WormBase-Caltech Weekly Calls
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Contents
Previous Years
2014 Meetings
July 3, 2014
WS245 Upload
- Tuesday, July 29th local citace upload (to Wen)
- Friday, August 1st citace upload to Hinxton
Data models freeze
- Next Friday July 11th
Automated Concise Descriptions
- James and Ranjana making progress
- Several examples of automated descriptions, proof of concept
- Based on 3 GO categories and homology
- Add tissue-specific expression, and go live
- Should add 1000s of descriptions (automated)
- Next, pick terms of higher granularity
- We should ask users what they want: e.g. Is an Ascaris suum gene ortholog in C. elegans essential?
- Manual annotations in future? How can edits be tracked? Gets a new tag?
- Automated descriptions for all objects?
- We will likely separate manual from automated descriptions to ease editing and tracking
- GO terms can be added as IDs and be converted (automatically) to the term name with hyperlink on the web site
New Tazendra machine
- Up and running at dhcp-52-226.caltech.edu; IP address: 131.215.52.226
- Juancarlos will sync the current Tazendra data to the new machine after meeting
- Curators will test forms and dumpers; compare dump outputs from new and old machine
- We can make the new machine live later in the month
July 10, 2014
CANTO
- CANTO - PomBase's Community Annotation Tool
- http://www.ncbi.nlm.nih.gov/pubmed/24574118
- Link to demo version: http://curation.pombase.org/demo
- Can try demo version with any S. pombe or S. cerevisiae gene names/ids
- GO annotations, mutant phenotypes, etc.
Construct model/annotation
- Need to add "Construct" under list of "Detection methods" in the ?Interaction model
- Chris will send corrected models.wrm file to Karen
- Karen will send models.wrm to Paul Davis by tomorrow
- Interaction OA dumper will need to be updated to accommodate constructs and transgene changes (Chris will work on with Juancarlos)
BioGRID data
- Mike Tyers agreed to release physical interaction data for C. elegans
- We will import data into the Interaction OA and WormBase
- Attribution? Reference to an ?Analysis object? Would need an additional field for Analysis objects? Could reference as Database accession number
- Chris will discuss with Kimberly
July 17, 2014
SAB
- Travel Arrangements for the October SAB in England and GO Meeting in Spain
- Have advisory board members been contacted? Are they all available?
Construct
- Model and OA are now live
- Transgenes have been replaced with appropriate construct objects
WOBr
- Pushing code to the live web site soon
July 24, 2014
SAB
- Happening on Oct 7 and 8th, 2014, with advisors
- Monday whole day
- Tuesday till 1pm
- Pre-meeting on Oct 6, Sunday afternoon
Nomenclature pages on the website
- See email from Mary Ann sent 18th July.
- Will still use single link under 'Nomenclature' in black banner in bottom of wormbase.org page, but add a link in widget to redirect to different link for 'other nematode'
WormBook chapter on wormbase
- to replace NAR article
- to show users what are data and the means to access these data
- gene function view, eg, gene expression, anatomy
- GBrowse
- WormMine
- Process/Topic page
Biotapestry
- canonical net works can be pre-constracted and display in Topic page
- dynamic display issue
Expression data
- data from Waterston group, 130 diagrams
- topo maps, mountain views data
Misc issues
- 'curated_by' tag is going to be retired. -D file is generated
- construct OA works well.
July 31, 2014
Agenda
- Topic 1
- Topic 2
