|
|
| Line 25: |
Line 25: |
| | | | |
| | [[WormBase-Caltech_Weekly_Calls_December_2011|December]] | | [[WormBase-Caltech_Weekly_Calls_December_2011|December]] |
| − |
| |
| − |
| |
| − | == 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
| |
