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Annotation Conf. Call 2018-02-27

GO wiki (new pages) - 3 hours 14 min ago

Vanaukenk: Created page with "= Agenda = == GitHub Projects Page == == Ontology Editors Report == = Minutes = *On call: Category:Annotation Working Group"

= Agenda =
== GitHub Projects Page ==

== Ontology Editors Report ==


= Minutes =
*On call:



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

Publications, Talks, Posters 2018

GO wiki (new pages) - Wed, 02/14/2018 - 02:44

Huntley: Created page with "Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Brecke..."

Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP. (2018) [http://circgenetics.ahajournals.org/content/11/2/e001813 Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology]. Circ. Genom. Precis. Med. 11:e001813.


[[Category:Reports]]
[[Category:Publications]] Huntley
Categories: GO Internal

GO-CAM Noctua Call 2018-02-14

GO wiki (new pages) - Tue, 02/13/2018 - 18:32

Vanaukenk:

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

= Agenda =
== Updates/Discussion on 1.0 Release Milestones ==
We will get an update from the software groups at Berkeley and USC on the status of the 1.0 release:

[https://github.com/orgs/geneontology/projects/6 Noctua 1.0 Release]

= Minutes =
*On call:


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

GO-CAM and Noctua 2018 Agenda and Minutes

GO wiki (new pages) - Tue, 02/13/2018 - 18:27

Vanaukenk: Created page with "* GO-CAM Noctua Call 2018-02-14 Category: Annotation Working Group"

* [[GO-CAM Noctua Call 2018-02-14]]



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

Annotation Conf. Call 2018-02-13

GO wiki (new pages) - Thu, 02/08/2018 - 13:24

Vanaukenk: /* Agenda */

= Agenda =
== Working Group Reports ==
=== GO Managers ===
*Documentation meeting in Berkeley, January 22nd - 28th
=== HTP Working Group ===
*Guideline updates
*Proteomics experiments
=== Protein Complexes ===
*Draft survey to GO users
*Follow-up call to discuss
== Annotation File Pipelines ==
*UniProtKB = namespace; UniProt = contributor
== Annotation Review ==

= Minutes =
*On call:


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

Annotation Conf. Call 2018-01-23

GO wiki (new pages) - Thu, 02/08/2018 - 13:24

Vanaukenk: Created page with "Cancelled due to documentation meeting in Berkeley the week of January 22nd. Category:Annotation Working Group"

Cancelled due to documentation meeting in Berkeley the week of January 22nd.


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

Manager Call 2018-02-15

GO wiki (new pages) - Thu, 02/08/2018 - 00:29

Pascale: Created page with "Category:GO Managers Meetings = Call in info= https://stanford.zoom.us/j/754529609 = Agenda = ==Agenda for GOC meeting and SAB meeting=== = Minutes = *On call:"

[[Category:GO Managers Meetings]]

= Call in info=
https://stanford.zoom.us/j/754529609

= Agenda =


==Agenda for GOC meeting and SAB meeting===




= Minutes =
*On call: Pascale
Categories: GO Internal

Manager Call 2018 Rota

GO wiki (new pages) - Thu, 02/08/2018 - 00:25

Pascale:

{| border="1" cellpadding="5" cellspacing="0"
!Date!!Agenda!!Minutes
|-
|[[Manager Call 2018-01-04|January 3]]|| || 
|-
|[[Manager Call 2018-01-18|January 17]]|| ||
|-
|[[Manager Call 2018-02-01|February 7]]|| ||
|-
|[[Manager Call 2018-02-15|February 21]]||Kimberly||Chris
|-
|[[Manager Call 2018-03-01|March 7]]||Chris|| Huaiyu
|-
|[[Manager Call 2018-03-15|March 21]]||Huaiyu||Pascale
|-
|[[Manager Call 2018-04-05|April 4]]||Pascale||Suzy
|-
|[[Manager Call 2018-04-19|April 18]]||Suzy||David
|-
|[[Manager Call 2018-05-03|May 2]]||David||Kimberly
|-
|[[Manager Call 2018-05-17|May 16]]||Kimberly||Chris
|-
|[[Manager Call 2018-06-07|June 6]]||Chris|| Huaiyu
|-
|[[Manager Call 2018-06-21|June 20]]||Huaiyu||Pascale
|-
|[[Manager Call 2018-07-05|July 4]] - July 4th holiday in US || ||
|-
|[[Manager Call 2018-07-19|July 18]]||Pascale||Suzy
|-
|[[Manager Call 2018-08-02|August 1]]||Suzy||David
|-
|[[Manager Call 2018-08-16|August 15]]||David||Kimberly
|-
|[[Manager Call 2018-09-06|September 5]]||Kimberly||Chris
|-
|[[Manager Call 2018-09-20|September 19]]||Chris|| Huaiyu
|-
|[[Manager Call 2018-10-04|October 3]]||Huaiyu||Pascale
|-
|[[Manager Call 2018-10-18|October 17]]||Pascale||Suzy
|-
|[[Manager Call 2018-11-01|November 7]]||Suzy||David
|-
|[[Manager Call 2018-11-15|November 21]]||David||Kimberly
|-
|[[Manager Call 2018-12-06|December 5]]||Kimberly||Chris
|-
|[[Manager Call 2018-12-20|December 19]]||Chris|| Huaiyu


