Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm (→August 8, 2013) |
m (→August 8, 2013) |
||
| Line 92: | Line 92: | ||
*Paper categorization | *Paper categorization | ||
*Depth vs breadth of topics (number of papers?) | *Depth vs breadth of topics (number of papers?) | ||
| + | **'Stress' has been a pilot topic, but is a very broad topic | ||
| + | **Will work on generating subcategories of 'Stress' on the Wiki page | ||
*Goals of 'covering' a topic? | *Goals of 'covering' a topic? | ||
| + | **'Complete' and vetted process page, Wikipathway | ||
| − | + | Curator's should check CGIs | |
| − | * | + | *Submission forms and other CGIs may have been altered |
Revision as of 18:45, 8 August 2013
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)
- form at http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi
- cronjob to get data from "Curation Statistics Page" button at
- /home/acedb/cron/curation_stats/get_daily_curation_stats.pl
- deposits files every day at 5am to :
- /home/acedb/cron/curation_stats/files/
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
August 8, 2013
New Spica now has a closed (private) 'citace' account
- citpub account is accessible to everyone with password
- People can create their own spica accounts
- Personal accounts are encouraged so as to avoid saving changes to citpub database
Worm Ontology Browser
- Raymond has set up a server
- Browsing should be faster now
- Should be transferable to the Amazon cloud
- Raymond will establish a WormBase development environment
Curation priorities
- Paper categorization
- Depth vs breadth of topics (number of papers?)
- 'Stress' has been a pilot topic, but is a very broad topic
- Will work on generating subcategories of 'Stress' on the Wiki page
- Goals of 'covering' a topic?
- 'Complete' and vetted process page, Wikipathway
Curator's should check CGIs
- Submission forms and other CGIs may have been altered
