GO Internal

Guidelines for creating relationships between terms

GO wiki (new pages) - Fri, 11/16/2018 - 06:23

Pascale:

See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.


# To create asserted relationships in GO, use the <code>Subclass</code> field

== Review Status ==
Last reviewed: November 16, 2018

[http://wiki.geneontology.org/index.php/Ontology_Editing_Guide Back to: Ontology Editing Guide]

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

QCQA call 2018-11-13

GO wiki (new pages) - Tue, 11/13/2018 - 06:43

Pascale: /* Questions about QC rules */

GOC meeting Presentation: https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.p

=Define duplicate annotations=
To decide how to implement the proposed rule: Verify that we are not creating a duplicate annotation

=Questions about QC rules=
* Do we want reciprocal annotations for IGI ? (P2GO has a rule that checks for reciprocal annotations for IPI, except for self-binding): https://github.com/geneontology/go-site/pull/911
-> We probably cannot always have an annotation to the same term.
* Do we want to implement: New rule: Identify annotations to the function term "mRNA binding involved in post transcriptional gene silencing" (GO:1903231) that lack a corresponding annotation to the process term "gene silencing by miRNA" (GO:0035195) or one of its descendants https://github.com/geneontology/go-site/issues/921
-> Decided not to implement this one.
* New gorule Verify that we are not creating a duplicate annotation: is this already in the Noctua tracker ?
-> We probably do not want to implement this - we may need the same annotation/annoton in different models (or in the same model)
* Implement gorule-0000007? IPI should not be used with catalytic activity molecular function terms - are we OK with this ?

==Action items from the Montreal meeting==

Pascale: TO DO: Create tickets
* Check groupcontacts.csv in go-site/metadata and please update for GO curators in your group [annotation group].
* Add more explanation text to the matrix rule check data html page so curators know what they’re actually looking at on this page.
* Val suggests a report/list of violations for review for groups per species: Seth: may require rewriting the tool
* Annotation review tickets will be classified better wrt priority (we also need to articulate how we will assess priority).
* Assess where we stand wrt the signaling workshop. What needs to be wrapped up? What are the sticking points and why? How do we capture downstream effects of signaling pathways?
* Develop guidelines for annotation metrics in light of the increased contribution of annotation review to curator efforts. Consider how prioritization of annotating previously unannotated genes will be taken into account. Include metrics for comprehensive annotations and develop guidelines and a system for flagging genes/gene products as annotation complete (gpi specs) and make this publically available.
* Suzi - develop a ‘white list’ for specific pathways
* Review guidelines with curators: http://wiki.geneontology.org/index.php/Tips_to_Produce_High_Quality_Annotations


----

Topics carried over from previous calls:

==Annotation redundancy - non-experimental annotations==
* We need to define what constitutes a redundant information, WRT to sources, evidences and references
* There is a ticket that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440
* '''AI: Rules for flagging redundant annotations need to be documented - Chris'''
* https://github.com/geneontology/go-annotation/issues/2060
* https://github.com/geneontology/go-annotation/issues/1879

Different types of redundancy
* identical experimental annotations from different sources https://github.com/geneontology/go-annotation/issues/1404
* inferred and IEA, ISO, ISM, IBA annotations when EXP exist
* Redundant inferred annotations from GOC F-P links pipeline e.g. https://github.com/geneontology/go-site/issues/576
* TAS /NAS (special case)

There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present.
If somebody wants a complete set of annotations from a mapping resource these could be made available separately.

==New error reports - status==
http://snapshot.geneontology.org/reports/gorule-report.html
https://github.com/geneontology/go-site/issues/709

==Annotation from mutant phenotypes==
Guidelines (draft) : http://wiki.geneontology.org/index.php/Annotating_from_phenotypes



[[Category:Quality Control]] Pascale
Categories: GO Internal

Annotation Conf. Call 2018-11-13

GO wiki (new pages) - Mon, 11/12/2018 - 05:37

Vanaukenk: /* Agenda */

= Meeting URL =
*https://stanford.zoom.us/j/976175422

== GO Conference Calls ==
*Tuesdays at 8am PDT
**1st Tuesday: Alliance Biological Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

= Agenda =

== Review Action Items, Decisions, and Future Plans from Montreal GOC Meeting ==

=== Annotation QC/QC Reports ===
*New reports page: http://snapshot.geneontology.org/reports/gorule-report.html

=== Annotation Review ===
*Discussed how priorities are set for annotation review
*Use labels on go-annotation tickets to indicate which annotation reviews are high priority.
*Some annotation review tickets are marked 'high priority'. This means that the Annotation Group would like curators to review these annotations as soon as possible. Tickets are marked high priority when they are relevant to major ontology projects (for example, in 2018, signaling and transcription), or when annotations are incorrect and should rapidly be fixed. The requestor of the annotation review can set the high priority level, but the manager of the annotation group ca decide to increase/decrease the priority of any ticket.

