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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

Ontology meeting 2017-10-13

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

David: Created page with "No meeting due to PRO meeting travel. Category: Ontology Category: Meetings"

No meeting due to PRO meeting travel.


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

Ontology meeting 2017-10-06

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

David: Created page with "No meeting due to GOC meeting Category: Ontology Category: Meetings"

No meeting due to GOC meeting


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

Ontology meeting 2017-09-29

GO wiki (new pages) - Thu, 10/19/2017 - 11:09

David: Created page with "No meeting due to GOC meeting Category: Ontology Category: Meetings"

No meeting due to GOC meeting


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

Manager Call 2017-10-18

GO wiki (new pages) - Thu, 10/05/2017 - 23:26

Pascale: Created page with "* GOC meeting action item review * GOC mailing lists clean up: ** Remove/merge some lists ** Remove some people for eg from Managers list ? Category: GO Managers Meetin..."

* GOC meeting action item review
* GOC mailing lists clean up:
** Remove/merge some lists
** Remove some people for eg from Managers list ?




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

GO-CAM Sept 27, 2017

GO wiki (new pages) - Wed, 09/27/2017 - 07:08

Vanaukenk: /* GPAD Outputs */

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

= Agenda =
== 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]

== 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]

= Minutes =
*On call:




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