GO Internal

Ontology meeting 2017-11-20

GO wiki (new pages) - Fri, 11/17/2017 - 10:41

Vanaukenk: /* Editors Discussion */

= Conference Line =

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

= Agenda =
== Documentation on Asserted Parents ==
*Deleting asserted parents was already included in the section on [https://github.com/geneontology/go-ontology/blob/master/docs/CreateNewTerm.md CreateNewTerm].
*Does it need to be somewhere else?
*Is it not clear enough?
==GH project link==
https://github.com/geneontology/go-ontology/projects/1

== Editors Discussion ==
*[https://github.com/geneontology/go-ontology/issues/14579 GO:0043683 type IV pilus biogenesis parentage]
**cellular component assembly vs biogenesis vs morphogenesis - any guidelines for deciding when to instantiate which terms?

= Minutes =
*On call:





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

Publications, Talks, Posters 2017

GO wiki (new pages) - Fri, 11/17/2017 - 07:45

Hdrabkin: Publications

Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 6:10. https://doi.org/10.1186/s13630-017-0054-8 Hdrabkin
Categories: GO Internal

Grant Progress reports 2017

GO wiki (new pages) - Fri, 11/17/2017 - 07:26

Hdrabkin: Catagory:Reports

== Subcontract Projects ==
===Infrastructure===

[[Berkely Software Infrastructure]] This is linked to 2015; rename to begin new


===MOD Annotation Groups===
[http://wiki.geneontology.org/images/3/39/MODProgressReportTemplate_2008.doc MOD template]

[[MGI December 2017]

[[WormBase December 2017]]

[[EcoliWiki December 2017]]

[[RGD December 2017]]

[[dictyBase December 2017]]

[[FlyBase December 2017]]

[[TAIR December 2017]]

[[GOA December 2017]]

[[PomBase_December 2017]]

[[SGD_December 2017]]

[[UCL_December 2017]]

[[ZFIN_December 2017]] Hdrabkin
Categories: GO Internal

Annotation Conf. Call 2017-11-28

GO wiki (new pages) - Wed, 11/15/2017 - 12:42

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = == Guidelines for Annotation Display == == Signaling Project == *Review of cAMP-related signaling and biosynt..."

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

= Agenda =
== Guidelines for Annotation Display ==
== Signaling Project ==
*Review of cAMP-related signaling and biosynthesis terms



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

Manager Call 2017-11-15

GO wiki (new pages) - Mon, 11/13/2017 - 02:18

Pascale: Created page with " PanTree IDs in 'with' column https://github.com/geneontology/go-annotation/issues/1673 Category: GO Managers Meetings"





PanTree IDs in 'with' column
https://github.com/geneontology/go-annotation/issues/1673



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

Ontology meeting 2017-11-13

GO wiki (new pages) - Fri, 11/10/2017 - 08:35

Vanaukenk: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = * Logical definition vs. asserted terms (Pascale): I have been removing SubClasses when they are..."

= Conference Line =

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

= Agenda =

* Logical definition vs. asserted terms
(Pascale): I have been removing SubClasses when they are redundant with the logical definition. But in some releases of the ontology they are not added back. Would it be safer to always assert both?
See for example: GO:0015603 - I would have removed the SubClasses.

==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==
*On call:



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

2017-11-08

GO wiki (new pages) - Wed, 11/08/2017 - 11:54

David:

= Agenda =

== Ontology ==
*Managing tickets, training, editors' calls for November
*Reviewing minimal information for new term requests
**https://github.com/geneontology/go-ontology/blob/master/CONTRIBUTING.md

== Annotation ==
*transport do not annotate
**[https://github.com/geneontology/go-annotation/issues/1648 improving specificity by banning high level terms]
*HTP data
**[https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]
*signaling workshop follow-up
*Noctua/GO-CAM
**groups in users.yaml



[[Category:GO Managers Meetings ]] Vanaukenk
Categories: GO Internal

GO-CAM November 8th, 2017

GO wiki (new pages) - Tue, 11/07/2017 - 12:46

Vanaukenk: /* Minutes */

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =

== Noctua GitHub Organization ==
*Using projects to organize tickets
*Using milestones for ticket prioritization

== Requirements/Roadmap ==
[[https://docs.google.com/document/d/1dfPnt8fHtO3gP9Xr76SUF90aiDtT3K_2KqhanMFfsXo/edit Noctua Requirements/Roadmap]]

