New member onboarding: Difference between revisions
Jump to navigation
Jump to search
m (→Review Status) |
|||
(27 intermediate revisions by 2 users not shown) | |||
Line 1: | Line 1: | ||
[[Category: | [[Category:GOC Overview]] | ||
'''Welcome to the GO Consortium!''' | '''Welcome to the GO Consortium!''' | ||
Line 5: | Line 5: | ||
=Project organization= | =Project organization= | ||
The Gene Ontology project is a consortium | 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. | ||
* '''[[ | * '''[[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]). | ||
Line 16: | Line 16: | ||
==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 '''[[ | *'''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#New_members:_joining_the_GO_project |New Member Onboarding: joining the GO project]]''' section of this document. | ||
*'''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# | * Within GitHub, group of related tasks are organized into 'projects'. See '''[[Instructions_for_GitHub_for_GO#GO_Projects |GO projects]]''' for details. | ||
= | =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]].''' | ||
==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. | ||
#'''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 | |||
#*'''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 | ||
Line 38: | Line 37: | ||
#*'''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, 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 also gives you emails to go-friends and go-discuss. | ||
#'''Get an ORCID''' at [https://orcid.org/signin ORCID] | |||
==Checklist for new Biocurators== | ==Checklist for new Biocurators== | ||
* Annotation documentation: '''[[Annotation]]''', including '''[[Noctua |Noctua documentation]].''' | * Annotation documentation: '''[[Annotation]]''', 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://gitter.im/geneontology/go-annotation go-annotation Gitter]''': Live chat with other GO curators. | ||
** 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?) | ** 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?) | |||
---> | |||
==Checklist for new Software Developers== | ==Checklist for new Software Developers== | ||
Line 60: | Line 62: | ||
** https://build.geneontology.org/ | ** https://build.geneontology.org/ | ||
* Communication: | * Communication: | ||
* https://groups.io/g/godev-internal/ | ** https://groups.io/g/godev-internal/ | ||
* Slack: function group on alliance slack | ** Slack: function group on alliance slack | ||
* [https://gitter.im/geneontology/noctua Gitter (for developers)] | ** [https://gitter.im/geneontology/noctua Gitter (for developers)] | ||
==Checklist for new Ontology Editors== | ==Checklist for new Ontology Editors== | ||
* '''[[Ontology Development| Ontology Development documentation]]''' | * Read the Ontology Editors manual: '''[[Ontology Development| Ontology Development documentation]].''' | ||
* Subscribe to the [https://mailman.stanford.edu/mailman/listinfo/go-ontology go-ontology email list]. | * 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 | * Be sure to 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 | * Do the '''[http://go-protege-tutorial.readthedocs.io/en/latest/ GO Protege/OWL tutorial]'''. | ||
==Checklist for new GO Managers== | ==Checklist for new GO Managers== | ||
* 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: '''[[GO_Managers_conference_call_minutes_and_rota |GO Managers calls agendas and minutes]]'''. | ||
==Useful links== | ==Useful links== | ||
Line 126: | Line 126: | ||
|- | |- | ||
|User Support | |User Support | ||
|Suzi | |Suzi Aleksander | ||
|@suzialeksander | |@suzialeksander | ||
|suzia-at-stanford.edu | |suzia-at-stanford.edu | ||
Line 134: | Line 134: | ||
== Review Status == | == Review Status == | ||
Last reviewed: | Last reviewed: July 9, 2019 |
Revision as of 04:35, 9 July 2019
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.
- 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
Checklist for all Gene Ontology Consortium Members and Contributors
- Create a GO wiki account
- Create a GitHub account at GitHub
- Check your mail (including spam), and accept the invitation when you receive it.
- 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, the name of your organization, and group.
- Sign up to the GO-consortium mailing list. This also gives you emails to go-friends and go-discuss.
- Get an ORCID at ORCID
Checklist for new Biocurators
- Annotation documentation: Annotation, 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.
- go-annotation Gitter: Live chat with other GO curators.
- Slack: Genome Alliance Function Group Slack.
Checklist for new Software Developers
- Relevant orgs: http://github.com/geneontology/
- See all pinned repos
- Javascript libs
- OWLTools
- APIs, python
- ontobio documentation (Python)
- Noctua Stack technical docs
- For continuous Integration, we use Travis for per-repo checks
- Communication:
- https://groups.io/g/godev-internal/
- Slack: function group on alliance slack
- Gitter (for developers)
Checklist for new Ontology Editors
- Read the Ontology Editors manual: Ontology Development documentation.
- Subscribe to the
go-ontology email list
. - Be sure to follow the Ontology GitHub repository.
- Get an id range in go-idranges.owl.
- Do the GO Protege/OWL tutorial.
Checklist for new GO Managers
- Subscribe to the
go-managers email list
. - Attend weekly calls: GO Managers calls agendas and minutes.
Useful links
Key contacts
Role | Name | GitHub handle | |
---|---|---|---|
Project management | Pascale Gaudet | @pgaudet | pascalegaudet-at-swib.swiss |
Technical Lead | Seth Carbon | @kltm | sjcarbon-at-lbl.gov |
Bioinformatics Outreach | Laurent-Philippe Albou | @lpalbou | albou-at-usc.edu |
Annotation | Kimberly VanAuken | @vanaukenk | vanauken-at-caltech.edu |
Ontology | David Hill | @ukemi | david.hill-at-jax.org |
Phylogenetic Annotation | Huaiyu Mi | @huaiyumi | huaiyumi-at-usc.edu |
User Support | Suzi Aleksander | @suzialeksander | suzia-at-stanford.edu |
Review Status
Last reviewed: July 9, 2019