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| | [[WormBase-Caltech_Weekly_Calls_June_2011|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2011|June]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_July_2011|July]] |
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| − | == July 7, 2011 ==
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| − | Root Passwords for all machines
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| − | *Send to Paul for emergency access
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| − | Issue Trackers
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| − | *All code in production use in BitBucket or equivalent
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| − | *Textpresso - Subversion (code can be shared)
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| − | *WormBase - Bitbucket, GitHub (can commit code)
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| − | *Todd says Github for code is best
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| − | Alex Bishop Help Desk E-mail
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| − | *Interolog Finder
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| − | *FlyBase will include links soon
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| − | *Is WormBase interested connecting to it?
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| − | *Can it be sustainably maintained?
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| − | *We should make a link under the Tools section of WormBase
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| − | *Interolog Finder provides cytoscape files
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| − | *Does Cytoscape have a web interface?
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| − | Elbrus is currently working stably
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| − | *Raymond stabilized Elbrus
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| − | *Elbrus is a frankenstein now
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| − | *Sanger/EBI taking over the RNAi mappings
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| − | *Will discuss with Igor once we determine the remaining issues
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| − | *Elbrus still needed for RNAi scripts to generate ACE files
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| − | Oliver Hobert correcting expression patterns occasionally
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| − | *Ask Oliver to point out what is missing
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| − | *Also ask Shawn Lockery
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| − | *Cell-specific markers
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| − | *Curated as transgenes
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| − | *Can link to specific promoters if transgenes present
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| − | *Bottom of every transgene page has a link to the static Marker table
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| − | *Check on new Beta version of WormBase website
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| − | Changing language of e-mail to authors to confirm data
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| − | *Non-nematode papers in WormBase via Cecilia?
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| − | *Authors sending all papers in their CV
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| − | Expression Cluster data curation
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| − | *Including GO terms, life stage, etc.
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| − | *Link to process pages?
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| − | Expression Cartoons
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| − | *Attempting to depict expression patterns by separate images for each tissue
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| − | *Would be nice to have a consolidated image with the option to expand to see individual tissue images
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| − | *Will maintain consolidated and expandable images for each gene as well as each expression pattern for each gene
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| − | *Trying to capture "Certain", "Uncertain", and "Partial" curation tags
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| − | Molecule curation
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| − | *Will need a molecule page on WormBase at some point
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| − | *Need a way to handle molecules that do not have a Mesh IDs
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| − | *Will replace WBMolecule IDs with Mesh IDs when they become available
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| − | *WBMolecule ID will be made a synonym of the molecule name alongside the Mesh ID
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| − | *Need to consider how the data will be stored and referred to in the long term (via ACE files etc.)
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| − | == July 14, 2011 ==
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| − | Concise descriptions
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| − | *OA being developed for concise descriptions
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| − | *Wiki page for concise descriptions
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| − | *User Community involvement - individual user curation/annotation
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| − | Diseases
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| − | *Managing disease relevance tags in appropriate models
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| − | *Relating human disease genes to C. elegans orthologous genes
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| − | *Developing an integrated view for users to browse human disease relevance
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| − | *Manual vs Automated curation processes
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| − | Worm Breeder's Gazette mass e-mails
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| − | *Users complained about e-mails going to old e-mail addresses
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| − | *Will only e-mail the most current e-mail on a user's profile
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| − | GitHub
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| − | *WormBase curation repository
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| − | *Should Juancarlos put postgres (and other) cgi's there?
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| − | *Make a separate Tazendra repository?
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| − | *Generate symbolic links for flat files (non-code)?
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| − | *Are we limited in the number of repositories we can have? Cost-dependent
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| − | *We could pay more for more repositories; is it worth it?
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| − | *Make another account separate from Todd's? Probably not; should keep consolidated in one account
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| − | *Do different dependencies cause problems?
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| − | *We will ask Todd about what he thinks is best
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| − | *OA code could eventually go to GitHub as well ''Code already in github -- J''
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| − | *Textpresso code can go to GitHub as well
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| − | Ontology Browser
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| − | *Aldrin installing Amigo
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| − | *How long should installing Amigo take?