=== GPAD as Main Annotation Exchange File Format ===
*Goal is to move to GPAD as the main annotation exchange file format within the GOC
*Some changes to the current GPAD specifications were discussed during one of the breakout sessions
*A formal specifications document with proposed changes will be presented for comments
*Timeline - roughly mid-to-late spring of 2019

= Minutes =
*On call:

[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-11-12

GO wiki (new pages) - Fri, 11/09/2018 - 10:42

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==Meetings== ===Ontology Developers' workshop=== * '''Logistics''': Geneva_ontology_editors_me..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

==Meetings==

===Ontology Developers' workshop===
* '''Logistics''': [[Geneva_ontology_editors_meeting-_Dec_10-13,_2018_-_Logistics]]
** Planning on Dec 8th arrival/Dec 14th departure; please let Pascale know if you arrive/depart on different days
* '''Agenda''': https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit

==Discussion topics==

===Preparation for Geneva===
* Progress update on Reactome xrefs
* Harold will use Docker to generate the Chebi import on the call.
** https://github.com/geneontology/go-ontology/pull/16601
* Import of Reactome into GO-CAM models.
** What are the issues?

===Report on RO meeting===
Chris
+ how to move forward with relations:
* What realtion do wee need for the Rhea alignment work?
* GO_REL versus RO
* P2GO versus GO_REL and RO (I think P2GO uses GO_REL- mostly)
* reaction participants and incorrect inferences in Noctua (for eg transcription)

===MetaCyc x reference===
Email by Tomer "MetaCyc2GO mapping file missing reactions"

24 Oct 2018

We didn't answer yet

*Wouldn't it make sense to roll this into the other xref work?

===Removing property chain transports_or_maintains_localization_of o part_of -> occurs_in===
https://github.com/geneontology/go-ontology/pull/16546

This was not in RO, it's injected via GO (we should check we are not injecting more)
How do we check that ?

= Minutes =
*On call:





[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

November 7, 2018

GO wiki (new pages) - Wed, 11/07/2018 - 06:42

Vanaukenk: Created page with "= Minutes = *Discussed ontology imports *Pascale will organize annotation review spreadsheets on Google drive into smaller time increments to make analysis easier **Review o..."

= Minutes =
*Discussed ontology imports

*Pascale will organize annotation review spreadsheets on Google drive into smaller time increments to make analysis easier
**Review outstanding spreadsheets on a future annotation call

*Progress reports due next month? Need to inform groups of due date

*Reviewed action items from Montreal meeting Vanaukenk
Categories: GO Internal

David, Kimberly, Pascale - Wednesday calls

GO wiki (new pages) - Wed, 11/07/2018 - 06:39

Vanaukenk: Created page with "November 7, 2018"

[[November 7, 2018]] Vanaukenk
Categories: GO Internal

Manager Call 2018-11-01

GO wiki (new pages) - Tue, 11/06/2018 - 02:02

Pascale: /* Montreal GOC Meeting Action Items and priorities */

= Meeting URL =

*https://stanford.zoom.us/j/754529609

= Agenda =

== Montreal GOC Meeting Action Items and priorities==
Reminder: SAB recommendations - high level priorities
* '''Major uses of GO'''
** mRNA expression analysis
** Proteomics data analysis
** Genetic data analysis
** DNA methylation analysis
** Other: (~50%) primarily comp biol and biomed informatics

* Keep doing: ontology + annotations = model of biology, broad accessibility to all
* And get even better: more expressive annotations, more QA and review, more collaboration, more APIs and better response times

'''SAB recommendations''':
* increase focus on QA
* Leverage authors of curated papers (~150K papers have been used, link from PubMed to GO for annotated papers) ----review (and curate new)
* Review of older annotations, highly annotated genes
* Develop GO-CAM use cases, promote in tool developer community
* Empower developer community (push use of recent GO annotations/ontology in tools, developer guide, website guide, APIs, build an R package to update GO annotations)



=== Public presence/Website===
* Deploy new website: see new design here: https://geneontology.github.io/
* PURLs for the ontology need to point to 'current' rather than 'snapshot' https://github.com/geneontology/go-site/issues/873



[[Category:GO Consortium]] [[Category:GO Managers Meetings ]] Pascale
Categories: GO Internal

When should you remove old annotations?

