WBConfCall 2013.10.17-Agenda and Minutes

Agenda

WormMine WS239

• maybe JD can give an overview of the new things
• Thoughts, reactions?

WormMine WS239 is now up for testing:

Please find the new WormMine build here: http://206.108.125.174:8080/wormmine/begin.do

Data changes from WS238:

• genomic fasta, protein fasta, genes from gff3, transcripts from gff3 has been expanded to represent all species in wormbase (besides any of the "sp" species)
• the fields of data for each Ace type has been expanded. Wiki has been updated: http://wiki.wormbase.org/index.php/WormMine#Data_contained_in_WormMine
• RNAi included
• CDS locations have been temporarily omitted due to them being loaded incorrectly in the last build.

Build released to curators for testing, will be pushed to production once approved.

database URL/URIs

• where should we store these?
  • acedb + website flat file
  • website flat file only with only database name and description stored in acedb
• can there be an easier way to update the URL/URIs on the web

ABM 2014

• when?
• where?

Minutes

WormMine

• 3d build time, checkpoints used to resume
• sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11
• richer classes to query (example RNAi, etc.)
• link to JDs wiki:
• CDS locations not included in WS239

URLs / URIs

• current: flatfile in the github repository (problem: wrong formatted commits)
• future: potentially an update form/site
• proposal: remove the URLs from database (to make it clear the repository is the canonical source)

Curation Focus ideas for themed releases

ncRNAs

• we could add ncRNAs to the other non-cores from other databases (Hinxton) and look through literature (CalTech)