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Ontology meeting 2018-12-17

GO wiki (new pages) - Mon, 12/17/2018 - 06:41

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

= Conference Line =

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

= Agenda =

==Meetings==

===Ontology Developers' workshop===
* '''Agenda''': https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit

==Discussion topics==

===Progress Report===
* Priorities for next year.

= Minutes =
*On call:





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

Annotation Conf. Call 2018-12-18

GO wiki (new pages) - Mon, 12/17/2018 - 06:13

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: Alliance Biological Function
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

= Agenda =

== Progress Reports ==
*Due this week
*Template is here: https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9
*Rename the file and save in the same location.
*Any questions or issues?

== Ontology Editor's Geneva Meeting ==
*The ontology editor's met in Geneva last week to discuss plans to align reactions amongst GO - Rhea - Reactome.
*The plan is that, going forward, Rhea reactions will be the authoritative source for GO catalytic activity terms.
*We also reviewed and discussed conversion of Reactome pathways to GO-CAM models (Ben Good's work).

== Annotation Guidelines ==
*We would like to discuss new guidelines written for annotating from mutant phenotypes:
**[http://wiki.geneontology.org/index.php/Annotation#Annotating_from_phenotypes Annotating from phenotypes]

== 2019 ==
*Next consortium-wide call: Tuesday, January 8th, 2019


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

Manager Call 2018-12-19

GO wiki (new pages) - Thu, 12/13/2018 - 08:52

Pascale:

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

= Agenda =

* Abstract for biocuration? Moving towards a common shared curation community. No-one volunteering to steer right now. Technical updates or curation-centric?

* Who is attending ISB (Please add here)?

==Annual report==
* Reminder that each WG (ontology, annotation, PAINT, outreach, QC) and annotation group needs to submit a report
* No template for WG.
* Reports are to be submitted in the Google drive: https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9
# Need to add plans for next year as well.

==Next few weeks==
* Alliance grant due Jan 31; Xmas holidays coming up
* What is the impact on the work that people can do on GO? (esp: Chris, Seth, Kimberly, David - anyone else directly involved in Alliance and also key in GO?)
# We need to be aware of this.

==Follow up on priorities==

* '''Release tasks update'''

* '''GO website migration''':
# Status
# What will happen with the help desk?

* '''Noctua+GO-CAM repository''': Moving existing non-GO-CAM annotations to GO central: Jim, Ben, Chris, Seth: strategy

# Created a project; https://github.com/orgs/geneontology/projects/34



==Next hackathon==
Early February in LA?

Proposed aims (David, Kimberly, Pascale):
* import of legacy annotations & GP2term relations
** also for importing legacy annotations - mapping existing annotation extensions to GO-CAM models

# We will follow up by email, but it is looking like late February.

==On call==




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

Outreach

GO wiki (new pages) - Thu, 12/13/2018 - 06:46

Pascale:



==GO helpdesk==
*[[gohelp|GO helpdesk]]

==GO seminars==
We will invite GO users and tool developers to present their work, to increase interactions with users and take user needs into account when we make new development.

Will start in 2019.

=Old working groups related to Outreach=
MUST REVIEW THESE PAGES

The purpose of the User Advocacy group is to establish lines of communication between the scientific community and the GO Consortium. The goal is to ensure that the GOC does not become insular and remains receptive to the needs of the scientific community. In addition, open lines of communication will increase the awareness and usefulness of GO in the scientific community.

This purpose includes:
#ensuring that changes in the GO are publicized and communicated to the community
#acting as a broker between the community and the GOC so that the GOC does not become insular
#providing user support for the products produced by GO
#providing documentation for the products produced by GO.

This group will ensure that GO remains useful, relevant, and accessible to the scientific community. This [[Media:Advocacy_diagram_v4.jpg|figure]] outlines this group's aims and organisation.

==Sections:==

*[[gohelp|GO helpdesk]]



'''Other:'''

*[[GO survey 2009/10]]
*[[users_meetings|Future Users Meetings]]
*[[tools_standards|Standards for GO tools]]
*[[journals_advice|RSC journals: marking up text]]

==Old pages to review==

* [[Mock-ups for GO website]]
*[[:Category:AmiGO working group | AmiGO Working Group]]

*[[Outreach and Advocacy]]
*[[Annotation Outreach group summary|Group summary]]
* [[Annotation Outreach group reports|Reports]]
* [[Metrics]]
* [[Priorities]]
* [[Annotation Outreach group meetings|Meeting minutes]]


* See also http://wiki.geneontology.org/index.php/Category:AmiGO

==Users meetings==
[[Avian GO Workshop May 2008]]<br>

==Retired==
*[[GO news digest| GO News Digest]]
*[[newsletter]] - discontinued as of Oct 2008. See [[news feed]].
*[[news feed|News pages]]
*[[News group]]
*[[Annotation_Outreach_group_reports|Annotation_Outreach_group Monthly Reports]]


*[[User Advocacy group summary (Retired)]]
*[[User Advocacy group aims 2006 (Archived)]]


*[[Web Presence Working Group: Meetings (Archived)]]
*[[AmiGO: Prototypes]]



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

Annotation Conf. Call 2018-11-27

GO wiki (new pages) - Thu, 11/29/2018 - 03:55

Pascale: 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: GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: Alliance Biological Function
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

= Agenda =

==GO Rules reports==
*Curators should begin reviewing their reports.html file under the snapshot release and begin to address any errors that have been flagged.
*Curators should think about what enhancements could be made to the annotation error reports most efficient to use/work with. Ruth’s suggestion: review Protein2GO email reports.