GO wiki (new pages) - Mon, 11/05/2018 - 07:14

Pascale: Created page with " Category: Annotation Category:Working Groups"




[[Category: Annotation]] [[Category:Working Groups]] Pascale
Categories: GO Internal

Annotating binding

GO wiki (new pages) - Mon, 11/05/2018 - 07:13

Pascale: Created page with " Category: Annotation Category:Working Groups"





[[Category: Annotation]] [[Category:Working Groups]] Pascale
Categories: GO Internal

Annotating regulation

GO wiki (new pages) - Mon, 11/05/2018 - 07:13

Pascale: Created page with " Category: Annotation Category:Working Groups"




[[Category: Annotation]] [[Category:Working Groups]] Pascale
Categories: GO Internal

Annotating from phenotypes

GO wiki (new pages) - Mon, 11/05/2018 - 07:11

Pascale: Created page with "Complete from https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.g44f4f58dad_0_96 What is the normal molecular function ? Being..."

Complete from https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.g44f4f58dad_0_96

What is the normal molecular function ?
Being ‘required for’ a process does not mean a protein is ‘part of’ a process
Pleiotropic effects should not usually be captured





[[Category: Annotation]] [[Category:Working Groups]] Pascale
Categories: GO Internal

QCQA call 2018-11-01

GO wiki (new pages) - Wed, 10/31/2018 - 04:45

Pascale: Created page with "Action items from the Montreal meeting * Check groupcontacts.csv in go-site/metadata and please update for GO curators in your group. * Add more explanation text to the matri..."

Action items from the Montreal meeting

* Check groupcontacts.csv in go-site/metadata and please update for GO curators in your group.
* Add more explanation text to the matrix rule check data html page so curators know what they’re actually looking at on this page.
* Val suggests a report/list of violations for review for groups per species.
* Annotation review tickets will be classified better wrt priority (we also need to articulate how we will assess priority).
* Assess where we stand wrt the signaling workshop. What needs to be wrapped up? What are the sticking points and why? How do we capture downstream effects of signaling pathways?
* Develop guidelines for annotation metrics in light of the increased contribution of annotation review to curator efforts. Consider how prioritization of annotating previously unannotated genes will be taken into account. Include metrics for comprehensive annotations and develop guidelines and a system for flagging genes/gene products as annotation complete (gpi specs) and make this publically available.
* Suzi - develop a ‘white list’ for specific pathways
* Review guidelines with curators: http://wiki.geneontology.org/index.php/Tips_to_Produce_High_Quality_Annotations



[[Category:Quality Control]] Pascale
Categories: GO Internal

Authorship guidelines

GO wiki (new pages) - Wed, 10/31/2018 - 03:43

Pascale: Created page with "=GOC publications: Author Guidelines= The GOC is a large and distributed group with multiple contributors and concurrent threads of development. In addition to the main NHGR..."

=GOC publications: Author Guidelines=

The GOC is a large and distributed group with multiple contributors and concurrent threads of development. In addition to the main NHGRI U41 grant, other funding lines support specific GOC activities and projects. Our program covers many aspects of research informatics including data integration, tool development, curation of molecular and genomic information, knowledge visualization, and community support. Our collective publication record is robust and growing. Here we detail guidelines for authorship in GOC publications.

# Publications that include authors funded by GOC U41 grant need to put funding source in Acknowledgements. The following text is recommended, particularly if the PIs are not authors.
“The Gene Ontology is funded by NIH NHGRI grant U41 002273 to multi-Pis Judith A Blake, J. Michael Cherry, Suzanna Lewis, Paul Thomas and Paul Sternberg."
# Papers with GOC-funded authors, whether or not a GO PI is an author, need sign-off from go-tops.
# Authorship is best discussed at the start of a project, with expected first and last authors on any projected papers discussed with those working on the project.
# Particularly with projects detailing work on a specific aspect of biology (such as apoptosis), it is important to consider including as authors all developers and curators who contributed to the specific project.
# Papers such as the GOC paper in the NAR special database issue in Jan, that include work from all active GOC funded people, can often be authored as ‘The Gene Ontology Consortium’ with a contributing author, and a list of Consortium members included at the end of the document.

