


Last reviewed: April 11, 2019
Last reviewed: February 28, 2022

Revision as of 12:48, 16 March 2022

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 (see also sidebar 'GOC Project' menu). Note that members of the different groups may overlap.

  • 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).
  • GO Managers oversee and prioritize projects.

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.

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

Checklist for all Gene Ontology Consortium Members and Contributors

  1. Create a GO wiki account
  2. Create a GitHub account at GitHub
    • 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):
    • Be invited to the Gene Ontology Project: Please mention your role: Biocurator, software developer or domain expert.
    • Get access to GO google drive: Please provide the email account you want to use
    • Be added to the GO Google calendar, so you can view conference call information
    • Be added to Group contacts: Please provide your expertise (1-3 keywords)
    • Be added to Users: Please provide your ORCID (can be obtained at ORCID), the name of your organization, and group.
  4. Sign up to the GO-consortium mailing list. This will automatically also send you emails from the go-friends list.

Checklist for new Biocurators

Checklist for new Software Developers

Checklist for new Ontology Editors

Checklist for new GO Managers, Product Owners, Technical Leads

Useful links

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