Annotation: Difference between revisions
Jump to navigation
Jump to search
(250 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
= Group Leaders = | |||
Pascale Gaudet and Kimberly Van Auken | |||
== | =Mission statement= | ||
* Educate GOC curators about best annotation practice | |||
* Enforce annotation rules/policies within GOC | |||
* Maintain the annotation/evidence code documentation | |||
* Train/assist new groups with annotations | |||
* Educate and keep all the annotating groups up-to-date with changes in file formats | |||
* Keep contributing groups up-to-date with ontology development and how it affects annotations | |||
= Annotation Documentation = | |||
[[Annotation Guidelines]] | |||
==General Annotation Documentation== | |||
{| class="wikitable" | |||
!Topic | |||
! Status | |||
! Last reviewed | |||
|- | |||
|[http://geneontology.org/docs/go-annotations/ General introduction to GO annotation - GO website] | |||
| Current | |||
| 2021-01-27 | |||
|- | |||
|[[Elements of an annotation]] | |||
| Current | |||
| 2019-04-11 | |||
|- | |||
|[[Guide to GO Evidence Codes]] | |||
| Current | |||
| 2018-02-23 | |||
|- | |||
|[[Tips to Produce High Quality Annotations]] | |||
| Current | |||
| 2019-04-11 | |||
|- | |||
| [[Annotation Relations]] | |||
| Draft | |||
| | |||
|- | |||
! colspan="3"| Annotation Extensions | |||
|- | |||
|[https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=1456134218 Annotation Extensions - Summary] | |||
| Current | |||
| 2021-06-10 | |||
|- | |||
| [[Annotation Extension | Annotation Extensions]] | |||
| Being reviewed | |||
| | |||
|- | |||
| [[Annotation Extension: Capturing cell and tissue types]] | |||
| To be reviewed | |||
| | |||
|- | |||
| [[Annotation Extension: Capturing participants]] | |||
| To be reviewed | |||
| | |||
|} | |||
==Topic-Specific Guidelines== | |||
{| {{Prettytable}} class='sortable' | |||
!Topic | |||
! Status | |||
! Last reviewed | |||
|- | |||
|[[Annotating from phenotypes]] | |||
| Current | |||
| 2018-12-18 | |||
|- | |||
| [http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual Apoptosis Curation Manual] | |||
| | |||
| | |||
|- | |||
| [[MicroRNA_GO_annotation_manual]] | |||
| Current | |||
| 2020-03-23 | |||
|- | |||
| [https://docs.google.com/document/d/1bqCxx7QUblrc9q4PIynbJzoCXv248UWBxJa7fguJyXs/edit# Transcription factors annotation manual] | |||
| Current | |||
| 2021-06-09 | |||
|- | |||
| [http://gocwiki.geneontology.org/index.php/Signaling Signaling] | |||
| | |||
| | |||
|- | |||
| [[Non-catalytic Molecular Functions]] | |||
| Current | |||
| 2022-05-19 | |||
|- | |||
| [[Annotating binding]] | |||
| Draft | |||
| 2020-05-04 | |||
|- | |||
| [[Annotating ligand-receptor pathways]] | |||
| To be reviewed | |||
| > 5 years old | |||
|- | |||
| [[Annotating regulation]] | |||
| To be reviewed | |||
| > 5 years old | |||
|- | |||
| [[Annotating downstream processes]] | |||
| Draft | |||
| | |||
|- | |||
| [[Guidelines for checkpoints]] | |||
| To be reviewed | |||
| | |||
|- | |||
| [[Response to x annotation guidelines]] | |||
| To be reviewed | |||
| | |||
|- | |||
| [[Multi-species processes]] | |||
| To be reviewed | |||
| | |||
|- | |||
| [[Experiment-Specific Annotation Guidelines]] | |||
| Draft | |||
| | |||
|} | |||
== Noctua and GO-CAM == | |||
{| class="wikitable" | |||
!Topic | |||
! Status | |||
! Last reviewed | |||
|- | |||
| [[Noctua |Noctua Curation Guide]] | |||
| Current | |||
| 2021- | |||
|- | |||
| [https://docs.google.com/document/d/1Yo2O7LWj1wdRGbbOlaxX_AFDl99T-P59JOf5YoebX0Q/edit# ART Documentation] | |||
| Current | |||
| 2021-05-26 | |||
|- | |||
| [[Noctua_MOD_Imports |Importing MOD annotations into Noctua]] | |||