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

2018 NYU GOC Meeting Logistics

GO wiki (new pages) - Wed, 02/07/2018 - 14:46

Peterd:

Details will be available by next week. Meanwhile, here is some information to help you make travel arrangements.<br>'''Meeting site:''' Translational Research Building, 227 East 30th Street, in the Murray Hill neighborhood of Manhattan.<br>'''Accommodations:''' A block of rooms has been reserved at a group rate at the Shelburne Affinia Hotel, a comfortable hotel a 10 or 15 minute easy walk from the meeting site and convenient to public transportation.<br>'''Getting to New York:''' by air from far away, Kennedy Airport is more convenient than Newark but both work. From closer to New York, LaGuardia also works although it lacks useful public transportation into Manhattan and is buried in construction aimed at improving its third-world amenities. Details on getting into the city from all three airports will follow. The meeting will start first thing on Saturday May 12 (so plan to arrive on Friday) and will end on Monday May 14 early enough in the afternoon to enable people to get to the airport for overnight flights to Europe.<br>'''Registration fee:''' Amount and payment details to be determined, but we hope to keep the amount low and find a convenient way to pay.<br>'''Food and other needs:''' A roster form for you to log this information is under construction.<br>See you in May!

[[Category: GO Consortium Meetings]] Peterd
Categories: GO Internal

Ontology meeting 2018-02-05

GO wiki (new pages) - Mon, 02/05/2018 - 07:18

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 == Editors Discussio..."

= Conference Line =

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

= Agenda =


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

== Editors Discussion ==
*The GH ticket-closing jamboree will be from Feb. 12-16th in Denver.
*I have created a page for this meeting here: [[2018 Ontology Editors' GH ticket Meeting]]

= Minutes =
*On call:


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

Ontology meeting 2018-01-29

GO wiki (new pages) - Mon, 01/29/2018 - 06:39

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 == Editors Discussio..."

= Conference Line =

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

= Agenda =


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

== Editors Discussion ==
*The GH ticket-closing jamboree will be from Feb. 12-16th in Denver.
*I have created a page for this meeting here: [[2018 Ontology Editors' GH ticket Meeting]]

= Minutes =
*On call:


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

2018 USC Noctua developers meeting

GO wiki (new pages) - Fri, 01/26/2018 - 16:57

Cjm: Created page with " == Venue == == Hotel == == Agenda == Items: *Reactome2GO *UI architecture: Angular, Vue, reusable components *Python code/biolink *Web APIs == Participants == Travelin..."


== Venue ==


== Hotel ==

== Agenda ==

Items:

*Reactome2GO
*UI architecture: Angular, Vue, reusable components
*Python code/biolink
*Web APIs

== Participants ==

Traveling

* Seth Carbon LBL
* Chris Mungall LBL
* Eric Douglass LBL
* Ben Good LBL

USC

*Tremayne Mushayahama
*Dustin Ebert
*Huaiyu Mi
*Paul Thomas
*?Laurent-Phillippe?

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

Annotation Quality Control

GO wiki (new pages) - Wed, 01/24/2018 - 14:17

Vanaukenk: /* Annotation Rules */

== Annotation Rules ==
[https://github.com/geneontology/go-site/tree/master/metadata/rules GO Rules]

==[[Annotation Review Request]] ==


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

Tips to Produce High Quality Annotations

GO wiki (new pages) - Fri, 01/19/2018 - 08:58

Vanaukenk: /* Check Term Parentage in the Ontology */

= Tips to Produce High Quality Annotations =

== 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

== Focus on the Research Hypothesis ==
Use prior knowledge to understand the hypothesis being tested and its relation to the experimental observation.