[[Category:GO Consortium]] Pascale
Categories: GO Internal

Ontology meeting 2018-11-05

GO wiki (new pages) - Wed, 10/31/2018 - 02:35

Pascale: /* Ontology Developers' workshop */

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

==Meetings==

===Ontology Developers' workshop===
* '''Logistics''': [[Geneva_ontology_editors_meeting-_Dec_10-13,_2018_-_Logistics]]
** Planning on Dec 8th arrival/Dec 14th departure; please let Pascale know if you arrive/depart on different days
* '''Agenda''': https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit

===Discussion topics===
====Removing property chain transports_or_maintains_localization_of o part_of -> occurs_in====
https://github.com/geneontology/go-ontology/pull/16546

This was not in RO, it's injected via GO (we should check we are not injecting more)
How do we check that ?






= Minutes =
*On call:





[[Category: Ontology]]
[[Category: Meetings]] Pascale
Categories: GO Internal

GO-CAM and Noctua FAQs

GO wiki (new pages) - Tue, 10/23/2018 - 07:49

Vanaukenk: Created page with "= GO-CAM and Noctua FAQs = Category: Annotation Guidelines Category: GO-CAM Category: Noctua"

= GO-CAM and Noctua FAQs =

[[Category: Annotation Guidelines]]
[[Category: GO-CAM]]
[[Category: Noctua]] Vanaukenk
Categories: GO Internal

GO-CAM Working Group Call 2018-10-22

GO wiki (new pages) - Mon, 10/22/2018 - 07:21

Vanaukenk: Created page with "= Meeting URL = https://stanford.zoom.us/j/976175422 = Agenda = == Review Action Items from Montreal Meeting == = Minutes = *On call: Category: Annotation Workin..."

= Meeting URL =
https://stanford.zoom.us/j/976175422

= Agenda =

== Review Action Items from Montreal Meeting ==


= Minutes =
*On call:








[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-10-22

GO wiki (new pages) - Mon, 10/22/2018 - 04:57

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==Meetings== ===Ontology Developers' workshop=== Fall 2018 ontology editors meeting - potentia..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

==Meetings==

===Ontology Developers' workshop===
[[Fall 2018 ontology editors meeting - potential agenda topics]]
* Airfare from BGR to Geneva searched on Monday Oct 22. Main cabin on American $1379, leaving from Boston is the same.

===Montreal GOC Meeting===
*Recap of the Montreal Meeting



= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Ontology meeting 2018-10-15

GO wiki (new pages) - Fri, 10/12/2018 - 13:26

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==Meetings== ===Montreal GOC Meeting=== *http://wiki.geneontology.org/index.php/2018_Montreal_GO..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

==Meetings==

===Montreal GOC Meeting===
*http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda

===Ontology Developers' workshop===
[[Fall 2018 ontology editors meeting - potential agenda topics]]

== Editors Discussion ==


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Ontology meeting 2018-10-08

GO wiki (new pages) - Fri, 10/12/2018 - 13:24

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==Meetings== ===Montreal GOC Meeting=== *http://wiki.geneontology.org/index.php/2018_Montreal_GO..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

==Meetings==

===Montreal GOC Meeting===
*http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda

===Ontology Developers' workshop===
[[Fall 2018 ontology editors meeting - potential agenda topics]]

== Editors Discussion ==


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Annotation Conf. Call 2018-10-09

GO wiki (new pages) - Mon, 10/08/2018 - 07:40

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 == GO Conference Calls == *Tuesdays at 8am PDT **1st Tuesday: Alliance Biological Function **2nd Tuesday: GO Consortium..."

= Meeting URL =
*https://stanford.zoom.us/j/976175422

== GO Conference Calls ==
*Tuesdays at 8am PDT
**1st Tuesday: Alliance Biological Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Biological Function/GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

= Agenda =

== Montreal Meeting, October Wednesday, 17th - Friday, 19th ==
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda Agenda]

== Molecular Function Refactor ==
=== Distal/Proximal Promoter Binding Terms ===

== Pipeline ==
http://wiki.geneontology.org/index.php/Release_Pipeline
===Annotation File Formats===
====GPAD/GPI for Internal Consortium Annotation Exchange====
*At NYC meeting in May, proposal was made that we would eventually switch to using GPAD/GPI file format for data exchange within the consortium
*Reasons to switch to GPAD/GPI:
**Less redundacy
**Ability to use expanded set of annotation relations (gp2term)
**Ability to use unique ECO identifiers instead of 3-letter GO codes
**Annotation properties field - allows for capturing annotation metadata
*Many groups consume GPAD (any external group using Protein2GO; groups consuming derived GPAD from GO-CAM models)
*Not all groups produce a GPAD
*Any barriers to moving to GPAD/GPI?
*Timeline - by start of new year (2019)?

= Minutes =
*On call:

[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal