Previous Years

2017 Meetings

Started curating expression clusters in 2007
Had been using text pattern match to identify expression cluster papers
Now with more papers for positive and negative training set, shifting to SVM identification
540 positive papers, 900 negative papers for training
Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)

Looks like it will get funded
Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
Paul put in a request for posting another curator position
- If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
Will need to consider re-allocation of curation responsibilities
Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
- Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
- Do other AGR members curate molecules? In some cases yes; don't capture metabolites
Transgene curation could be distributed
- Karen will be working on more automated curation of transgenes from papers; maybe also for molecules

What would we like to see in WB for metabolomics?
Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
WB enzyme gene pages link out to respective gene pages on WormFlux
How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?

What are the best ways to capture empirical evidence as support for pathway models?
Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
How can micropublications be used to fill in the gaps?

What would be a good set of genes to test?
If we omit IEAs (most from mouse), are we left with substantial data for human genes?