== Capture the Conclusion, not the Assay ==

== Use Caution when Inferring 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.

== Check Term Placement in the Ontology ==

== 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.

Back to: [[Annotation]]

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

Manager Call 2018-02-01

GO wiki (new pages) - Fri, 01/19/2018 - 08:48

Pascale:

[[Category:GO Managers Meetings]]

= Call in info=
https://stanford.zoom.us/j/754529609

= Agenda =

==Noctua V1.0 progress report==


==NYU meeting==
*Do we have any info on logistics? Hotel is all set
*Start working on agenda?

==Docathon report==
==What is a GO contributor, GO collaborator, and a GO resource?===
* http://wiki.geneontology.org/index.php/Main_Page#GO_Consortium_Resources
see also website


==Revisit mailing lists==
While working on this: http://geneontology.org/page/go-mailing-lists
we wondered if they are all necessary and should we advertise all 3 on the GO website ?

==EC2GO mappings==
*We are missing about 1,500 reactions (25%) of EC (it's possible that we are also missing the corresponding terms
*What is the goal: (a) keep up to date? (b) remove incorrect (moved) mappings?
*Back in 2013 there was a Plan of action with respect to EC and Rhea, is this still our plan? What's the priority? http://wiki.geneontology.org/index.php/Enzymes_and_EC_mappings#Plan_of_Action




= Minutes =
*On call: Pascale
Categories: GO Internal

Noctua

GO wiki (new pages) - Wed, 01/17/2018 - 10:54

Paul Thomas:

[[Category: Annotation]]
=Summary=
Noctua is an online system for making extensible GO annotations, which we call "GO-CAM models". Anything from simple annotations to complicated pathways are supported. However, the overall goal should be for a model to represent a unit that roughly corresponds to a biological pathway. This document describes how to make GO-CAM models using Noctua.

=Requirements=
A web browser. Chrome is recommended.

=Launching Noctua=
* Go to http://geneontology.org/cam.

=Setup=
* Before using Noctua to edit or create models, please follow this procedure to request edit access. You will need a ORCID (https://orcid.org), so you can be uniquely identified. Each part of a Noctua model is individually attributed to an editor, as well as the project that provided their funding (if applicable).

=Using Noctua=

==Login==
You can view models without logging in, but you must log in before creating new annotations (by editing an existing model, or creating a new model). Click on the Login button in the right upper corner of the page. There are several options for logging in. We recommend using Github (if you don't already have an account just go to http://github.com).

==Editing an existing model==
Just click on the "Edit" button in the rightmost column of the model list. The model list can be filtered using the search box just above the list of available models.

==Starting a new model==
Just click on the blue "Create Noctua Model" button.

==What is a Noctua model?==
===Molecular activity===
Each Noctua model consists of at least one MOLECULAR ACTIVITY (FUNCTION), carried out by at least one GENE PRODUCT. Ideally, all of the following “aspects” of the gene product’s function will be specified in the model. However, in cases where some or most of these aspects are unknown, a model may still be constructed with details added as more information becomes available. Users should attempt to specify functions as fully as possible, but partial models are expected and still contribute to the GO knowledgebase. The following aspects are represented in a model:
*Molecular function (MF): the molecular activity carried out by a gene product as part of a larger biological process; this is specified by a term from the GO molecular function ontology. MF may be qualified, using defined relations, as follows:
**If the function acts upon another “target” molecule, this can be specified using a gene product identifier (for a protein or a gene) or term from the ChEBI ontology (for a small molecule)
**If the function acts during a particular “biological phase” (e.g. a particular stage in organism development), this can be specified using a term from an appropriate ontology
*Cellular component (CC): the location of the gene product when it is carrying out its activity; this is specified by a term from the GO cellular component ontology. CC may be qualified, using defined relations, as follows:
**If the activity occurs in a specific cell type, this can be specified using a term from a Cell Type or Anatomy Ontology.
**If the activity occurs in a specific anatomical structure, this can be specified using a term from the Uberon, or other organismal Anatomy, ontology.
*Biological process (BP): the larger “biological program” to which the activity contributes; this is specified by a term from the GO biological process ontology. BP may be qualified, using defined relations, as follows:
**If the process is a part of a larger biological program, it can be linked to the larger biological program with another GO biological process term.
All of these aspects together constitute a unit of annotation, which we call an “annoton”. Each annoton is centered on the molecular activity, as this is the most basic description of gene product function.
===Molecular activities can be linked by causal relations===
Activities can be linked together by relations that describe their causal dependence. The most common relations are “regulates” and “provides input for”, but there are other relations of greater and lesser specificity, depending on what is known. “Regulates” should be used to denote biological control of a downstream activity. “Provides input for” should be used when there is no control, but an upstream function creates a molecular entity that is the target of the downstream function, such as in a metabolic pathway.