== Progress Reports ==
*Due December 19th
*Template is here: https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9
*Rename the file and save in the same location.


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

Manager Call 2018-12-05

GO wiki (new pages) - Thu, 11/29/2018 - 03:47

Pascale: Created page with "*https://stanford.zoom.us/j/754529609 = Agenda = ==Annual report== * Reminder that each WG (ontology, annotation, PAINT, outreach, QC) and annotation group needs to submit a..."

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

= Agenda =

==Annual report==
* Reminder that each WG (ontology, annotation, PAINT, outreach, QC) and annotation group needs to submit a report
* No template for WG.
*Reports re to be submitted in the Google drive: https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9




==On call==

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

Ontology meeting 2018-12-03

GO wiki (new pages) - Wed, 11/28/2018 - 05:28

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
* '''Draft Agenda''': https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit

==Discussion topics==

===Preparation for Geneva===
In preparation for the meeting, we should all have a look at the project describing our tasks:
* https://github.com/geneontology/go-ontology/projects/10


= Minutes =
*On call:





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

GO-CAM Working Group Call 2018-11-27

GO wiki (new pages) - Mon, 11/26/2018 - 10:31

Vanaukenk: /* GO-CAM Relations */

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

== Progress Reports ==
* 2018 progress reports are due Wednesday, December 19th
* For working groups, [https://drive.google.com/drive/folders/0B8kRPmmvPJU3NnNzdnBFSlRwam8 folder for 2018 reports], with [https://docs.google.com/document/d/15HObk9-uPxYrgHaOK6RKKCbGJybnOrdoIr4JtkUTdjM/edit template], is on the GO's Google drive.

== GO-CAM Relations ==
*causally upstream of, positive effect - http://wiki.geneontology.org/index.php/Causally_upstream_of,_positive_effect
*contrast causally upstream of, positive effect with direct regulation
**In the clocka model, the activity of the clocka TF is 'part of' a process that is 'causally upstream of, positive effect' on the activity of its transcriptional target, smad3a
**Contrast this with the activity of a gene product, such as

== GO-CAM GPAD - Pipeline ==
*Currently, GPAD files are available here:
**http://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/
*Check with Seth on status of:
**[https://github.com/geneontology/pipeline/issues/65 Port build.berkeleybop.org export-lego-to-legacy to give new home to GO-CAM pick-ups]
* Proposed new (transitional) location for Noctua GO-CAM pick up:
**"noctua_RESOURCE.gpad.gz" in http://snapshot.geneontology.org/products/annotations/
***Example: "noctua_wb.gpad.gz"

= Minutes =
*On call:





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

Causally upstream of, positive effect

GO wiki (new pages) - Mon, 11/26/2018 - 07:23

Vanaukenk: /* Review Status */

== Overview ==
The 'causally upstream of, positive effect' relation is used to relate two GO Biological Processes or a GO Biological Process to a GO Molecular Function.

=== Definition ===

*Needs formal RO definition.
*Proposal: p is causally upstream of, positive effect on q if and only if p precedes q and p and q are linked in a causal chain whereby completion/execution/progression of p increases the frequency, rate or extent of q

*RO comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

=== Child Terms ===

== Examples of Usage ==
Exemplar:http://noctua.geneontology.org/editor/graph/gomodel:5a5fc23a00000137

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect]

== Review Status ==

Last reviewed: November 26, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-11-26

GO wiki (new pages) - Wed, 11/21/2018 - 05:09

Pascale: 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===


===Inferred Taxon constraints==
(Pascale): Is there any way to view inferred taxon constraints somewhere? See question here: https://github.com/geneontology/go-ontology/issues/16047#issuecomment-440631092

= Minutes =
*On call:





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

QCQA call 2018-11-27

GO wiki (new pages) - Tue, 11/20/2018 - 08:09

Pascale: Created page with " GOC meeting Presentation: https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.p ==Annotation review status== Pascale - update..."


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


==Annotation review status==
Pascale - update ?


==GO rules status==
Seth - update ?


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

==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].
* 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.