== GPAD Outputs ==
*[https://github.com/geneontology/noctua/issues/500 GPAD missing annotations via 'causally upstream of'?]
*[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000110 TEST: causally upstream of - KRC]
*With Chris, Jim, and Karen out for today's call, I suggest that we take up these issues again on the next GO-CAM call on November 8th

*ACTION ITEM: on a future GO-CAM call, review the Inference Explanations for some models

== Attribution ==
[https://github.com/geneontology/noctua/issues/458 Attribution with GO-CAM exports to GOC annotation files]

== Simple Annoton Editor ==

[https://github.com/geneontology/noctua/issues/492 dealing with blank MF in the simple annoton editor]

[https://github.com/geneontology/simple-annoton-editor/issues/12 Extend form to include standard GO-CAM model fields]

[https://github.com/geneontology/simple-annoton-editor/issues/10 Bare MF annotation should generate part-of triples]

*Editor enhancements to come:
**Ability to add basic set of annotation extensions, e.g. has_input for an MF
**Ability to just add a CC annotation and get the resulting part_of annotation in the graphical interface

= Minutes =
*On call:




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

2017 November Berkeley Noctua Developers Meeting

GO wiki (new pages) - Mon, 11/06/2017 - 12:49

Cjm: Created page with " = Agenda (Draft) = = Logistics = == Accommodations == You can get the lab rate and any of these hotels: * http://travel.lbl.gov/air_car_hotel/preferred_hotels.html * Clos..."


= Agenda (Draft) =

= Logistics =

== Accommodations ==

You can get the lab rate and any of these hotels:

* http://travel.lbl.gov/air_car_hotel/preferred_hotels.html
* Closest hotel: http://www.fourpointssanfranciscobaybridge.com/ -- However, it is still 30 mins walk away
* The most pleasant option is to stay in downtown berkeley and get the lab shuttle in the morning. Others may be staying here: http://www.senshotelberkeley.com
* Non-lab employees may want to look on airbnb

== Parking ==

Park temporarily and grab a parking pass from the person at the gate, you can then park in the garage:

* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/

== Meeting Location ==

[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]

Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley
Physical address: 717 Potter Street, Berkeley, CA 94710

Meeting room: room 181

=== Travel between hotel and meeting ===

* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]
* Taxi/Lyft/Uber

Aim to be at the lab for 9.30am



== Participants ==

USC:

*Tremayne Mushayahama
*Anushya?

LBL:

* Chris Mungall
* Eric Douglass
* Seth Carbon
* HyeongSik Kim
* Suzi Lewis


[[Category:Meetings]]
[[Category:Protege]] Cjm
Categories: GO Internal

Annotation Conf. Call 2017-11-14

GO wiki (new pages) - Mon, 11/06/2017 - 09:25

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = == Ontology Term Requests == *Refresher on information required for term requests: **Term name **Parents **Te..."

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

= Agenda =
== Ontology Term Requests ==
*Refresher on information required for term requests:
**Term name
**Parents
**Term definition
**Reference(s)
*If you need help with parentage or definitions, the ontology editors can help with this, but please make a first-pass at parentage and defs to help expedite the ticket.
== Annotation QC ==
* Manual annotation to uninformative high-level terms is strongly discouraged
** See: [https://github.com/geneontology/go-annotation/issues/1648 improving specificity by banning high level terms #1648]
** For example: direct annotation to 'transport' (GO:0006810) is one case where a more specific annotation can likely be made
** In AmiGO, there are 53 experimentally supported annotations to 'transport'.
** Can groups check these annotations to see if a more granular term is appropriate?
** Annotations according to group:
(8) EcoCyc
(7) EcoliWiki
(7) MGI
(7) PseudoCAP
(6) SGD
(5) UniProt
(4) BHF-UCL
(3) RGD
(3) TAIR
(2) GR
(1) SynGO
* PomBase has a list of >1300 high-level terms that have a 'do not manually annotate' flag
* The proposal is to work through this list so annotations are consistent amongst all GOC members

== Ontology Updates ==
*Pascale:
** [https://github.com/geneontology/go-ontology/projects/7 Transcription factor activity refactor]
** Molecular Function terms describing 'transcription factors'
** See: [https://github.com/geneontology/go-ontology/issues/13588 Make parent term for transcription factor activity]
** See: [https://github.com/geneontology/go-annotation/issues/1668 Transcription factor branch refactoring: overview of annotations of TFIIIC and TFIIB complexes]

