Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
Line 113: Line 113:
 
**Papers up to year 2000 were carefully, manually scored for expression data
 
**Papers up to year 2000 were carefully, manually scored for expression data
 
*We can present the form at SAB meeting
 
*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 form
+
*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
 
*Microarray datatype to be added to form
 
**GEO data with no reference? Ignore
 
**GEO data with no reference? Ignore

Revision as of 20:47, 17 January 2013

2009 Meetings

2011 Meetings

2012 Meetings


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)


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