Revision as of 19:37, 11 April 2014

Previous Years

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.

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.

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, ClinGene(?)
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

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

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

@@ Line 37: / Line 37: @@
 ===Apologies===
 * Karen: attending impromptu OICR group meeting, won't be on the Caltech call.
-===ISB2014===
-Karen: I'd like to propose that the attendees combine our notes on the meeting and post them [http://wiki.wormbase.org/index.php/ISB2014_WormBase_notes#Speakers here]<br>
-Perhaps we can go over the meeting next week when I'm in town?  In the meantime people can check over the minutes of the meeting taken mainly by Abby (amazing job!), which I will copy onto our wiki.
 === BioCurator Meeting ===
+[[ISB2014_group_notes]]
 * many text mining tools
 * many ontology systems, mapping ontologies