WormBase-Caltech Weekly Calls January 2013

January 10, 2013

Site-of-action pages

• No cell function pages exist
• Tried to display cell function info on anatomy pages
• Trying to display site-of-action data on relevant gene pages

Process pages

• Rudimentary process page up
• Has overview widget with all relevant entities
• Should be something by SAB

Intermine

• JD is working on; should have something ready by SAB
• Will replace WormMart entirely
• We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
• We can perform queries for users in the meantime, if necessary
• Intermine interface isn't very intuitive; maybe we can improve it in time
• Can build queries with a query builder and perform complex queries
• Precanned queries could be made and proposed to users
• Curators can try YeastMine or FlyMine to try it out

Species expression data from Itai Yanai

• Importing pictures; potentially flagging each to a particular species
• Pictures typically linked to Expr_pattern objects
• Can images be linked to sequences, rather than gene objects?

Documentation for Protein-2-GO tool

Brugia database

• Mark Blaxter offered to donate his Brugia database into WormBase
• Papers from 1600s!!!

Nematode Textpresso

• ~10,000 new papers available (open access?)

Species in Phenotype curation

• Species tag in phenotype
• Default dumping with species as C. elegans; some data was removed during the dump
• Do phenotypes need a species tag? We should add species tag to everything, to be safe
• Do we create a separate Citace for each species (potentially 100s)?
• Dump all data for all species in one file for testing, and individual files for upload?
• Should discuss with Kevin Howe

Upload Stats

• Wen will process upload statistics as curators submit data
• Curators can check for discrepancies right away, rather than wait for the build and submission to notice errors

Legacy info complete!

Curation Status Form

• Will be live (on Tazendra) once some SVM reruns are done

INDI (Interesting, Not-yet-modeled Data Index)

• Wiki page generated to capture data types that do not fit cleanly into current data models
• http://wiki.wormbase.org/index.php/INDI

Community Annotation of Concise Descriptions, WikiPathways

• Concise Descriptions
  • Ranjana wrote up a template; Kimberly and Ranjana were stress testing the form
  • Goal: Useful to WB curators, specific community members (experts) for trial curation, and finally general users
  • Scripting simple descriptions, manual annotation of complex descriptions
  • Prioritizing genes that have no descriptions
  • Form should allow a user comment box to indicate data that is missing from WormBase (must have reference or data to support)
• WikiPathways
  • How do we engage the community in WikiPathways? Prepopulating pages with lists of genes?
  • WormBase-approved models vs. community suggestions/ideas
• We could focus on specific data types (for this year, say) and really push a public agenda to get community annotation rolling

SAB Meeting

• Few weeks away
• What do we present?
• We want to discuss our process: curation pipeline, Curation Status Tool
• Human disease relevance
• Generate consistent theme or topic flow; divy up to people to present
• How do we engage the community? What tools do we develop? How will they work? Educational outreach?
• Display
  • How do we display transcription regulatory networks (TRNs)?
  • How do we display/capture pathways?
• Topics: Multiple genomes, Natural variants, Transcriptomics, TRNs, Community Annotation, Pathways, Human relevance, Drugs/molecules

January 17, 2013

Curation Status Form

• Expression data
  • Daniela going through and validating negative papers
  • No record of truly negative papers during Andrei's first pass
  • ~2000 papers flagged positive for other_expr but not curated
  • Papers up to year 2000 were carefully, manually scored for expression data
• We can present the form at SAB meeting
• Transgene, antibody, and disease are coming from Textpresso, not SVM; papers will be flagged through Curator First Pass tables
• Microarray datatype to be added to form
  • GEO data with no reference? Ignore
• Need to add a "Positive but not curatable" pre-canned comment

SAB Meeting agenda

• Chris' will present flagging and curation pipeline overview
• Human relevance
  • Diseases, disease ontology
• "Spontaneous" updates to DB/website? Mirrors?
• Processes and pathways
• Transcription Regulatory Networks
  • Show Cytoscape view of regulatory interactions
  • Show GBrowse with PWMs, for example
  • Cytoscape cell lineage?
  • BioTapestry
  • Cytoscape network filters? (temporal, spatial, process)
• OICR and Hinxton will present first
• Kimberly can present on LEGO
• GO curation pipeline
• Future plans
• Community Annotation
• Meeting at Millikan boardroom
• SAB Monday night dinner @ Morgan Library
• Sunday meeting
  • Discuss Cytoscape options with OICR team

Gene Disaese OA

• Ranjana and Juancarlos developed OA for gene/disease relationships
• Connections to Reactome via human genes

Cori Bargmann

• Giving talk this Tuesday 4pm
• She'll meet WormBase Wednesday morning ~9am-10:30am

Prioritization of Allele/Phenotype curation

• Lack of data
• Process-based curation
• Top priority: phenotypes for genes that have no existing data
• Consider throughput of data sets (large scale may be less reliable/granular)

