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| | [[WormBase-Caltech_Weekly_Calls_January_2015|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2015|January]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_February_2015|February]] |
| − | = February 2015 =
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| − | | |
| − | == February 5, 2015 ==
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| − | | |
| − | === Community Annotation ===
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| − | * Mary Ann discussed with Paul S.
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| − | * Mary Ann would like to develop a prototype curation form (for variations/molecular lesions) for the international meeting
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| − | ** Test version in 6 weeks?
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| − | ** Juancarlos would need a list of required fields, field types, data connections, etc.
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| − | ** Could take advantage of existing forms
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| − | * Ranjana and Juancarlos working on the concise description form
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| − | | |
| − | === Changing GAF format ===
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| − | * What implications does this have for the WormBase Ontology Browser?
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| − | * What testing of generation of the GAF could be done (and sent to Raymond)?
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| − | * Kimberly will discuss with Kevin
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| − | | |
| − | === Automated descriptions with updated release schedule ===
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| − | * WS247 database will not be ready with enough time for Ranjana and James to incorporate into the automated description generation
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| − | * They can make do with older files
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| − | | |
| − | === Citace upload for WS248 ===
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| − | * Tuesday March 3rd
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| − | | |
| − | | |
| − | | |
| − | == February 12, 2015 ==
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| − | | |
| − | === Physical Interaction Curation ===
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| − | * We have begun physical interaction in Interaction OA
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| − | * We are establishing a pipeline to share all physical and genetic interactions with BioGRID
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| − | * It would be good to clarify which curators can/will curate physical interactions
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| − | * Would be good if phenotype curators could curate genetic AND physical interactions in the same paper
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| − | * Something that John DeModena could do?
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| − | * Xiaodong capturing protein-DNA interactions
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| − | * We still need to decide what level of detail we would like to capture
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| − | * We could try to capture specific protein sequences used in experiments
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| − | * We don't have individual protein/peptide sequence objects, maybe we want them? IDs for domain instances?
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| − | * We have an SVM pipeline "geneprodgo"
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| − | * A lot of GO protein interaction data to extract; might use ?Analysis objects to track attribution of curation
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| − | | |
| − | === BioGRID interaction sharing ===
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| − | * Provenance and attribution issues
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| − | * ?Analysis object can be created for BioGRID attribution
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| − | * WormBase has imported all worm (C. elegans) physical (protein-protein) interactions from BioGRID
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| − | * Working on importing BioGRID genetic interactions, or at least resolving overlap
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| − | * WormBase will send physical and genetic interaction data to BioGRID at every upload
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| − | * Rose et al are considering regulatory interaction data, currently discussing
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| − | | |
| − | === WormBook WormBase Chapter ===
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| − | * Feb 28 deadline coming up
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| − | * Can be about 3 pages per chapter
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| − | * Sections can be written as stand alone and merged as necessary
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| − | * Putatively 8 - 10 chapters being written
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| − | | |
| − | === User submitted Phenotype (RNAi) data ===
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| − | * A user recently requested addition of RNAi data for a handful of papers
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| − | * I (Chris) directed them to our trial [https://docs.google.com/a/wormbase.org/spreadsheets/d/1lLxMZ016g81EpR11eKILm3H17DbcrsUuwq5lqmIIKWk/edit#gid=0 RNAi data submission table]
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| − | * Would be good to embed community annotation forms into WormBase website so that users could log in and add data without having to re-enter personal information
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| − | * Can we map user login info to WBPerson ID? Is that already the case? Would be good.
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| − | | |
| − | === Clone Mapper Software ===
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| − | * We will adopt Clone Mapper for RNAi clone mapping
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| − | * Chris and Kevin working with Jonathan Ewbank
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| − | * Important issue remains: what cutoff for the Clone Mapper tool do we choose?
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| − | * We are working on creating RNAi reagent objects in WormBase to capture targets (and off targets) independently of any RNAi experiments
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| − | | |
| − | === WormBase PI meeting for database migration ===
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| − | * Next week to discuss current new database considerations
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| − | * Datomic, MongoDB, etc. front runners
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| − | | |
| − | === Virtual Fly Brain ===
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| − | * Paul S will talk to group
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| − | * 8:30am meeting next Monday
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| − | * Coordination with fly and fish groups
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| − | * Working out applicable ontologies
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| − | | |
| − | | |
| − | == February 19, 2015 ==
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| − | | |
| − | === Citace Upload ===
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| − | * 10am March 3rd
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| − | | |
| − | === International Meeting Workshop ===
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| − | * Raymond will cover WormBase Ontology Browser
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| − | * Ranjana will cover concise description submission/correction
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| − | * Paul S. will present at plenary session to make a call for community annotation
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| − | * Kevin will present Parasite and sequence repositories/submission
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| − | | |
| − | === Int. Mtg. Booth and Posters? ===
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| − | * Would be good to have a projector at booth like last time; show people how to get data, etc.
