WormBase-Caltech Weekly Calls
From WormBaseWiki
2013 Meetings
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