WBConfCall 2012.05.03-Agenda and Minutes

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1. converting the Life_stage dump from names into IDs (Daniella)

Hi everyone

here at Caltech we discussed the topic of converting the Life_stage dump 
from names into IDs. We need to make sure to change it for each and every 

Could you please tell me if in your curation you use Life_stage objects?



2. including Authors in RNAi objects (Chris)

Hello everyone,

 The issue of including Authors in RNAi objects just came up here at
Caltech. Those of us who curate RNAi don't usually deal with this data as
it has been included automatically into our .ACE files by scripts. The
question came up as to whether to keep this data in RNAi objects or not.
Does anyone have a reason for keeping the "Author" tag in the RNAi class
model? It seems pretty redundant with the Paper information and I'm not
sure if it serves any particular purpose at the moment.



3. Variation and RNASeq data from non-core species (Mary Ann)

David Bird from the M. hapla genome group has asked "We also have
sequence data from VW8 and LM (2 other isolates of M. hapla), as well
as a huge amount of RNASeq data. Is there a mechanism to add this also
to WormBase?"

We don't currently have the mechanisms in place to accept this data,
but should we?

Mary Ann

4. Outstanding helpdesk items

Reported by Marjolein Wildwater (wildwaterm@gmail.com) 
03 May 12 09:37

  Dear Sir, In the previous Wormbase when you typed a gene name, you could 
immediately find all the gene information, like whether there were RNAi 
clones available which alleles were there, wheter there were GFP fusions 
and who had those, where the gene was expressed (with references). Now, with
 the new wormbase I can only find the coding sequence and some basic info. 
Is there still a possibility to find all the info that we could previously 
find on wormbase? Did I forget to switch on something? Could you help me 
out here so I can use wormbase effectively again? Or alre all those things 
no longer possible? Kind regards, Marjolein Wildwater


1. converting the Life_stage dump from names into IDs (Daniella)

  • Caltech sorted this
  • other sites?

ACTION: in a few days will send out conversion table (DR)

2. including Authors in RNAi objects (Chris)

  • Michael P responded - if we receive RNAi obj before papers published - can use evidence hash
  • ACTION: CG to Formal request PD to remove Author tag from RNAi model

3. Variation and RNASeq data from non-core species (Mary Ann)

  • how hard to handle non-core data?
    • no infrastructure for non-acedb species
    • can we convert to vcf for upload? BAM for gbrowse?
    • WB can't remap for every assembly every species (burden), unless extra resources
    • need to look at competing demands and resources over next 5 yrs
    • concentrate on priority species until pipeline solution?
    • ACTION: discuss when Todd is back - making archive sites avail (different releases)
      • like in GBrowse
      • instead of remapping for each release

4. Outstanding helpdesk items

ACTION: I will email (AC). Turn on widgets

5. Open table

CG: PCR products mapped as we go

  • way to distinguish data put it by curators vs. data calculated by mapping?
  • confusing to look at
  • turn on timestamp() for tags : curator specific view

ACTION: CG will make a ticket