Difference between revisions of "WBConfCall 2013.10.17-Agenda and Minutes"
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Jump to navigationJump to search| Line 21: | Line 21: | ||
= Minutes = | = Minutes = | ||
== WormMine == | == WormMine == | ||
| − | * | + | * 5.3 days build time, checkpoints used to resume |
| + | ** | ||
* sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11 | * sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11 | ||
* richer classes to query (example RNAi, etc.) | * richer classes to query (example RNAi, etc.) | ||
* link to JDs wiki: | * link to JDs wiki: | ||
* CDS locations not included in WS239 | * CDS locations not included in WS239 | ||
| + | |||
| + | JD's announcement email: | ||
| + | |||
| + | 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. | ||
== URLs / URIs == | == URLs / URIs == | ||
Revision as of 16:29, 17 October 2013
Contents
Agenda
WormMine WS239
- maybe JD can give an overview of the new things
- Thoughts, reactions?
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?
Release Themes
- protein folding / pathways WS241
- ncRNA / specific ncRNAs (lincRNA/snoRNAs) WS242
Minutes
WormMine
- 5.3 days 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
JD's announcement email:
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.
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)
- proposal: remove the URL_constructor from model
ABM
- early next year
- Hinxton
Nameserver
- JSON dumper too slow
- delay between GeneAce <=> NameDB synch
- make sure that NameDB <=> GeneAce is synched weekly
- proposal: do a nightly JSON dump
- proposal: put the database on the cloud
InterMine
- call for letter of support for their new funding cycle
Themed Curation
- collaborate to curate the protein folding pathways for WS241
- potentially comparative analysis across species
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)
