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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. | 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= | =[[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 | There are different groups within the project. Note that members of the different groups may overlap. | ||
* '''[[Project_organization#GO_Managers|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_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. | ||
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* '''[[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]). | ||
==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#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>[https://mailman.stanford.edu/mailman/listinfo/go-consortium 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>. | ||
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=All 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== | ||
# '''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/new?assignees=&labels=&projects=&template=new-member-onboarding.md&title=New+User+Onboarding Helpdesk repository] to request to''' (please copy the following list in the ticket): | ||
#'''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): | # * '''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 <br /> If you are a consortium member, your permissions are handled by being added to the "go-consortium" Google Group <br /> If you are <i>not</i> a consortium member, your permissions are handled by being added to the "go-guest" Google Group | ||
#*'''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.yaml]:''' 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]. | ||
#*'''Be added to [https://github.com/geneontology/go-site/blob/master/metadata/users.yaml | # '''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. | ||
#'''Sign up to the [https://mailman.stanford.edu/mailman/listinfo/go-consortium GO-consortium mailing list]'''. This also | # '''[http://wiki.geneontology.org/index.php/Special:CreateAccount Create a GO wiki account] (optional)''' | ||
#''' | |||
==Checklist for new Biocurators== | ==Checklist for new Biocurators== | ||
* | * [[Annotation|Annotation documentation]], including [[Noctua |Noctua documentation]]. | ||
* Communication: | * Communication: | ||
** Attend | ** 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 | ** 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 | *** 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]]. | ||
** | ** used regularly for smaller discussions, specific technical channels: [https://geneontologyworkspace.slack.com/home GO Slack] | ||
** | ** less active: [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/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 | * For continuous Integration, we use GitHUb Actions for per-repo checks | ||
* | * For data pipeline, we use Jenkins https://build.geneontology.org/ (GO pipeline) | ||
* Communication: | * Communication: | ||
** https://groups.io/g/godev-internal/ | ** https://groups.io/g/godev-internal/ | ||
** [https://geneontologyworkspace.slack.com/home GO Slack]: Informal group chats | |||
** [https:// | |||
==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>. | ||
* | * 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 <code>[https://mailman.stanford.edu/mailman/listinfo/go-managers go-managers email list]</code>. | * Subscribe to the <code>[https://mailman.stanford.edu/mailman/listinfo/go-managers go-managers email list]</code>. | ||
* Attend weekly calls: '''[[ | * 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 | * '''[http://amigo.geneontology.org AmiGO]''' | ||
* '''[http://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 | ||
|- | |- | ||
|Annotation | |Annotation | ||
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|vanauken-at-caltech.edu | |vanauken-at-caltech.edu | ||
|- | |- | ||
| | |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 Aleksander | |Suzi Aleksander | ||
|@suzialeksander | |@suzialeksander | ||
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== Review Status == | == Review Status == | ||
Last reviewed: | Last reviewed: February 28, 2022 |
Latest revision as of 16:59, 27 February 2024
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
- 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
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 - * 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.yaml: Please provide your ORCID (can be obtained at ORCID), the name of your organization, and group.
- Sign up to the GO-consortium mailing list. This will automatically also send you emails from the
go-friends
list. - 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
Key contacts
Role | Name | GitHub handle | |
---|---|---|---|
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