2015 Washington DC GOC Meeting Agenda: Difference between revisions

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(Helen offered to chair this discussion)
(Helen offered to chair this discussion)
* General issues (Sandra)
* General issues (Sandra)
** ID co-ordination between GO, PRO, and Intact (Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD)
** ID co-ordination between GO, Intact, and PRO [Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD]
* Annotation guidance (Rama)
* Annotation guidance (Rama)
* Ontology issues (David OS?)
* Ontology issues (David OS?)

Revision as of 14:05, 14 August 2015

Please plan to join us this fall from August 30th through September 2nd for the next meeting of the Gene Ontology Consortium. We will host the meeting at the Marvin Conference Center, George Washington University, at the heart of Washington, DC.

The GOC meeting will be held on August 30-31, 2015.
A GOC Symposium day will be held on September 1, 2015. (Details will be posted here: http://wiki.geneontology.org/index.php?title=2015_Washington_DC_GOC_Symposium_Agenda)
The GOC SAB will convene on September 2, 2015. (Details will be posted here: http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Scientific_Advisory_Board_Meeting_Agenda)

Details to follow soon.

Daily schedule

  • Start: ??
  • Morning coffee break: ??
  • Lunch: ??
  • Afternoon session: ??
  • Afternoon coffee break: ??

Minutes

http://wiki.geneontology.org/index.php?title=2015_Washington_DC_GOC_Meeting_Minutes

Agenda for the main GOC meeting (August 30-31 2015)

Please ensure that all outstanding items from the trello board are covered here in the agenda under the appropriate heading.

User support and interaction

  • GO survey and user experience
  • GO enrichment analysis
  • GO website and FAQs
  • AmiGO
  • GO helpdesk
  • GO Facebook page
  • Protein2GO: 15 min - demo/new features + 5 min discussion (ECO codes) - Aleksandra Shypitsyna
  • PSIQUIC GO annotations (5 min) - Ruth

Phylogenetic Annotation

Literature Annotation

Annotation issues

  • Guidelines for annotation to x-catabolism to capture the product of a reaction rather than the end product of a pathway (Pascale)



Proteome sets

Traceability of annotations

  • When one annotation is derived from another (manually or logically) it would be useful to have an easy way to point back to the existing annotation. Tony Sawford

Annotating complexes to GO

(Helen offered to chair this discussion)

  • General issues (Sandra)
    • ID co-ordination between GO, Intact, and PRO [Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD]
  • Annotation guidance (Rama)
  • Ontology issues (David OS?)

Compounding Evidence codes

  • Is it possible to do this and is it appropriate? An example of this would be capturing the evidence when a direct enzymatic assay is used to test the loss of function in a mutant enzyme (IDA or IMP) - Rama?
  • Continuing discussion of IGI example from May annotation call - Rama

Annotation extension relationship progress

Usefulness of annotation extensions, intelligent querying (5 min) - David OS?

Survey how many groups who are actively annotating are using or are capable of using annotation extensions (5 min) - Rama?

Dealing with annotation extension inconsistencies (30 min) - Ruth/Rachael (e.g. dependent_on https://github.com/geneontology/annotation_extensions/issues/17)

Progress on documentation (10 min) - David OS/Rama

MicroRNA guideline summary

Brief overview (15 min) - Rachael Huntley

Resolution on chromatin binding

chromatin binding vs localization to chromatin (15 min) - Ruth, Karen, others?

Software, Database and API

  • New architecture (Chris)
  • GAF/GPAD version and file naming (Tony S)

Making use of annotation extensions

Very few tools consume annotation extensions usefully. For example, an annotation to 'cytosol' part of 'postsynapse' will NOT be grouped under postsynapse by the vast majority of tools. How can we fix this!?

Can we provide 'folded' temp terms for at least some AE relationships: @ a minimum, part_of + occurs_in.

Common Curation Environment and LEGO annotations

  • Noctua update (Seth, Chris)
  • Combined GO/Phenotype annotation (Chris)

Ontology Production and R&D

Molecular Function refactoring

David OS/Paul T?

Deepening annotations - develop ontology patterns e.g. protein binding

(David H/Chris/Paul T) https://trello.com/c/J9jFm8Ex/95-deepening-annotations-develop-ontology-patterns-e-g-protein-binding

Update on focused projects (vesicles, autophagy…)

Vesicles (Paola)

Biochemical pathways (David H)

Autophagy (David H)

Synapse project (David OS)

Cilia (Paola/Karen)

Other ontology issues

Protein production https://github.com/geneontology/go-ontology/issues/10787 (Pascale)


Ontology stats

Moving to GitHub (Chris)

A brief introduction to GitHub- getting accounts, submitting and updating tickets etc. With a focus on ontology requests.