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| − | * Keep the poster for advertisement/outreach and displaying the most current WB poster (Xiaodong's SeqFeat)
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| − | * Could have prepared presentation/slides displayed on projector at booth by default as a background; change to live demo as needed
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| − | * Could demonstrate community annotation?
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| − | * Advertisement & Outreach
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| − | * Community annotation poster?
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| − | | |
| − | === WS247 WormBase Ontology Browser built ===
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| − | * Number of genes with Gene Ontology annotations dropped
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| − | * May be explained by lack of Phenotype-to-GO annotations
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| − | * Raymond can send numbers to Kimberly
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| − | | |
| − | | |
| − | == February 26, 2015 ==
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| − | | |
| − | === WormBook chapter(s) ===
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| − | * We'll do a round of reviews and edits on Google Docs
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| − | * Eventually we'll transition to Word Docs
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| − | * We can hand in next week sometime
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| − | * WRT community annotation, we can discuss what we already have
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| − | | |
| − | === 2015 International C. elegans meeting ===
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| − | * Posters
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| − | ** Could submit abstracts for 1-2 posters
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| − | ** Could project slides/posters projected at Help Desk booth
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| − | ** Self explanatory slides projected?
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| − | * Workshop
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| − | ** Volunteers:
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| − | *** Raymond : WOBr
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| − | *** Mary Ann : Community annotation (for variation)
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| − | *** Ranjana : Concise descriptions
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| − | *** Kevin : Parasite, sequence repositories & submission
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| − | *** Chris : WormMine
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| − | *** Kimberly : Finding and using GO annotations
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| − | *** Scott Cain : JBrowse
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| − | * WormBase staff could have distinctive outfits (shirts or hats)
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| − | ** Paul S could wear it at opening plenary talk
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| − | * Maybe Kevin Howe could request a booth for ParaSite?
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| − | | |
| − | === Model change errors for WS248 upload ===
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| − | * Main problem is fixing a model after it has been tagged. We want to avoid having to do this because once a model has been tagged it is employed at different centers, fixing a tagged model would required extra work at all these centers.
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| − | * Historical_gene tag accidentally removed from ?Construct model
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| − | * Would be good for all curators to see an explicit diff output to confirm all changes made
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| − | * Before tagging the models, would be good for Paul Davis to send a formal diff of all changes made to confirm; Paul summarizes the changes in CVS. All curators should look at the CVS summary of changes to make sure only the requested changes had been made.
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| − | | |
| − | === Automated concise descriptions ===
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| − | * Orthology pipeline needed to be reworked
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| − | * Find best match by multiple orthology searching methods
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| − | * 120,000+ total automated descriptions
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| − | ** 5 Caenorhabditis species
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| − | ** Pristionchus pacificus
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| − | ** Brugia malayi
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| − | ** Onchocerca volvulus
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| − | * One-to-many orthologies start to become unwieldy
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| − | * Because of upload time crunches, we may want to fall back on older files if necessary
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| − | | |
| − | === Database infrastructure ===
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| − | * Narrowed down to Datomic and MongoDB
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| − | * Thomas, Lincoln thought Datomic was better
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| − | * Datomic *could* possibly be bought out
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| − | ** Could still be changed over; would require work, but would have technology in place, worth it
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| − | * Will have timestamps
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| − | * Still planning to have a single all-encompassing database
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| − | | |
| − | === BioGRID data sharing pipeline ===
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| − | * Juancarlos developed a BioGRID TAB2 dump file from the Interaction OA
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| − | * Eventually will send all worm genetic and physical interactions to BioGRID
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| − | * Will omit genetic no_interactions
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| − | * Will omit interactions with no PubMed ID: reviews or person evidence only
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| − | * Will omit interactions with uncloned genes (no Entrez ID)
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| − | * As of Feb 25, 2015, we have ~8220 total novel* genetic interactions to submit to BioGRID (*novel to BioGRID)
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| − | | |
| − | === Species for genes in Postgres ===
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| − | * We will talk to Michael Paulini about getting species info for genes
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| − | * Need to get from GeneACE or some place else
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| − | * Added after meeting - yes, all Species are in Geneace. (Mary Ann)
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