2019 Berkeley GOC User Meeting Agenda: Difference between revisions

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Additional topics are under consideration.
Additional topics are under consideration.


[[Category: GO Users Meetings]]
[[Category: Meetings]]
[[Category: GO Consortium Meetings]]

Revision as of 15:36, 28 August 2019

GO User Meeting

General

The GO User Meeting will be held on Monday, October 7, 2019 at 717 Potter St., Berkeley, CA. There is no formal sign-up at this point, but if you are interested in attending, please contact the organizers. For access and other logistic points, see the Logistics page for the main meeting: http://wiki.geneontology.org/index.php/2019_Berkeley_GOC_User_Meeting_Agenda


The GO has a broad base of users, including biologist researchers, computational biologists, and bioinformaticians. This meeting is an opportunity for users at LBNL and in the SF Bay Area to interact with members of the GO Consortium, to share research and existing GO use cases, learn more about best practices using GO, and future developments such as GO-CAMs.

Schedule

Note: speakers and talk titles to be finalized

9am-noon: Presentations

Introductory session

  • 9:00-9:20: Welcome (Chris)

How GO and GO annotations are made

  • 9.20-9.35 Literature biocuration and ontology development in GO -- GO Consortium
  • 9.35-9.50 GO annotation pipelines: interpro2go, PAINT/PantherDB -- Huaiyu Mi, GO Consortium
  • 9.50-10.00 Getting GO annotations -- Seth Carbon, GO Consortium
    Where to go to get official GOC downloads, AmiGO, APIs.
  • 10.00-10.10 Fungal functional annotation pipeline at JGI -- Igor Grigoriev, JGI
  • 10.10-10.20 Microbial functional annotation pipeline: JGI/NMDC perspective -- NERSC/JGI/NMDC
  • TBD - GO annotation in GMOD/Apollo -- Ian Holmes, UCB/LBNL
  • 10.20-10.30 GO in KBase -- Paramvir Dehal, KBase/LBL
  • 10.30-10.45 Group discussion
  • 10.45-11.00 Coffee

Using GO and functional annotation for data analysis

  • 11.00-11.15 Introduction to GO enrichment -- GO Consortium
    Best practice, use official GO enrichment, perils of using old sites.
  • 11.15-11.25 GO in space: using functional annotations to analyze brain radiation exposure omics data -- Laurent-Phillipe Albou (GO) or Andy Wyrobek (BSE)
  • 11.25-11.35 Analysis of mouse QTL data using GO -- Antoine Snijders, BSE
  • 11.35-11.45 TBD -- Axel Visel or Diane Dickel, BSE
  • 11.45-11.55 Metabolomics use cases and MAGI -- Ben Bowen, JGI
  • 11.55-12.15 Lies, damn lies and annotations -- Morgan Price, EGSB
  • 12.15-12.30 Group discussion

Lunch 12.30-1.30

This will not be provided--everybody will need to feed themselves.

GO: New developments

  • 1.30-1.50 GO Causal Activity Models -- Chris Mungall or Paul Thomas, GO Consortium
    Overview GO-CAM talk--the next generation of functional modeling.
  • 1.50-2.10 GO and Reactome -- Ben Good (GO) or Peter d’Eustachio (Reactome)
  • 2.10-2.30 GO, metabolic pathways, and enzymatic reactions with Rhea -- TBD
  • 2.30-2.45 GO and other ontologies -- Chris Mungall

Afternoon Breakout Sessions

Possible topics:

  • GO-CAM (with possible enrichment)
  • GO and Microbial annotation: mappings from existing systems, pipelines
  • Alliance (AGR) data flow use cases
  • GO APIs and Data access, Jupyter notebooks etc

TBD

Additional topics are under consideration.