==Creating a new activity and its properties==
After either selecting an existing model or starting a new one, you will see the graph view by default. To create new activities, you should use the “Simple annoton editor” tool, available in the Workbench menu:
Workbench -> Simple annoton editor
[[File:Launch_noctua_activity_form.png|thumb|Fig. 1 Launching the simple annoton editor|400px]]
This will launch a new browser tab
===Step 1. Fill in the form===
Fill in as many fields as possible in the form, by typing in the field, and then selecting from the autocomplete suggestions by moving the mouse over your selection and clicking. Tips:
*The required fields are gene product, molecular function and evidence for the function. All other fields are optional.
*You can annotate a complex instead of a single gene product, by choosing "macromolecular complex" from the drop-down menu
*For gene products, you can type in the gene symbol, e.g. Wnt3a. If necessary to narrow down the choices, type a space after the symbol, and enter the three letter code for the species (first letter from genus and two from species name, e.g. mmu for Mus musculus). Each entry in the autocomplete will also show the associated unique database identifier or accession, so curators can confirm that they are selecting the appropriate entity for annotation.
* In general, enter a space after a complete word, to narrow down the choices.
Just as in conventional GO annotation, you must fill in the Evidence and Reference fields for each line of annotation, or an annoton will not be created.
We recommend that you fill in as many fields as possible before creating the annoton, as after it is created, you will need to edit it from the graph canvas, which requires more steps to do.
===Step 2. Add the new activity to a model===
Press the CREATE button. A new activity will appear on the graph canvas (the main window). Tips:
*Each new activity will appear on the same part of the canvas, so if you add more than one activity you will need to move them around on the canvas (by clicking and dragging) to see the ones underneath.
*If the CREATE button is grayed-out, there is some information missing from the form that you still need to fill in. You can press the "why is the save button disabled?" for a list of missing fields.

The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).

--------- Paul Thomas
Categories: GO Internal

Annotation File Pipelines

GO wiki (new pages) - Tue, 01/16/2018 - 08:48

Vanaukenk:

= Annotation File Pipelines =
== SVN ==
*[[How to run Mike Cherry's filtering script locally before checking the GAF into SVN?]]
== Jenkins Jobs ==
== LBNL File Retrieval from GOC Members ==

Back to: [[Annotation]]

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

Annotation Extensions

GO wiki (new pages) - Tue, 01/16/2018 - 08:32

Vanaukenk:

= Annotation Extensions =
*[[Annotation Extension Relation Subsets]]
*[[Column 16: Cell Type]]
*[[Column 16: Targets]]
*[[Issues with Annotation Extension relations]]
*[[Annotation Extension Relation Documentation Jamboree]]
*[[Guidance for updating deprecated Annotation Extension Relations]]

Back to: [[Annotation]]


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

Cellular Component

GO wiki (new pages) - Tue, 01/16/2018 - 08:28

Vanaukenk: /* Annotation Relations for Cellular Component Annotations */

= Cellular Component Annotation Guidelines =
== Meaning of a GO Cellular Component Annotation ==
== Annotation Relations for Cellular Component Annotations ==
=== part of ===
=== colocalizes with ===

== Annotation Extensions for Cellular Component Annotations ==
== Term-specific Guidelines for Cellular Component ==


Back to: [[Annotation]]

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

Molecular Function

GO wiki (new pages) - Tue, 01/16/2018 - 08:25

Vanaukenk: /* Molecular Function */

= Molecular Function Annotation Guidelines =

== Meaning of a GO Molecular Function Annotation ==
== Annotation Relations for Molecular Function Annotations ==
=== enables ===
=== contributes_to ===

== Annotation Extensions for Molecular Function Annotations ==
== Term-specific Guidelines for Molecular Function ==

Back to: [[Annotation]]

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