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| [[WormBase-Caltech_Weekly_Calls_December_2011|December]] | | [[WormBase-Caltech_Weekly_Calls_December_2011|December]] |
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− | == December 1, 2011 ==
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− | WORM paper
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− | *Sorted out at conference call
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− | *EBI will take lead on rewrite
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− | *We want a paper on the new website to go to a broader audience
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− | Interaction model
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− | *Almost sorted out and working
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− | *Chris & Kimberly will discuss
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− | Elsevier linking (images)
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− | *Caltech attorney's want the agreement with Elsevier to be under US law
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− | *Usage data relating to Elsevier content access must be deleted within 3 months(???)
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− | *Should not be an issue?
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− | Local AQL queries
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− | *Running on Caltech mirror? Currently getting an error: "Connection closed by remote server"
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− | *Can run AQL from xace on spica
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− | == December 8, 2011 ==
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− | Bio Curator Meeting
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− | * In Washington DC next April
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− | * Wen will send an abstract on SPELL
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− | * Kimberly, Arun and Michael will be there as well
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− | * Abstracts to submit: 3 in total (Kimberly, Arun, Wen)
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− | WomrBase curator ad officially posted
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− | WormBase meeting announcement
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− | * What is our policy? Should we send info to everyone?
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− | * We can send to PIs only
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− | * Meeting announcements are an appropriate use of the list (if a bonafide ''C. elegans'' meeting)
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− | Beta site Protein Page review
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− | * Common protein name e.g. 'UNC-26' or 'Synaptojanin'
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− | * Use GO curation, PAINT/PANTHER tool to assign name?
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− | * What's the best method (automated, if possible) to assign a useful name?
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− | * Refer to Uniprot for names; can EBI pull names directly from Uniprot?
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− | * GO: Molecular Function and Cell Component are annotated to gene, in some cases an isoform is attributed
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− | * Want to enable curation to isoforms when info is available
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− | Interactions
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− | * Interaction model still being tweaked
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− | * Will try to 'swallow up' Gene Regulation objects and tags into main Interaction model
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− | * #Interaction_info and #Interacor_info may be removed
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− | Anatomy nomenclature discrepancies
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− | * Oliver Hobert raised issue of consistency of names
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− | * For example, sometimes "DA neurons" refers to dopamine neurons as opposed to the anatomical 'DA' neuron
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− | * DA neurons are actually cholinergic
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− | * Maybe post on the blog
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− | * Make synonym for dopaminergic neuron as 'DA neuron'?
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− | Citace upload date (WS230)?
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− | * Monday, December 19th
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− | * Scripts to be run manually
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− | GSA Markup at FlyBase
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− | * Flybase's role in markup and QC?
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− | * 3 month notice to stop curator QC at FB
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− | * FB curators do not want to QC, even with the 'QCFast' tool
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− | * How to make the tool user-friendly for authors?
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− | == December 15, 2011 ==
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− | Interactions display on Beta
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− | *Under 'Phenotype' reads "Interaction_Phenotype" e.g. let-60
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− | *On interaction page, no reference
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− | Dead genes in interaction objects
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− | *In citace minus, dead genes hidden in hashes
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− | *Some data stored as .ace files, others (large-scale) in flat files; flat files easier to manage
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− | *We don't want large-scale data in the OA; take up too much space? (Megabytes of data, ~quarter million objects?)
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− | *Interaction objects have to be edited one-by-one to clean up dead genes, very tedious
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− | *Keep data in flat files? Who will manage the flat file? Xiaodong
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− | *Juancarlos has script to screen all objects for dead genes
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− | *Still need to upload the data (from OA and flat file) for every release/upload/build
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− | *Old interaction objects still in Citace Minus (never removed); Wen will erase
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− | *Keep dead genes in large-scale interactions for now, script their removal later
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− | *Suppress entire objects from loading to ACEDB if has dead genes? No, still dump, but add cautionary remark?
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− | *RNAi interaction objects likely have dead gene assigments (need to check)
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− | *'Dead genes' 29128, totally 'dead' vs. 'merged' genes?
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− | *Juancarlos will generate list of 'killed' genes (not 'merged')
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− | *Move 'killed' genes to flat files?
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− | *OA will throw error in interaction has only one gene if dumped
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− | *Need to reconcile the fact that the Interaction objects require a GeneID for Interactor tag
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− | *Need to deal with RNAi-to-gene mapping for interactions
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− | Preparation for Arun's departure
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− | *Arun will check all code into SVM repository
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− | *Repository has taken in a bunch of unnecessary data (PDF files, etc.); will avoid from now on
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− | *Daniela will meet with Arun and Yuling, to extract images from PDFs, and marking positive/negative figure legends
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− | *SGD QCFast editor finished (although may not be able to test extensively before Arun leaves)
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− | *Arun will discuss maintenance of QCFast with Michael
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− | *Arun will prepare documentation
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− | *How much work will it take to generate FlyBase editor?
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− | **Providing capacity/functionality to delete as well as add links in paper
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− | IAIC (International Arabidopsis Information Consortium)
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− | *Imagine 10+ years from now; what data does Arabidopsis researcher have access to?
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− | *People listed features wish-list
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− | *What specifications required to achieve wish-list? APIs, user documentation, code, etc.
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− | *Ideas fall to the side based on difficulties
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− | *Optimistic vs pessimistic approach
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− | *People then start writing specifications in grant format
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− | *At end, 38 page document capturing all ideas/thoughts
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− | *Divide into 4 groups, to pick up all ideas that fell through the cracks
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− | *NSF, MRC, German, Austrian groups
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− | *Community annotation focus
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− | *Core references developed upon consistent, repeated user-generated annotations
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− | *Wikipedia-type monitoring and annotation (minimal staff)
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− | *Moving from single gene queries to multi-gene/process queries
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− | *Looking for appropriate PIs to take charge
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− | *Publicly available document (Jan 2012?)
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− | *NSF has spent $1B on Arabidopsis research, cannot let data just wither
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− | BioCreative group conference
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− | *BioCreative is text mining research/development group
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− | *After BioCurator meeting in April
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− | *Requires submission of 2-page document describing curation workflow
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− | *Kimberly has written a draft and would like feedback (will send out)
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− | *Track II section of BioCreative
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− | *Document = Description of biocurative workflow (for a text miner audience)
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− | Communicating Script function and maintenance pipeline
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− | *How to best document script generation, development, updating, and maintenance
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− | Ian Hope's New Expression data set
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− | *Daniela handling importing of data
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− | *Ian will update us when data is available
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− | *Method paper is out
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