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| − | = January 10, 2013 =
| + | 2013 Meetings |
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| − | Site-of-action pages
| + | [[WormBase-Caltech_Weekly_Calls_January_2013|January]] |
| − | *No cell function pages exist
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| − | *Tried to display cell function info on anatomy pages
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| − | *Trying to display site-of-action data on relevant gene pages
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| − | Process pages
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| − | *Rudimentary process page up
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| − | *Has overview widget with all relevant entities
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| − | *Should be something by SAB
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| − | | |
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| − | Intermine
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| − | *JD is working on; should have something ready by SAB
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| − | *Will replace WormMart entirely
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| − | *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
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| − | *We can perform queries for users in the meantime, if necessary
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| − | *Intermine interface isn't very intuitive; maybe we can improve it in time
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| − | *Can build queries with a query builder and perform complex queries
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| − | *Precanned queries could be made and proposed to users
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| − | *Curators can try YeastMine or FlyMine to try it out
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| − | Species expression data from Itai Yanai
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| − | *Importing pictures; potentially flagging each to a particular species
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| − | *Pictures typically linked to Expr_pattern objects
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| − | *Can images be linked to sequences, rather than gene objects?
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| − | Documentation for Protein-2-GO tool
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| − | Brugia database
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| − | *Mark Blaxter offered to donate his Brugia database into WormBase
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| − | *Papers from 1600s!!!
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| − | Nematode Textpresso
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| − | *~10,000 new papers available (open access?)
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| − | Species in Phenotype curation
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| − | *Species tag in phenotype
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| − | *Default dumping with species as C. elegans; some data was removed during the dump
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| − | *Do phenotypes need a species tag? We should add species tag to everything, to be safe
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| − | *Do we create a separate Citace for each species (potentially 100s)?
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| − | *Dump all data for all species in one file for testing, and individual files for upload?
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| − | *Should discuss with Kevin Howe
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| − | Upload Stats
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| − | *Wen will process upload statistics as curators submit data
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| − | *Curators can check for discrepancies right away, rather than wait for the build and submission to notice errors
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| − | Legacy info complete!
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| − | Curation Status Form
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| − | *Will be live (on Tazendra) once some SVM reruns are done
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| − | INDI (Interesting, Not-yet-modeled Data Index)
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| − | *Wiki page generated to capture data types that do not fit cleanly into current data models
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| − | *http://wiki.wormbase.org/index.php/INDI
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| − | Community Annotation of Concise Descriptions, WikiPathways
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| − | *Concise Descriptions
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| − | **Ranjana wrote up a template; Kimberly and Ranjana were stress testing the form
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| − | **Goal: Useful to WB curators, specific community members (experts) for trial curation, and finally general users
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| − | **Scripting simple descriptions, manual annotation of complex descriptions
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| − | **Prioritizing genes that have no descriptions
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| − | **Form should allow a user comment box to indicate data that is missing from WormBase (must have reference or data to support)
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| − | *WikiPathways
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| − | **How do we engage the community in WikiPathways? Prepopulating pages with lists of genes?
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| − | **WormBase-approved models vs. community suggestions/ideas
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| − | *We could focus on specific data types (for this year, say) and really push a public agenda to get community annotation rolling
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| − | SAB Meeting
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| − | *Few weeks away
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| − | *What do we present?
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| − | *We want to discuss our process: curation pipeline, Curation Status Tool
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| − | *Human disease relevance
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| − | *Generate consistent theme or topic flow; divy up to people to present
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| − | *How do we engage the community? What tools do we develop? How will they work? Educational outreach?
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| − | *Display
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| − | **How do we display transcription regulatory networks (TRNs)?
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| − | **How do we display/capture pathways?