| Draft | |||
| 2021- | |||
|} | |||
== | ==Annotation quality control== | ||
{| class="wikitable" | |||
!Topic | |||
! Status | |||
! Last reviewed | |||
|- | |||
|[[Annotation Review Request]] | |||
| Current | |||
| 2022-04-22 | |||
|- | |||
|[[Annotation maintenance]] | |||
| Current | |||
| 2020-08-20 | |||
|- | |||
|[[Proposal for Author Feedback for annotations]] | |||
| Draft | |||
| 2019-04-16 | |||
|- | |||
|[[QC procedures from contributing groups]] | |||
| Draft | |||
| 2019-03-14 | |||
|} | |||
==Guidelines for new Groups/new submissions == | |||
{| class="wikitable" | |||
!Topic | |||
! Status | |||
! Last reviewed | |||
|- | |||
| [[General guidance to submit annotations to the GO consortium]] | |||
| Under review | |||
| > 5 years ago | |||
|} | |||
= Communication = | |||
== Annotation Conference Calls == | |||
=== When === | |||
[ | * Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST | ||
* Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it. | |||
* Reminder emails are sent out to the go-consortium mailing list; [https://mailman.stanford.edu/mailman/listinfo/go-consortium sign up here.] | |||
=== How to Join === | |||
*Please consult the GO calendar for the meeting URL. | |||
*to join via phone: enter Meeting ID found on the GO calendar after dialing in | |||
*from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll) | |||
*from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717 | |||
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622 | |||
* | |||
( | |||
* | |||
* | |||
=== Agenda and Minutes === | |||
*[[ | *[[Annotation Call 2022 Agenda and Minutes]] | ||
*[[Annotation Call 2021 Agenda and Minutes]] | |||
*[[ | |||
*[[Annotation Call 2020 Agenda and Minutes]] | |||
[[ | |||
*Please contact Kimberly if there are items you would like to add to the agenda | |||
[[ | * Past Annotation Call Minutes: [[Annotation Call 2010 Minutes | 2010]] | [[Annotation Call 2011 Minutes |2011]] | [[Annotation Call 2012 Minutes | 2012]] | [[Annotation Call 2013 Minutes | 2013]] | [[Annotation Call 2014 Minutes | 2014]] | [[Annotation Call 2015 Minutes | 2015]] | [[Annotation Call 2016 Minutes | 2016]] | [[Annotation Call 2017 Minutes | 2017]] | [[LEGO Discussion Rota | LEGO Discussion Rota 2017]] | [[Annotation Call 2018 Agenda and Minutes | 2018]] | [[Annotation Call 2019 Agenda and Minutes | 2019]] | ||
== GO-CAM and Noctua Calls == | |||
Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls. | |||
We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation. | |||
=== Agenda and Minutes === | |||
[[ | *[[GO-CAM and Noctua 2019 Agenda and Minutes]] | ||
[[ | * Past Annotation Call Minutes: [[LEGO Annotation Calls 2015 Minutes | 2015]] | [[GO-CAM and Noctua 2016 Agenda and Minutes | 2016]] | [[GO-CAM and Noctua 2017 Agenda and Minutes | 2017]] | [[GO-CAM and Noctua 2018 Agenda and Minutes | 2018]] | ||
[[ | == GO Annotation on GitHub == | ||
* The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues. | |||
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-annotation here]. | |||
* Contact information for each group that contributes to the consortium is available [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv here] | |||
[[ | == GO Annotation on Slack == | ||
*The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service. | |||
*Curators are free to ask questions or share ideas on Slack, with issues elevated to more formal tracking (i.e. [https://github.com/geneontology/go-annotation github/go-annotation] or [[Annotation#Annotation_Documentation |wiki documentation]]), as appropriate. | |||
[ | == GO Annotation on Google Drive == | ||
