2019 Berkeley GOC User Meeting Agenda

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GO User Meeting


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.


Note: speakers and talk titles to be finalized

Morning: How GO and GO annotations are made

  • 9.00-9.30 Overview of GO -- Chris Mungall
  • 9.20-9.35 Literature biocuration and ontology development in GO -- Kimberly or David, GO Consortium
  • High-level, emphasize that neither ontologies nor annotations are static, we are responsive to community
  • 9.35-9.50 GO annotation pipelines: interpro2go, PAINT/PantherDB -- Huaiyu Mi, GO Consortium
  • Specifically mention new work on plants as this would be of interest
  • Have a separate phylogenes.org presentation from Peifen Zhang?
  • 9.50-10:00 phylogenes project: Peifen Zhang, Phoenix Bioinformatics/TAIR
  • 10:00-10.10 Getting GO annotations -- Seth Carbon, GO Consortium
  • High level - where to go to get official GOC downloads, AmiGO, briefly mention APIs
  • 10.10-10.20 Fungal functional annotation pipeline at JGI -- Igor Grigoriev, JGI
  • 10.20-10.30 Microbial functional annotation pipeline: JGI/NMDC perspective -- Kjiersten? NERSC/JGI/NMDC
  • 10:30-10:35 Phytozome GO annotation pipeline - Joe Carlson, JGI/Phytozome

Break (15 mins)

  • 10:50-11:00 GO annotation in GMOD/Apollo -- Ian Holmes, UCB/LBNL
  • 11:00-11:05 Multi-organism annotation with GO: Michelle Gwinn Giglio, UoM
  • 11:05-11.15 Unknowns -- Val Wood, PomBase, GO Consortium
  • 11:15-11:30 Group Discussion

Lunch 11.30-1.00


Using GO and functional annotation for data analysis

  • 1.00-1.15 Introduction to GO enrichment -- Huaiyu Mi or Paul T, GO Consortium
  • Most in the audience will be somewhat familiar, this is an opportunity to promote best practice, use official GO enrichment, perils of using old sites e.g DAVID
  • 1.15-1.25 GO in space: using functional annotations to analyze brain radiation exposure omics data -- Laurent Phillipe (GO) or Andy Wyrobek (BSE)
  • 1.25-1.30 TBD -- Ruth Lovering, UCL, GO Consortium
  • 1.25-1.35 Analysis of mouse QTL data using GO -- Antoine Snijders, BSE
  • 1.35-1.45 TBD -- Axel Visel or Diane Dickel, BSE
  • 1.45-1.55 Metabolomics use cases and MAGI -- Ben Bowen, JGI
  • 1:55-2.05 GO in KBase -- Paramvir Dehal, KBase/LBL
  • 2.05-2.25 Lies, damn lies and annotations -- Morgan Price, EGSB


GO: New developments

  • 3.00-3.20 GO Causal Activity Models -- Chris M or Paul T, GO Consortium
  • Standard GO-CAM talk, many will be hearing for first time
  • 3.20-3.30 GO and Reactome -- Ben Good (GO) or Peter d’Eustachio (Reactome)
  • 3.30-3.45 GO, metabolic pathways, and enzymatic reactions with Rhea -- Chris M or David H or Alan B
  • Emphasize high-quality reaction annotations, EC not moving fast enough, uniprot curating directly to RHEA now, GO tightly coupled. Also mention links to other databases
  • 3.45-4pm GO and other ontologies -- Chris M