Difference between revisions of "WormBase-Caltech Weekly Calls"
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Revision as of 16:37, 5 January 2012
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?
December 15, 2011
Interactions display on Beta
- Under 'Phenotype' reads "Interaction_Phenotype" e.g. let-60
- On interaction page, no reference
Dead genes in interaction objects
- In citace minus, dead genes hidden in hashes
- Some data stored as .ace files, others (large-scale) in flat files; flat files easier to manage
- We don't want large-scale data in the OA; take up too much space? (Megabytes of data, ~quarter million objects?)
- Interaction objects have to be edited one-by-one to clean up dead genes, very tedious
- Keep data in flat files? Who will manage the flat file? Xiaodong
- Juancarlos has script to screen all objects for dead genes
- Still need to upload the data (from OA and flat file) for every release/upload/build
- Old interaction objects still in Citace Minus (never removed); Wen will erase
- Keep dead genes in large-scale interactions for now, script their removal later
- Suppress entire objects from loading to ACEDB if has dead genes? No, still dump, but add cautionary remark?
- RNAi interaction objects likely have dead gene assigments (need to check)
- 'Dead genes' 29128, totally 'dead' vs. 'merged' genes?
- Juancarlos will generate list of 'killed' genes (not 'merged')
- Move 'killed' genes to flat files?
- OA will throw error in interaction has only one gene if dumped
- Need to reconcile the fact that the Interaction objects require a GeneID for Interactor tag
- Need to deal with RNAi-to-gene mapping for interactions
Preparation for Arun's departure
- Arun will check all code into SVM repository
- Repository has taken in a bunch of unnecessary data (PDF files, etc.); will avoid from now on
- Daniela will meet with Arun and Yuling, to extract images from PDFs, and marking positive/negative figure legends
- SGD QCFast editor finished (although may not be able to test extensively before Arun leaves)
- Arun will discuss maintenance of QCFast with Michael
- Arun will prepare documentation
- How much work will it take to generate FlyBase editor?
- Providing capacity/functionality to delete as well as add links in paper
IAIC (International Arabidopsis Information Consortium)
- Imagine 10+ years from now; what data does Arabidopsis researcher have access to?
- People listed features wish-list
- What specifications required to achieve wish-list? APIs, user documentation, code, etc.
- Ideas fall to the side based on difficulties
- Optimistic vs pessimistic approach
- People then start writing specifications in grant format
- At end, 38 page document capturing all ideas/thoughts
- Divide into 4 groups, to pick up all ideas that fell through the cracks
- NSF, MRC, German, Austrian groups
- Community annotation focus
- Core references developed upon consistent, repeated user-generated annotations
- Wikipedia-type monitoring and annotation (minimal staff)
- Moving from single gene queries to multi-gene/process queries
- Looking for appropriate PIs to take charge
- Publicly available document (Jan 2012?)
- NSF has spent $1B on Arabidopsis research, cannot let data just wither
BioCreative group conference
- BioCreative is text mining research/development group
- After BioCurator meeting in April
- Requires submission of 2-page document describing curation workflow
- Kimberly has written a draft and would like feedback (will send out)
- Track II section of BioCreative
- Document = Description of biocurative workflow (for a text miner audience)
Communicating Script function and maintenance pipeline
- How to best document script generation, development, updating, and maintenance
Ian Hope's New Expression data set
- Daniela handling importing of data
- Ian will update us when data is available
- Method paper is out