* The Gene Ontology uses Google drive to host notes and spreadsheets for annotation review and annotation working groups. | |||
* The GO Annotation folder on Google Drive may be accessed [https://drive.google.com/drive/folders/0B8kRPmmvPJU3fmNRM2dYTnJmVXg4bG52bTZIdk8wdU53R2F1MDlubG90Rll5LTZqbEVVN3c here]. | |||
[ | == GO Consortium Mailing List == | ||
* Reminders about conference calls are sent to the go-consortium mailing list. | |||
* To subscribe to the go-consortium mailing list, please click [https://mailman.stanford.edu/mailman/listinfo/go-consortium here]. | |||
[[ | =Focused annotation projects= | ||
* [[Kidney Development]] (2009/2010) | |||
* [[Immunology]] (2006) | |||
=PAGES TO REVIEW= | |||
[[ | ==Intro to GO== | ||
* [[Submit_GO_annotations]] | |||
* [[Beginning Annotation SOP]] | |||
* Can we use the way this is presented ? [http://wiki.geneontology.org/images/b/b1/GOA_training_cutdown.pdf GOA Training slides] | |||
* [[Guidelines_for_literature-based_curation]] | |||
* [[Guidelines for electronic annotation methods]] | |||
* MGI IEA pipeline 2008: [[Electronic - Harold and Evelyn]] | |||
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1176400/ Clark et al., 2005] | |||
* [[Contributing_GO_Annotations]] | |||
* [[With_field]] | |||
* [[Authoritative_Database_Groups]] | |||
* Regulation [http://wiki.geneontology.org/index.php/Category:Regulation] | |||
* https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit | |||
* http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management | |||
* http://wiki.geneontology.org/index.php/Annotation_Issues_and_Management | |||
* [[GO annotation activities by central GO Consortium members]] | |||
[[ | ==To delete, archive, or retire== | ||
* [[Database_Objects]] | |||
* [[GO_annotation_fields_required_for_correct_display]] | |||
== | =To review= | ||
* [[Tools_ID_Mapping]] | |||
=== | = History = | ||
== [[Archived Pages]] == | |||
[[ | [[Category: GOC Overview]] |
Revision as of 05:32, 19 May 2022
Group Leaders
Pascale Gaudet and Kimberly Van Auken
Mission statement
- Educate GOC curators about best annotation practice
- Enforce annotation rules/policies within GOC
- Maintain the annotation/evidence code documentation
- Train/assist new groups with annotations
- Educate and keep all the annotating groups up-to-date with changes in file formats
- Keep contributing groups up-to-date with ontology development and how it affects annotations
Annotation Documentation
General Annotation Documentation
Topic | Status | Last reviewed |
---|---|---|
General introduction to GO annotation - GO website | Current | 2021-01-27 |
Elements of an annotation | Current | 2019-04-11 |
Guide to GO Evidence Codes | Current | 2018-02-23 |
Tips to Produce High Quality Annotations | Current | 2019-04-11 |
Annotation Relations | Draft | |
Annotation Extensions | ||
Annotation Extensions - Summary | Current | 2021-06-10 |
Annotation Extensions | Being reviewed | |
Annotation Extension: Capturing cell and tissue types | To be reviewed | |
Annotation Extension: Capturing participants | To be reviewed |
Topic-Specific Guidelines
Topic | Status | Last reviewed |
---|---|---|
Annotating from phenotypes | Current | 2018-12-18 |
Apoptosis Curation Manual | ||
MicroRNA_GO_annotation_manual | Current | 2020-03-23 |
Transcription factors annotation manual | Current | 2021-06-09 |
Signaling | ||
Non-catalytic Molecular Functions | Current | 2022-05-19 |
Annotating binding | Draft | 2020-05-04 |
Annotating ligand-receptor pathways | To be reviewed | > 5 years old |
Annotating regulation | To be reviewed | > 5 years old |
Annotating downstream processes | Draft | |
