WormBase-Caltech Weekly Calls

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August 1, 2013

Quarterly Progress Reports

  • Capturing curation stats from the Curation Status form
  • What data types do we want to capture curation stats for that we are not currently?
  • We have frequent database dumps that can be read for stats
  • We can capture the stats table statically on a regular basis (daily)

RNA-Seq and Tiling Array data

  • Data in SPELL
  • Wen found a lot more non modENCODE data sets
  • May use SVM for expression cluster data
  • Gene IDs can be found from original paper or data set
  • Up-to-date mapping to genes is not currently done

AMIGO2 (Wormbase Ontology Browser)

  • Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase
  • GO Term focus page demo
  • Graph view shows path to root (DAG view)
  • Inferred tree view shows:
    • Ancestor terms, no annotation numbers
    • Main term and children, with annotation numbers (inferred, term and descendant annotations)
    • Annotation numbers link to list of genes
    • Will not show "direct" annotations, only inferred
  • Sibling term displays: list parents with option to expand to see siblings of the main term
  • Separate expandable/collapsible tree of ontology ("Browse entire ontology")
  • Widget can be coded to integrate the ontology browser

Paper Categorization

  • Word frequency
    • We chose papers from the Author First Pass (AFP) list with 'stress'
    • About 40 papers in list, varied topics ('stress' is a broad term)
    • Curation essentially now complete for most data types
    • Expanding beyond AFP?
  • Chris will draw up preliminary tree of topics and send around
    • We can discuss, edit, and expand as a group
    • We want to 1) Collect positive and negative training papers and 2) Manually generate a list of key words to use for training
  • Todd proposes for paper pages on WormBase:
    • Show a table of flagged data types for a paper?
    • Give users a sense of where paper is in the curation pipeline