Community Concise Descriptions

• Focus on C. briggsae and Brugia malayi

Dead genes

• Plan is to maintain record of original genes (dead or not) referred to by objects in Postgres (and other curation databases)
• At dump, genes will be recognized as dead and replaced where applicable
• ACEBD and website will display only updated genes but have a "Historical_gene" tag and a remark indicating original reference to a dead gene

January 24, 2013

SAB Meeting

• Curation pipeline
  • Flagging methods
    • SVM
    • Author First Pass
    • Curator First Pass
    • Textpresso
  • Curation progress over time
    • Where are we? How much do we have to do? What's our rate?
    • Do we reprioritize curation? Deprecate some curation?
    • Group data types by phenotype related classes
    • Compare current numbers to WS220 and WS200
    • Numbers by object # versus paper #
    • Large-scale vs small-scale data sets
    • High vs low numbers

• Transcription Regulatory Networks and Gene Expression
  • modENCODE data in GBrowse (ChIP-Seq, RNA-Seq)
  • Cytoscape view - can filter for regulatory interactions
  • FlyBase TRN data
  • BioTapestry
  • What questions can we ask? What do we want to ask?
  • How much do we need to develop tools? Can we co-opt what has already been developed?
  • Transgenomics

• Interactions
  • New model, consolidating interaction types
  • New genetic interaction ontology with BioGrid, SGD, etc.
  • New OA
  • Will get data from and share with BioGrid
  • Genetic interactions done in parallel with phenotype curation
  • Regulatory interactions done by Xiaodong
  • Large-scale predicted interaction datasets

• Focus on processes and pathways
  • Process pages and Wikipathways
  • LEGO vs Wikipathways: Redundant? How are they complementary?

• Community Annotation

• Curation Priority & Efficiency
  • Curation by paper, data type, topic/process?
  • Should we pilot different curation pipelines?
  • What data types are more easily curated in parallel (e.g. phenotype and genetic interactions)?
  • Hybrid approach: spend some time acquiring specific (and related) data types, then switch to some other curation focus
  • Week focused on particular topic; curator jamboree
  • Experiment with different approaches: What's most fun? Efficient? Productive? Satisfying?

January 31, 2013

SAB Review

• Blog
  • Use blog more; user advice like: how to open all a page's widgets
  • Coming soon info: new data, new displays
    • Maybe just focus on existing content for now
  • We now have XXX number of XXX objects (Expr pattern, RNAi, phenotypes, etc.)
  • Distributing tasks/efforts
  • WormBase You Tube Channel
  • Recycling notices of features: Make sure all features that we make notice of
  • Report broken things and when things are fixed
  • Need a concise, comprehensive Table of Contents for the site; Site Map to help users know about data and features
  • How is WBPerson class growing/changing?
• Bug Fixes
  • Prioritizing bugs to be fixed
  • Everyone checks the staging site for a full day, once per release or month
  • Don't show features that are broken on site
• Intermine priority
  • What do we need to do to get it running ASAP?
  • What is the minimal function required for going live?
  • Start with gene class, see how much we can get ready
  • June 2013 release?
  • Work with existing capabilities of Intermine, not holding out on new query features/capabilities
  • Bottom-up vs top-down approach to development?
  • What are the biological priorities for Intermine?
  • Integrate one class at a time, starting with most important data
  • Get a freeze ready by April 2013, then start testing cycles and make tutorials
• Incremental updates
  • Easiest thing if we (Caltech) make pages here and send of to OICR to place in widget
  • Curators should decide what type of data they would like to see in incremental updates and discuss with Juancarlos
  • Concise description updates; how to handle typos?
  • Minor vs Major changes? Let's not distinguish right now
  • New data widget open by default on pages?
• Release notes
  • Need to send Hinxton a list of items (numbers) to be reported on release notes
  • Chris will compile a list of putative release stats to report and send around
• Resequencing strain issues
  • Curating phenotypes to strains vs. alleles, because of potential background mutations
  • Linking phenotypes to strain, but VIA a presumed allele
• Pathways - who is an expert? Can they help?
  • Gene pre-populating in Wiki Pathways
• Transcription Regulatory Networks
  • Can we have FlyBase-like GBrowse tracks?
  • When do we say a Transcription Factor is regulating a target gene? Corroborating evidence
• Paper Annotation Tool
  • Make tool available at the PubMed site?
• Expression page revamp
  • RNA-seq graphs, microarray graphs
  • Displaying genotype of transgenes on expression page
  • Displaying all anatomy terms associated with all Expr patterns
  • Yanai data as graphs/images
  • Expression clusters: re-annotating now, working on display and querying
• Brief IDs vs. concise descriptions

Table of Contents for Future Discussion

• Strain-to-Phenotype curation
• Intermine
• Incremental updates
• Bug fix prioritization
• Pathways
• Brief IDs vs. concise descriptions
• LEGO
• Community Annotation
• Phenotype-based curation; jamboree-style curation; Flagging papers by topic/process
• Phenotype-to-GO issues
• Quarterly update reports
• Relational DB vs ACEDB
• Hiring more developers?