Guidelines for checkpoints | To be reviewed | |
Response to x annotation guidelines | To be reviewed | |
Multi-species processes | To be reviewed | |
Experiment-Specific Annotation Guidelines | Draft |
Noctua and GO-CAM
Topic | Status | Last reviewed |
---|---|---|
Noctua Curation Guide | Current | 2021- |
ART Documentation | Current | 2021-05-26 |
Importing MOD annotations into Noctua | Draft | 2021- |
Annotation quality control
Topic | Status | Last reviewed |
---|---|---|
Annotation Review Request | Current | 2022-04-22 |
Annotation maintenance | Current | 2020-08-20 |
Proposal for Author Feedback for annotations | Draft | 2019-04-16 |
QC procedures from contributing groups | Draft | 2019-03-14 |
Guidelines for new Groups/new submissions
Topic | Status | Last reviewed |
---|---|---|
General guidance to submit annotations to the GO consortium | Under review | > 5 years ago |
Communication
Annotation Conference Calls
When
- Calls are held on Tuesdays at 4:00pm GMT, 11:00am EST, 8:00am PST
- Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it.
- Reminder emails are sent out to the go-consortium mailing list; sign up here.
How to Join
- Please consult the GO calendar for the meeting URL.
- to join via phone: enter Meeting ID found on the GO calendar after dialing in
- from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)
- from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
- from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622
Agenda and Minutes
- Please contact Kimberly if there are items you would like to add to the agenda
- Past Annotation Call Minutes: 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | LEGO Discussion Rota 2017 | 2018 | 2019
GO-CAM and Noctua Calls
Note that as of 2020, we are no longer distinguishing GO-Annotation and GO-CAM/Noctua calls.
We will meet regularly on Tuesdays at 8am PST to discuss annotation issues related to both standard and GO-CAM annotation.
Agenda and Minutes
GO Annotation on GitHub
- The Gene Ontology uses an issue tracker hosted on GitHub to record and track annotation issues.
- The go-annotation repo on GitHub may be accessed here.
- Contact information for each group that contributes to the consortium is available here
GO Annotation on Slack
- The GO consortium uses GO Slack as an informal chat service.
- Curators are free to ask questions or share ideas on Slack, with issues elevated to more formal tracking (i.e. github/go-annotation or wiki documentation), as appropriate.
GO Annotation on Google Drive
- The Gene Ontology uses Google drive to host notes and spreadsheets for annotation review and annotation working groups.
- The GO Annotation folder on Google Drive may be accessed here.
GO Consortium Mailing List
- Reminders about conference calls are sent to the go-consortium mailing list.
- To subscribe to the go-consortium mailing list, please click here.
Focused annotation projects
- Kidney Development (2009/2010)
- Immunology (2006)
PAGES TO REVIEW
Intro to GO
- Submit_GO_annotations
- Beginning Annotation SOP
- Can we use the way this is presented ? GOA Training slides
- Guidelines_for_literature-based_curation
- Guidelines for electronic annotation methods
- MGI IEA pipeline 2008: Electronic - Harold and Evelyn
- Clark et al., 2005
- Contributing_GO_Annotations
- With_field
- Authoritative_Database_Groups
- Regulation [1]
- https://docs.google.com/document/d/1HyOW6oYu9ZxQlHRbZqIgv73L-_fdaXmFhtZPi83DBSU/edit
- http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management
- http://wiki.geneontology.org/index.php/Annotation_Issues_and_Management
- GO annotation activities by central GO Consortium members
To delete, archive, or retire
To review