WormBase-Caltech Weekly Calls

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2013 Meetings

2014 Meetings

January

February

March

April 3, 2014

WOBr

• Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser)
• As one-offs, Raymond can take newly generated GAFs from curators and process for testing.

Murray Expression datasets

• Still need to acquire primary expression data from Waterston lab
• Problems with handling inferred expression of genes in cells
• Thus inferred expression data will be removed
• Expression object will retain graphical representations supplied by Murray et al.
• A friendly reminder will be sent to Waterston requesting tabulated, processed primary expression data.

April 10, 2014

Apologies

• Karen: attending impromptu OICR group meeting, won't be on the Caltech call.

BioCurator Meeting

ISB2014_group_notes

• many text mining tools
• many ontology systems, mapping ontologies
  • Aging ontologies
  • Anatomy ontology mapping (Uberon)
  • Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files
  • How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning
• Community Annotation
  • CANTO (Community ANotation TOol) workshop (Wen attended)
    • PombeBase use CANTO and works well
• Big data curation open discussion/workshop
  • Enormous datasets (e.g. genome sequencing of all cancer patients)
  • Data storage issue
  • Data stability issue
  • Clinical data, portal set up by Michael Cherry, ClinGen
• Lincoln's talk
  • International Cancer Genome Consortium (ICGC) project (petabyte datasets)
  • 10,000 cancer patients already sequenced (18 PB by 2018)
  • Torent P2P data sharing
• BioCreative workshop
  • Text mining
    • Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
      • Curates sentences, marks up entities, only applied to abstract
  • GO annotation
    • GO Cat (http://eagl.unige.ch/GOCat/)
• Amazon "Mechanical Turk" community annotation
• EcoCyc, MetaCyc - pathway curation (will hear from Karen)
• Reactome
  • May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)
  • Add a Reactome display to WormBase?
• SPELL - anything to replace SPELL? No.
  • Still lacking other tools for microarray and RNA-Seq data

Heartbleed SSL security issue

• Raymond updated all servers/machines
• All machines need to be rebooted
• Any user passwords should be changed
• Do we care about any non-root users? Best to change all passwords on machines that have been updated

BioGrid C. elegans physical interactions

• Kimberly has been using BioGrid's curation tool
• We have a table of C.elegans large scale genetic and physical interaction data
• We're still trying to get all data

Timestamps

• Curator evidence vs. history of curation
• Kevin and Juancarlos still looking for use-cases
• Need to consider for future database migration and potential use of a common central database
• Curators use timestamps for culling out bogus data objects/cleaning up data

April 17, 2014

BioGrid followup

What are the roadblocks to protein-protein interaction curation and incorporation into WormBase?

AmiGO verification manager

Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis.
I'm thinking this would be a good tool for analyzing and setting rules for phenotype annotation.

http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix
https://sourceforge.net/apps/trac/pombase/wiki/MatrixProject
http://build.berkeleybop.org/job/check-shared-annotations/lastBuild/console

They can include worm checks in this project as well. I don't know what we would need to do for that.
I can send along Val's poster to anyone who wants to know more

Reactome training sessions

Peter D'Eustacio is setting up WebEx training sessions for curating in Reactome for the different MODs- this includes WB, SGD, Flybase and PomBase, at least. Right now the thought is that there will be a couple intro WebEx sessions, and eventually an in-person curate-athon (jamboree) where all curators will get together and do a shared project (place to be determined). I will definitely be participating, but this can be open to anyone.