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| − | *Topics: Multiple genomes, Natural variants, Transcriptomics, TRNs, Community Annotation, Pathways, Human relevance, Drugs/molecules
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| − | | |
| − | = January 17, 2013 =
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| − | | |
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| − | Curation Status Form
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| − | *Expression data
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| − | **Daniela going through and validating negative papers
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| − | **No record of truly negative papers during Andrei's first pass
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| − | **~2000 papers flagged positive for other_expr but not curated
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| − | **Papers up to year 2000 were carefully, manually scored for expression data
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| − | *We can present the form at SAB meeting
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| − | *Transgene, antibody, and disease are coming from Textpresso, not SVM; papers will be flagged through Curator First Pass tables
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| − | *Microarray datatype to be added to form
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| − | **GEO data with no reference? Ignore
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| − | *Need to add a "Positive but not curatable" pre-canned comment
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| − | SAB Meeting agenda
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| − | *Chris' will present flagging and curation pipeline overview
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| − | *Human relevance
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| − | **Diseases, disease ontology
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| − | *"Spontaneous" updates to DB/website? Mirrors?
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| − | *Processes and pathways
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| − | *Transcription Regulatory Networks
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| − | **Show Cytoscape view of regulatory interactions
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| − | **Show GBrowse with PWMs, for example
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| − | **Cytoscape cell lineage?
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| − | **BioTapestry
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| − | **Cytoscape network filters? (temporal, spatial, process)
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| − | *OICR and Hinxton will present first
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| − | *Kimberly can present on LEGO
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| − | *GO curation pipeline
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| − | *Future plans
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| − | *Community Annotation
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| − | *Meeting at Millikan boardroom
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| − | *SAB Monday night dinner @ Morgan Library
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| − | *Sunday meeting
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| − | **Discuss Cytoscape options with OICR team
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| − | Gene Disaese OA
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| − | *Ranjana and Juancarlos developed OA for gene/disease relationships
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| − | *Connections to Reactome via human genes
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| − | | |
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| − | Cori Bargmann
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| − | *Giving talk this Tuesday 4pm
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| − | *She'll meet WormBase Wednesday morning ~9am-10:30am
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| − | Prioritization of Allele/Phenotype curation
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| − | *Lack of data
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| − | *Process-based curation
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| − | *Top priority: phenotypes for genes that have no existing data
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| − | *Consider throughput of data sets (large scale may be less reliable/granular)
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| − | Community Concise Descriptions
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| − | *Focus on C. briggsae and Brugia malayi
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| − | Dead genes
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| − | *Plan is to maintain record of original genes (dead or not) referred to by objects in Postgres (and other curation databases)
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| − | *At dump, genes will be recognized as dead and replaced where applicable
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| − | *ACEBD and website will display only updated genes but have a "Historical_gene" tag and a remark indicating original reference to a dead gene
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| − | | |
| − | = January 24, 2013 =
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| − | | |
| − | SAB Meeting
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| − | *Curation pipeline
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| − | **Flagging methods
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| − | ***SVM
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| − | ***Author First Pass
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| − | ***Curator First Pass
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| − | ***Textpresso
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| − | **Curation progress over time
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| − | ***Where are we? How much do we have to do? What's our rate?
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| − | ***Do we reprioritize curation? Deprecate some curation?
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| − | ***Group data types by phenotype related classes
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| − | ***Compare current numbers to WS220 and WS200
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| − | ***Numbers by object # versus paper #
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| − | ***Large-scale vs small-scale data sets
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| − | ***High vs low numbers
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| − | | |
| − | *Transcription Regulatory Networks and Gene Expression
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| − | **modENCODE data in GBrowse (ChIP-Seq, RNA-Seq)
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| − | **Cytoscape view - can filter for regulatory interactions
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| − | **FlyBase TRN data
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| − | **BioTapestry
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| − | **What questions can we ask? What do we want to ask?
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| − | **How much do we need to develop tools? Can we co-opt what has already been developed?
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| − | **Transgenomics
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| − | *Interactions
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| − | **New model, consolidating interaction types
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| − | **New genetic interaction ontology with BioGrid, SGD, etc.
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| − | **New OA
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| − | **Will get data from and share with BioGrid
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| − | **Genetic interactions done in parallel with phenotype curation
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| − | **Regulatory interactions done by Xiaodong
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| − | **Large-scale predicted interaction datasets
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| − | *Focus on processes and pathways
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| − | **Process pages and Wikipathways
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| − | **LEGO vs Wikipathways: Redundant? How are they complementary?
