WormBase-Caltech Weekly Calls
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2011 Meetings
December 1, 2011
WORM paper
- Sorted out at conference call
- EBI will take lead on rewrite
- We want a paper on the new website to go to a broader audience
Interaction model
- Almost sorted out and working
- Chris & Kimberly will discuss
Elsevier linking (images)
- Caltech attorney's want the agreement with Elsevier to be under US law
- Usage data relating to Elsevier content access must be deleted within 3 months(???)
- Should not be an issue?
Local AQL queries
- Running on Caltech mirror? Currently getting an error: "Connection closed by remote server"
- Can run AQL from xace on spica
December 8, 2011
Bio Curator Meeting
- In Washington DC next April
- Wen will send an abstract on SPELL
- Kimberly, Arun and Michael will be there as well
- Abstracts to submit: 3 in total (Kimberly, Arun, Wen)
WomrBase curator ad officially posted
WormBase meeting announcement
- What is our policy? Should we send info to everyone?
- We can send to PIs only
- Meeting announcements are an appropriate use of the list (if a bonafide C. elegans meeting)
Beta site Protein Page review
- Common protein name e.g. 'UNC-26' or 'Synaptojanin'
- Use GO curation, PAINT/PANTHER tool to assign name?
- What's the best method (automated, if possible) to assign a useful name?
- Refer to Uniprot for names; can EBI pull names directly from Uniprot?
- GO: Molecular Function and Cell Component are annotated to gene, in some cases an isoform is attributed
- Want to enable curation to isoforms when info is available
Interactions
- Interaction model still being tweaked
- Will try to 'swallow up' Gene Regulation objects and tags into main Interaction model
- #Interaction_info and #Interacor_info may be removed
Anatomy nomenclature discrepancies
- Oliver Hobert raised issue of consistency of names
- For example, sometimes "DA neurons" refers to dopamine neurons as opposed to the anatomical 'DA' neuron
- DA neurons are actually cholinergic
- Maybe post on the blog
- Make synonym for dopaminergic neuron as 'DA neuron'?
Citace upload date (WS230)?
- Monday, December 19th
- Scripts to be run manually
GSA Markup at FlyBase
- Flybase's role in markup and QC?
- 3 month notice to stop curator QC at FB
- FB curators do not want to QC, even with the 'QCFast' tool
- How to make the tool user-friendly for authors?