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| − | *Get some input from GO Consortium
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| − | Genetic Interactions from Textpresso
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| − | *Where are relevant paper sentences stored? ''on tazendra /home/postgres/work/pgpopulation/genegeneinteraction/<date>/ggi_<something> -- J''
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| − | *Should we pull out sentences used by Andrei for interactions curation?
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| − | *Alternatively, redo a Textpresso search for relevant gene names, etc.
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| − | *Can we adequately find allele information?
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| − | Interolog Finder
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| − | *How to incorporate Interolog Finder into relevant gene pages?
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| − | *Maybe make a database object for each C. elegans Interolog Finder interaction
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| − | *Can we display our own data in Cytoscape? Interolog Finder data?
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| − | *Are Wei-wei's data being updated?
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| − | Rearrangements
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| − | *Want to change the variation auto-complete file
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| − | *Dead allele objects
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| − | *Problem: some Rearrangment objects are considered alleles/variations, others are dead or are not considered alleles
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| − | *How do we define/distinguish between Rearrangements/Deficiencies and Alleles?
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| − | *All are variations
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| − | *Do we make alleles and rearrangements mutually exclusive?
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| − | *Since all are variations, we handle each generically as a WBVar### object
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| − | *The distinction would just need to be made at the point of object creation
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| − | Anatomy Ontology
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| − | *Obsolete terms dumped from the Anatomy Ontology
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| − | *Will flag obsolete terms or try to remove from dump
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| − | == July 28, 2011 ==
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| − | Condition Form
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| − | *No one is using
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| − | *Juancarlos will remove
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| − | Concise Description OA
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| − | *Almost done
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| − | *Can this be of use for other nematode (other species) groups?
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| − | *Those studying other nematode are collecting functionally relevant information for genes
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| − | Life Stage tags
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| − | *Do we need a species tag for Life Stages?
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| − | *How closely do different nematode species have similar or the same life stages (and stage names)?
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| − | *Example, Infective Juveniles (IJs) (analogous to dauer?)
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| − | *Example, are all "L1"s the same across species?
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| − | *Let's leave out the species tag for now
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| − | Tracking Gene Name Changes
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| − | *Juancarlos fixed script for tracking and updating gene names in the OA
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| − | *Names will still not be updated (in the OA) until the new release, so there will be a lag
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| − | *Solution for now is to look up WBGeneID in WormBase and query the OA using that
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| − | *(This came up because the official name of a gene changed and the OA hadn't caught up yet)
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| − | Concise Description records with no genes?
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| − | *Some invalid genes disappeared from the name server all together, but should have stayed in tagged as "obsolete"
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| − | Author First Pass forms for transgene
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| − | *Overexpression phenotype
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| − | *Transgene phenotype
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| − | Streamlining Molecule curation
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| − | *Karen gave Michael a list of molecules to run through Textpresso
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| − | *Can save sentences related to molecules
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| − | GSA
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| − | *FlyBase linking moving forward
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| − | *GO-term linking
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| − | **3 Papers have come through pipeline
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| − | **Curators will discuss once gone through
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| − | Outline for NAR paper in the works
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| − | WormBase paper for "Worm" journal
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| − | *"Fun" paper
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| − | *Discuss who we are and what is being done
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| − | Worm Breeder's Gazette
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| − | *WormBase can use Worm Breeder's Gazette as a forum for discussion
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| − | *We should have a presence for every Gazette
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| − | *Replacement for the news letter?
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| − | *SPELL related article? Virtual Worm?
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| − | SVM
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| − | *Ruihua will be here until late September
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| − | *We have an opportunity to update and tighten up the SVM code/process
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| − | *FlyBase interested in implementing
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| − | *Will take some effort to convert for fly
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| − | Expression Cluster Model
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| − | *Last week Wen finished processing Array Express microarray data
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| − | *Not a problem to keep up importing data from Array Express and GEO into SPELL
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| − | *Some authors do not provide spot IDs or respond to e-mails
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| − | *Gene IDs used rather than spot IDs
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| − | *New model will accommodate data from RNA-seq and tiling arrays (not just microarrays)
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| − | *Tag the Expression Cluster with applicable WormBase build/release for reference
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| − | *Capture treatment conditions (temperature, molecules, pathogens, etc.)
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