WormBase-Caltech Weekly Calls

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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