== GOC Meetings Cambridge ==
*Review key action items from signaling workshop and GOC meeting
**[https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit GOC Cambridge 2017 Meeting Minutes]
** Focus on annotation to signaling pathways
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Folder on Google drive for signaling pathways working group]
*** [https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit Signaling Workshop Meeting Minutes]
*** [https://github.com/geneontology/go-annotation/issues/1597 How to name specific MAPK pathways]
*** [https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”]
*** [https://github.com/geneontology/go-ontology/issues/13912 MP cell surface receptor signaling pathway]
** Adoption of expanded set of BP relations
** Review use of contributes_to and colocalizes_with
** Noctua into full production mode
*** Meetings on second and fourth Wednesdays at 8am PST to discuss issues
** Representation of protein complexes, and their constituent members, in GO and GO-CAM models
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGTTJfbXY4OUxUU1k Folder on Google drive for protein complexes working group]
*** [https://github.com/geneontology/go-annotation/issues/1662 inferring MFs from annotations to complex portal IDs to individual complex participants]
***[https://github.com/geneontology/go-annotation/issues/1661 Protein complex representation in Noctua]
** Review HTP annotations
*** [https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]
***[https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit Draft of HTP guidelines]
*** [https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit#gid=0 HTP data currently in GO]

= Minutes =
*On call:

== Annotation QC ==
* Action Item: Need curators to review experimental annotations to 'transport'
* Report back on any annotations that can't reasonably be transferred to a more granular term
* We will continue to look at the PomBase list and prioritize additional flags and error checks

== Ontology Updates ==
* Will merge DNA binding transcription factor activity into nucleic acid binding transcription factor activity
* Goal: trying to more easily distinguish 'general' transcription factors (generally only described wrt pol II TFs) from specific, regulatory TFs
* Pascale will tag groups/people if annotations need review
* Pascale, Karen, Paul T. will discuss further

== GOC Cambridge Meetings ==
=== Signaling Pathways ===
* Will follow-up on signaling workshop with items using the go-annotation tracker
=== HTP Evidence Codes ===
* Helen will finish updating guidelines
* How doe the HTP evidence codes map up to existing GO evidence codes?
** They are in a separate branch, although still experimental.



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

Ontology meeting 2017-11-06

GO wiki (new pages) - Fri, 11/03/2017 - 06:32

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 ==Discussion==..."

= Conference Line =

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

= Agenda =



==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==




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

Ontology meeting 2017-11-03

GO wiki (new pages) - Wed, 11/01/2017 - 09:39

Pascale:

= Conference Line =

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

= Agenda =



==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==

===DOS patterns - what are the next steps?===
https://github.com/geneontology/go-ontology/issues/14473
* What's already implemented ? For eg, if you change a DOS pattern, will it propagate in the ontology?
* How will we keep track of changes ? Will the DOS patterns get an identifier ?



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

2018 NYU GOC Meeting Agenda

GO wiki (new pages) - Wed, 11/01/2017 - 09:04

Pascale: Created page with " == Suggestions for topics== 'Response to' workshop (similar to the signaling WS) Category:Meetings"


== Suggestions for topics==
'Response to' workshop
(similar to the signaling WS)


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

Biological Process

GO wiki (new pages) - Wed, 10/25/2017 - 11:48

Vanaukenk:

= Biological Process Annotation Guidelines =

== Do I annotate to the process or regulation of the process? ==


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

Ontology meeting 2017-10-27

GO wiki (new pages) - Wed, 10/25/2017 - 11:37

Vanaukenk: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Should we pick a different time for this meeting? == == Feedback from Barbara == == Compound..."

= Conference Line =

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

= Agenda =

== Should we pick a different time for this meeting? ==

== Feedback from Barbara ==

== Compound Functions and Multiple Parentage ==

https://github.com/geneontology/go-ontology/issues/14161

==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==
*On call:



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

GO Annotation Basics

GO wiki (new pages) - Wed, 10/25/2017 - 07:12

Vanaukenk:

GO annotation guidelines

1. Generalities

1.1 Semantics of a GO annotation
The association of a GO class with a gene product is a statement that means:

* molecular function: molecular activities of gene products
* cellular component: where gene products are active
* biological process: pathways and larger processes made up of the activities of multiple gene products.
In other words, annotations represent the normal, in vivo biological role of gene products.