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

November 21, 2018

GO wiki (new pages) - Tue, 11/20/2018 - 06:12

Vanaukenk: Created page with "*Review progress report format"

*Review progress report format Vanaukenk
Categories: GO Internal

Manager Call 2018-11-21

GO wiki (new pages) - Mon, 11/19/2018 - 08:41

Pascale: /* Agenda */

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

= Agenda =

==Follow up on priorities==
* '''Release''': came out on Nov 16:
** Suzi, will you announce ? Do we have a process?
** Why was it delayed? Do we need more resources on releases ?
* '''GO website migration''': Suzi L/Laurent-Philippe: Aim: Dec 1 -> Are there any delays?
** Requires many technical tasks that mostly require Seth
* '''Data release pipeline''': Pascale/Seth: Are there any blocking issues remaining? If not, we can de-prioritize this for now
** Many steps are inefficient and slow
** More work needs to be done: Most work is done by Eric right now - can anyone else help on that ? Paul can find more resources - what do we need ?
** In the longer term: We need a person who will be responsible for the pipeline - possibly 25% (long-term estimate)
* '''Noctua+GO-CAM repository''': Kimberly/Seth/David:
** A developer is needed full time to develop until the Cambridge meeting:
** Tasks: (just a teaser):
*** getting in all existing annotations in - including implementing gp2term relations implemented
**** Chris: We will not be able to bring in everyone's annotations in by Cambridge
**** Back end: how much work will that be? Issues, we need to figure out how to partition annotations. We have some research work about this, there are many possible ways. We need to decide on the strategy.
**** Paul: is there a solution where nothing is connected at first (ie, 1 model for every annotation)? This would avoid create dependencies on connections AT FIRST. Advantage is that every group could move to Noctua as soon as that's in place. Otherwise we will likely be delayed.
**** David: we need to have a plan for how models/individual annotations will be handled/re-merged
**** Kimberly: AI we should make a Google doc - TO DISCUSS at the next managers call (?)
**** Pascale: we also need to think about doing QC on the automatic tools that would predict connectivity - that will take quite some time too, so prefers a more simple solution
**** Chris suggests doing an experiment in which we test integrating unconnected annotations, for example starting with dictyBase
**** Proposed import process: take triples out of each model
*** improve RO – who should do that? Including testing property chains:
**** Chris: We can have a bit of Jim's time on this.
**** David: What will we do about the different 'participants' relations - are we just moving forward ? Chris: yes
*** work on reasoning
*** fixing issues with pipeline (including GPAD output)
**** required GPAD2, which will require some plumbing and will break for a lot of people: people importing GPAD
**[https://docs.google.com/document/d/1FSWy7mvsSN7yZ10TL5CzSeJrzverub_oYwHY25bKD9o/edit Noctua Roadmap]
* '''GO rules (includes QC)''': Pascale/Eric: Improving reports: end of 2018, implement/fix some rules 4 rules /month?
* '''Tools''':
** GO API implementation (Laurent-Philippe / Deepak)
** Bioinformatics Guide (how to):
*** Ontology manipulation / traversal (parents, children, slim, related terms, etc)
*** Search / Browse / Aggregate annotations (e.g. per gene, taxon, pathway, aspect, etc)
*** Interactive Online Notebooks:
**** Jupyter (Python)
**** R Markdown (R)

Projects:
* '''Data release pipeline''': Pascale/Seth
* '''GO rules (includes QC)''': Pascale/Eric
* '''GO website migration''': Suzi L/Laurent-Philippe
* '''Noctua''': Kimberly/Seth
* '''GO-CAM integration with other pathway resources''': Paul/Ben/David
* '''QC''': ->
* '''Annotation & ontology''': no specific project
'''External'''
* CHEBI
* Complete proteomes
* Contributing groups

==Next hackathon==
Early February in LA?

Proposed aims (David, Kimberly, Pascale):
* import of legacy annotations & GP2term relations
** also for importing legacy annotations - mapping existing annotation extensions to GO-CAM models

===Action items===
https://docs.google.com/document/d/13BIc-zYaxIkIfK21Jhfk74pNq2jvtjepFdSGd6twpdw/edit#




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

GO-CAM Working Group Call 2018-11-20

GO wiki (new pages) - Mon, 11/19/2018 - 05:48

Vanaukenk: /* Progress Reports */

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

== Progress Reports ==
* 2018 progress reports are due December 19th, 2018
* Folder for 2018 reports, with template, and 2017 reports for reference is on the [https://drive.google.com/drive/folders/0B8kRPmmvPJU3NnNzdnBFSlRwam8 Google drive]

= Minutes =
*On call:





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

Ontology meeting 2018-11-19

GO wiki (new pages) - Mon, 11/19/2018 - 03:48

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 'currency chemicals'.
** https://github.com/geneontology/go-ontology/pull/16597
* 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?


===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

QCQA call 2018-11-20

GO wiki (new pages) - Mon, 11/19/2018 - 02:01

Pascale:


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


==Annotation review: capturing correct annotations==

see for example:
https://docs.google.com/spreadsheets/d/1AYSL_Lzy-BgmYKwaXyjEIOuSK2gankC1EOtSlCW_Vfo/edit#gid=0

==Annotation review - incomplete responses stats==
Pascale created new spreadsheet: https://docs.google.com/spreadsheets/d/1eBVWKfpYFBPC--sSiipzakGswFTTNLPgNsiqDH8-keU/edit#gid=0


==Annotation review==
https://drive.google.com/drive/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_
Separate completed Google spreadsheets by date - see

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

----


==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.



[[Category:Quality Control]] Pascale
Categories: 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