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