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| − | *Community Annotation
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| − | *Curation Priority & Efficiency
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| − | **Curation by paper, data type, topic/process?
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| − | **Should we pilot different curation pipelines?
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| − | **What data types are more easily curated in parallel (e.g. phenotype and genetic interactions)?
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| − | **Hybrid approach: spend some time acquiring specific (and related) data types, then switch to some other curation focus
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| − | **Week focused on particular topic; curator jamboree
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| − | **Experiment with different approaches: What's most fun? Efficient? Productive? Satisfying?
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| − | | |
| − | = January 31, 2013 =
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| − | | |
| − | SAB Review
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| − | *Blog
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| − | **Use blog more; user advice like: how to open all a page's widgets
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| − | **Coming soon info: new data, new displays
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| − | ***Maybe just focus on existing content for now
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| − | **We now have XXX number of XXX objects (Expr pattern, RNAi, phenotypes, etc.)
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| − | **Distributing tasks/efforts
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| − | **WormBase You Tube Channel
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| − | **Recycling notices of features: Make sure all features that we make notice of
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| − | **Report broken things and when things are fixed
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| − | **Need a concise, comprehensive Table of Contents for the site; Site Map to help users know about data and features
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| − | **How is WBPerson class growing/changing?
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| − | *Bug Fixes
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| − | **Prioritizing bugs to be fixed
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| − | **Everyone checks the staging site for a full day, once per release or month
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| − | **Don't show features that are broken on site
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| − | *Intermine priority
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| − | **What do we need to do to get it running ASAP?
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| − | **What is the minimal function required for going live?
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| − | **Start with gene class, see how much we can get ready
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| − | **June 2013 release?
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| − | **Work with existing capabilities of Intermine, not holding out on new query features/capabilities
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| − | **Bottom-up vs top-down approach to development?
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| − | **What are the biological priorities for Intermine?
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| − | **Integrate one class at a time, starting with most important data
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| − | **Get a freeze ready by April 2013, then start testing cycles and make tutorials
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| − | *Incremental updates
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| − | **Easiest thing if we (Caltech) make pages here and send of to OICR to place in widget
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| − | **Curators should decide what type of data they would like to see in incremental updates and discuss with Juancarlos
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| − | **Concise description updates; how to handle typos?
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| − | **Minor vs Major changes? Let's not distinguish right now
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| − | **New data widget open by default on pages?
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| − | *Release notes
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| − | **Need to send Hinxton a list of items (numbers) to be reported on release notes
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| − | **Chris will compile a list of putative release stats to report and send around
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| − | *Resequencing strain issues
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| − | **Curating phenotypes to strains vs. alleles, because of potential background mutations
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| − | **Linking phenotypes to strain, but VIA a presumed allele
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| − | *Pathways - who is an expert? Can they help?
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| − | **Gene pre-populating in Wiki Pathways
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| − | *Transcription Regulatory Networks
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| − | **Can we have FlyBase-like GBrowse tracks?
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| − | **When do we say a Transcription Factor is regulating a target gene? Corroborating evidence
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| − | *Paper Annotation Tool
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| − | **Make tool available at the PubMed site?
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| − | *Expression page revamp
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| − | **RNA-seq graphs, microarray graphs
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| − | **Displaying genotype of transgenes on expression page
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| − | **Displaying all anatomy terms associated with all Expr patterns
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| − | **Yanai data as graphs/images
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| − | **Expression clusters: re-annotating now, working on display and querying
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| − | *Brief IDs vs. concise descriptions
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| − | | |
| − | | |
| − | Table of Contents for Future Discussion
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| − | *Strain-to-Phenotype curation
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| − | *Intermine
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| − | *Incremental updates
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| − | *Bug fix prioritization
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| − | *Pathways
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| − | *Brief IDs vs. concise descriptions
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| − | *LEGO
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| − | *Community Annotation
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| − | *Phenotype-based curation; jamboree-style curation; Flagging papers by topic/process
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| − | *Phenotype-to-GO issues
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| − | *Quarterly update reports
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| − | *Relational DB vs ACEDB
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| − | *Hiring more developers?
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