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| | [[WormBase-Caltech_Weekly_Calls_March_2011|March]] | | [[WormBase-Caltech_Weekly_Calls_March_2011|March]] |
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| − | ==April 7, 2011==
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| − | Transgene Model
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| − | *On Wiki
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| − | *Sent out to people
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| − | *Have a look; report any concerns
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| − | *Can follow on BitBucket; search for transgene; link to Wiki
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| − | *No objections at Caltech; Karen will send to Paul Davis
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| − | *Changes to ACE dumping script; Karen will talk to Juancarlos
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| − | *Changes needed in OA (softer deadline than dump)
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| − | Interactions
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| − | *Murky genetic interaction curation?
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| − | *Err on the side of generality/trusting author statements
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| − | *When in doubt, curate as "genetic interaction"
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| − | *Chris is working on decision tree/pipeline for curation
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| − | *Kimberly working on Physical Interaction model
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| − | BioGRID meeting at Princeton in May
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| − | *Call in
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| − | *What will Rose propose?
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| − | Expression Pattern Curation (Daniela/Wen)
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| − | *Daniela sent out picture page for review
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| − | *Expr Pattern OA wiki is in place:
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| − | **http://wiki.wormbase.org/index.php/Expression_Pattern
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| − | *As soon as Juancarlos is done with the modularization will start working on the code.
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| − | *In the meanwhile Daniela will curate expression pattern writing .ace files
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| − | *Expr_pattern OA should be ready by the next upload (May26th). (I really doubt this, parsing in data, writing dumpers, and checking it take a long time. Picture and Interaction each probably took longer than 2 months, and we're not starting Expr until May at the earliest -- Juancarlos)
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| − | Patch file/Interbuild (Raymond)
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| − | *Developed good patch file
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| − | *Tested patch file to update WS224 to WS225 - seems OK
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| − | *Less than 5 minutes for upload
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| − | *Testing now should be done by Todd/OICR team
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| − | Uma started
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| − | *Working on concise descriptions of gene classes
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| − | *Karen has reviewed with Uma; Uma is reading papers
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| − | *Discussing details of descriptions
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| − | *Inconsistencies/discrepancies of gene class names
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| − | *>2400 gene classes
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| − | *Can work on generating formula for this curation
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| − | *Arun can help with automation
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| − | *May need to get Uma an interface to enter data into postgres
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| − | *Adapt concise description CGI for her? (probably write a whole new interface depending on goal -- Juancarlos)
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| − | *Gene class name and a text field
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| − | *Using Textpresso/WormMart output; sentence saver?
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| − | eggNOG data into citace?
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| − | *Who's going to handle the data? curate?
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| − | *Michael? OK
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| − | ==April 14, 2011==
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| − | Gene Class Descriptions
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| − | *Concerns about maintenance and redundancy
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| − | *Uma here for ~ 3 months
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| − | *How many gene classes have alleles?
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| − | *How many are named by phenotype rather than just molecular data?
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| − | *How is this different from gene concise descriptions?
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| − | *Should it be a summary of all gene concise descriptions of the class?
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| − | *Things currently focused on:
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| − | **using WormMart to look at genes in a class
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| − | **pulls out all concise descriptions
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| − | **look at similarities
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| − | **interesting things to highlight
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| − | *Gene concise descriptions vs class descriptions
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| − | **Gene-centric vs Class-centric
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| − | **Consolidating/pooling all concise descriptions from individual genes?
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| − | *Going for maintenance-free statements
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| − | *Potentially building an interface
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| − | *Richard Durbin: development vs behavior?
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| − | *Prioritization?
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| − | *Focus on phenotype-based classes like UNC?
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| − | *Factors for prioritization:
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| − | **Numbers of genes curated
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| − | **molecular vs phenotype-based
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| − | **Amount of info currently available?
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| − | **Historical points
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| − | **Most actively worked currently? (most mentioned in last year's publications?)
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| − | *Uma and Karen could communicate with Kimberly and Ranjana about
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| − | *What is most efficient for Uma to focus on?
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| − | *Uma can look at gene class description makes sense
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| − | *Skip gene classes for which only one gene exists
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| − | *GO term stats on each class?
