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| | [[WormBase-Caltech_Weekly_Calls_October_2011|October]] | | [[WormBase-Caltech_Weekly_Calls_October_2011|October]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_November_2011|November]] |
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| − | == November 3, 2011 ==
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| − | | + | == December 1, 2011 == |
| − | Gene ID mapping problems (as discussed in site-wide call)
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| − | *Does CIT need to worry about consistency of gene IDs over database builds?
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| − | *Hyper-linking entities in papers could be an issue
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| − | *Acquire an ID for every gene for every new genome?
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| − | *When mark a paper, separate into two different types of genes :stable vs unstable
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| − | **Stable genes map to stable ID
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| − | **Unstable genes map with a version number
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| − | *WormBase communicate/work with DCC personnel for data wrangling during post-DCC era?
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| − | Updating Predicted Gene Interactions
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| − | *Wei wei asking about how to update with WormBase
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| − | *WormBase predicted interaction objects can be updated simply via link to Gene Orienteer
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| − | *If we want a live interaction browser, we would need to pull the data into the build process
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| − | *Do we want a single object per pair of genes? One object per instance of evidence (per paper)?
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| − | == November 10, 2011 == | |
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| − | Worm Publication is under review
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| − | | |
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| − | NAR paper is published - has DOI
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| − | *Williams et al has to be added to bibliography
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| − | Citace, Development Release
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| − | *Cron-jobs/scrips used to update the database, but now requires manual manipulation
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| − | *Manual versus automated updating of database
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| − | *Need a plan for the future
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| − | *Migration to EBI affecting the process; will things change again
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| − | *Where will WS release files exist
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| − | | |
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| − | SVM
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| − | *Collecting feedback from curators
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| − | *Curators need to review results
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| − | Motifs in WormBase
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| − | *Xiaodong working on it
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| − | | |
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| − | Interaction Model
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| − | *Discuss with Todd the integrated model of 4 types (physical, genetic, predicted, regulatory)
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| − | *Change WBID names (WBInteraction versus WBPhysicalInteraction, WBGeneticInteraction, WBRegulatoryInteraction, WBPredictedInteraction)
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| − | *Put together series of example data objects; send to Todd/Paul to test out
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| − | *Need Interaction_type tag to distinguish the 4 basic types
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| − | *Types will need to be parsed/extracted after the build for FTP download etc.
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| − | | |
| − | | |
| − | Human Disease Relevance Descriptions
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| − | *Started going in from last build
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| − | *Ranjana will discuss with Web Team
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| − | *Disease-paper connections
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| − | | |
| − | | |
| − | | |
| − | == November, 17, 2011 ==
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| − | | |
| − | | |
| − | Handling 50-100+ genomes
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| − | *Annotation, gene finding, storage, handling
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| − | *~1 week to build all genome browsers and BLAT/BLAST servers
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| − | *Homology run takes longer; from Compara pipeline
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| − | *Species-by-species build processes?
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| − | *Lookup if genome in ACEDB; if not, look up gene models in GFF databases
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| − | | |
| − | | |
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| − | Beta site
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| − | *What is needed:
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| − | **Need eyes to look at current pages
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| − | **Suggestions as to what is needed on individual pages
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| − | *Currently not adding a lot of new features
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| − | *Data models browsable/searchable?
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| − | *If we provide AQL, need to provide data models
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| − | *Intermine will eventually make AQL obsolete(?)
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| − | *Run AQL queries from a local ACEDB instance for better performance (and fewer time outs)
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| − | *Time out limits currently set to 2 minutes on AQL queries
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| − | | |
| − | | |
| − | | |
| − | Expression pattern curation
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| − | *Confidence flags
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| − | *Ex: expressed in HSNs, in HSNL
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| − | *Annotate to parent term unless explicitly (and confidently) stated observed in child term/object
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| − | *Consistency of curation?
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| − | *Discussion between Raymond, Wen, Daniela, etc.
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| − | *Want list of ALL genes expressed in a cell (with some cutoff)
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| − | *Also want list of genes expressed ONLY in that cell and not others
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| − | *New technology generating paradigm shift; how to best represent data
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| − | *Categorize data sets (based on methods)
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| − | *Use evidence codes (text?) to categorize (ECO?)
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| − | | |
| − | | |
| − | ncRNA transcripts
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| − | *To pull out ncRNA genes and GO terms (Sarah Burge)
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| − | *Need to exclude protein-coding genes from query
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| − | | |
| − | | |
| − | | |
| − | GO Meeting (Kimberly)
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| − | *A lot of changes to be put in place
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| − | *Infrastructure, annotation changes - we'll need to sort out what this means for WormBase
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| − | *Annotation: "Annotation extension" column to add additional info
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| − | *Make explicit annotations for gene products
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| − | *Next meeting in February at Stanford (focused annotation meeting)
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| − | **Workout specifications for common annotation framework
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| − | | |
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| − | WormMart status
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| − | *Are we switching over to BioMart-run WormMart?
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| − | *OICR crew working on new data-loading tool
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| − | *Update still pending...
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| − | *Check modmine (http://intermine.modencode.org/)
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| − | | |
| − | | |
| − | Reviews in on SVM paper
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| − | *Maybe done in 3 weeks
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| − | *Reviewer wanted more metrics
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