1.2 Tips to produce high quality annotations

1.2.1 Get the wider perspective
* Favor a gene-by-gene or pathway-by-pathway approach for curation rather than paper-by-paper
* Read recent publications
* Look at existing annotations for the same protein and for the term you have chosen to annotate, to ensure consistency. This may trigger the need to revise other annotations
* Remove incorrect annotations based on invalidated hypothesis


1.2.2 Focus on the research hypothesis
Use prior knowledge to understand the hypothesis being tested and its relation to the experimental observation.

1.2.3 Capture the conclusion, not the assay


1.2.4 Infering normal functions based on phenotypes
Phenotypes can help understand the function of proteins, but also provide insights into mechanisms leading to disease
The scope of the GO, though, is to capture the normal function of proteins, so special care must be taken to understand how a phenotypic observation helps understand the nomal function of a protein.

Beware of indirect effects of mutations.
- Housekeeping genes, such as RNA polymerase, affects essentially all cellular processes (cell proliferation, development, etc) but does not *mediate* these processes.

Phenotypes not supported by a molecular role for the protein.
- Knockout/knock downs may result in pleiotropic effects on cell biology, development, etc. Without understanding the molecular mechanis, be careful no to make annotations to Biological Processes terms that are more specific than the experiment allows to conclude.

1.3 GO aims to represent current knowledge
The GO is not an archive or all findings published on a protein. Do no hesitate to remove older annotations that are inconsistent with the current state of knowledge for a protein' role.

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

Manager Call 2017-11-01

GO wiki (new pages) - Wed, 10/25/2017 - 07:06

Pascale: Created page with " ===Groups contacts=== We need to know which is the correct file for group contacts and remove old files: https://github.com/geneontology/go-ontology/blob/master/curator_grou..."


===Groups contacts===
We need to know which is the correct file for group contacts and remove old files:
https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv
or the yaml file ?


Continue to review the action items from the GOC meeting
===Noctua===
*Data flow - Work with the users.
*The priority is to push Noctua to the production level. Huaiyu suggested to use this project for a project management exercise. Pascale will work with Chris to set up deadlines for all requirements. Chris pointed out that there was no real requirement documents. Everything is in github tickets. There are two types of tickets: bugs and new features.
*End-user tool (visualization)


To be finished at the next manager call.

The other two items on the agenda were not discussed, and will be postponed to the next call.


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

GO-CAM October 25th, 2017

GO wiki (new pages) - Tue, 10/24/2017 - 19:13

Vanaukenk: /* Agenda */

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =
== Contributors ==
* What constitutes a 'contribution'?
* I have opened some models to look at what other curators have created and either moved annotons to see something better or looked at the annotation preview and then notice the asterisk in the tab.
** Should I be saving here? What would happen if I don't save?
** I haven't made any real contribution to the model so it seems wrong to have my orcid listed.

== GPAD Outputs ==
[https://github.com/geneontology/noctua/issues/500 GPAD missing annotations via 'causally upstream of'?]

[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000110 TEST: causally upstream of - KRC]

*ACTION ITEM: on a future GO-CAM call, review the Inference Explanations for some models

== Attribution ==
[https://github.com/geneontology/noctua/issues/458 Attribution with GO-CAM exports to GOC annotation files]

== Simple Annoton Editor ==

[https://github.com/geneontology/noctua/issues/492 dealing with blank MF in the simple annoton editor]

[https://github.com/geneontology/simple-annoton-editor/issues/12 Extend form to include standard GO-CAM model fields]

[https://github.com/geneontology/simple-annoton-editor/issues/10 Bare MF annotation should generate part-of triples]

*Editor enhancements to come:
**Ability to add basic set of annotation extensions, e.g. has_input for an MF
**Ability to just add a CC annotation and get the resulting part_of annotation in the graphical interface

= Minutes =
*On call:

== GPAD Outputs ==

== Attribution ==

== Simple Annoton Editor ==





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

Annotation Conf. Call 2017-10-24

GO wiki (new pages) - Fri, 10/20/2017 - 06:48

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = = Minutes = *On call: Category: Annotation Working Group"

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

= Agenda =

= Minutes =
*On call:



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

Ontology meeting 2017-10-20

GO wiki (new pages) - Thu, 10/19/2017 - 11:13

David:

= Conference Line =

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

= Agenda =

== Review of the GOC meeting paying particular attention to ontology tasks ==

== Should we pick a different time for this meeting? ==

==GH project link==

https://github.com/geneontology/go-ontology/projects/1

David H will be away next week and for several weeks in November. We need a volunteer to host these meetings.


==Discussion==
*On call:



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