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| − | Papers missing from Textpresso
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| − | *Issue: Genetics papers for GSA markup are missing from SVM analysis
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| − | *Juancarlos' file on caprica
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| − | *Discrepancy between papers on Textpresso and those gone through SVM
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| − | *SVM doesn't pick up GSA papers
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| − | *Generate a filtering to detect which ones have been missed by SVM
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| − | *Michael looking into reasons why the pipeline isn't working
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| − | *Tazendra vs Textpresso discrepancies?
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| − | *Ruihua will process 56 missing papers retroactively
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| − | *Still working on how to avoid this in the future
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| − | ==April 21, 2011==
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| − | WormMart
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| − | *Stable for IWM?
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| − | *WormMart presentation for WormBase workshop
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| − | **Query examples
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| − | **Data content
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| − | **Features
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| − | **Plans for the next year; what data to be made available
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| − | **Discuss stability?
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| − | Igor's machine: elbrus
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| − | *Can have problems
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| − | *Input info has changed for WS225
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| − | *RNAi script stopped working
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| − | *Migration issues
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| − | **Decide on priorities
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| − | **Who will maintain what?
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| − | **Migrate things over to newer machines, locally
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| − | *On elbrus now:
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| − | **RNAi scripts (sequence mapping); Migrating to EBI
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| − | **Anatomy ontology browser (optional)
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| − | **Microarray tool (Wen will take over)
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| − | **Get-Sequence CGI (how many people use it?)
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| − | *Meet with Norie at IWM?
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| − | *We should write everything down first
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| − | BioGRID-WormBase data exchange:
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| − | *Questions about how to best do this
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| − | *How to handle/organize genetic interactions
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| − | *BioGRID meeting in May; will not be sufficient to solve the genetic interaction issues
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| − | *Still working on genetic interaction organization scheme
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| − | SPELL/Microarray
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| − | *Discuss at IWM?
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| − | *Patching changes into WS225
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| − | ModENCODE Meeting
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| − | *Gary Williams should go
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| − | Picture Page
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| − | *New developments
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| − | *Elsevier publishing; how to handle them? ($17.5 per figure!!!)
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| − | Informatics Resources Assessment
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| − | *Can we develop plan to determine informatics resources available
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| − | *Long-term plans for sustainable informatics resources
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| − | ==April 28, 2011==
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| − | Cecilia - Person report
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| − | *"AKA" ("Also Known As") added manually
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| − | **"also publishes as" created automatically based on verified author-person connections
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| − | **Over populating AKA manually is redundant
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| − | **Populating unique or new AKAs manually are still necessary
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| − | *Verified names happen automatically
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| − | **Author-Person connections happen with a script that Cecilia runs weekly manually
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| − | **Creating connections if an author name matches to exactly 1 person's name / aka (if 0 or 2+ matches then no connection occurs)
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| − | **Connection verifications happen weekly with a script that Cecilia also runs manually based on other verified authors in the paper sharing a Lineage or Laboratory
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| − | **Manual verification are emailed monthly to Persons who verify.
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| − | *Connection to person in GSA markup pipeline
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| − | **Automatic if script unambiguously identifies one individual person
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| − | **Karen (/ Daniela ?) will keep manual touch with Cecilia to create people for GSA because people links are necessary for the URLs.
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| − | *Extracting person info from lab web pages, papers, worm meeting registration?
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| − | **This takes varying amounts of time for questionable benefit
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| − | **Concensus at meeting was that lab website + PI website + papers + meetings are good sources.
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| − | *WormBase policy? Should unverified person info be included?
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| − | **Raymond had question about whether it's a good idea in general to create people without explicit contact with the person via email.
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| − | **Juancarlos agrees that it's better data if they explicitly contact, but it's not necessarily better in a practical sense and anyone can spoof an email.
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| − | *Address? Remove details irrelevant to mailing address? Institute name?
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| − | **Leave it as is
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| − | *Prioritize name and e-mail verification for new paper/person connections?
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| − | **Juancarlos + Cecilia + Raymond will talk to Paul about priorities
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| − | Karen - Abby, Aldrin Montana - Google Summer of Code
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| − | *Aldrin didn't get accepted
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| − | *asks if he could work with us anyway?
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| − | *11 weeks during summer, full time
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| − | *would work remotely
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| − | *any ideas? modENCODE, microarray, pre-canned queries, Reactome (assigning confidence values to pathways)
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| − | *we can collect more ideas
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| − | *has coding experience (js, Perl, CSS), just not much with bioinformatics, he wants to learn
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| − | *Aldrin is working on a bioinformatics masters
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