WBConfCall 2021.04.01-Agenda and Minutes

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Help Desk

  • Karen handing over to Wen
  • As of 12:098 BST all helpdesk tickets are being dealt with or closed, except github ticket #8156
  • Erich highlighted the deprecation of the ftp protocol in some browsers as an issue.
    • Made him aware of the issue and suggested WB can't really do much about the ftp protocol security.
  • https://github.com/WormBase/website/issues/8156 - - needs a reply from textpresso group -Valerio will take care of it

Agenda and Minutes


1. IWM: what needs to be prepared?
Update: Workshop accepted, latest ask is for a more detailed schedule.
'Action: Chris and Ranjana will get back to people. '

2. Daniela brought up model changes for CENGen expression data
Paul D. will try to get it in for WS281
Paul S. Oliver Hobert anticipate Cell paper coming out in next couple months- good to have the model in for this. Will have another paper with males single-cell RNASeq.
Chris asks about XREFs between microarray experiments and pictures.
Paul D. Datomic may be able to allow query of pictures for microarray

3. Daniela: can we stick chronograms into the same bucket - as full expression data needs to be transferred to alliance, these data do not have all the required data (eg. anatomy, lifestage, and others are missing) for the Alliance model, what should we do about these data?
Wen, Paul S: chronograms (we have 2084) were from the COPUS WormSorter, we have expression clusters (98) for chronograms. Wen, suggests we keep the expression clusters but not the chronograms.
Chronograms are 1-D projection of GFP expression data over developmental time

Paul suggests
a. if people want to keep them b. ask Marc Vidal how to handle them

Chris: these are important data and we need to keep, although perhaps if there is only ~2000...
Raymond: We have only stored the image and final analysis
Paul: current single cell -3000 genes per cell, so doesn't cover everything, so...

Wen, treat as any other GFP expression pattern, image data for individual reporter. homol_homol tag
Daniela: homol_homol tag may not be needed anymore the gene name will be hardcoded, no need to put in model changes for the Alliance schema
'Action: keep chronograms, try to see if we can use top level terms for all missing model tags'

WB Paper Data to Alliance

Agreement to export data from postgres to Alliance; only dumping paper data (bibliographical info, author objects, eventually person objects, eventually flags-and-tags data that doesn't make it into acedb). We loose foreign characters in acedb, so we'll be able to keep those in postgres and pass them on to Alliance.

General Alliance and WB data discussion

Raymond: One postgres, two data streams one to acedb and a second to alliance
Juancarlos: Once everything is in place, we there can only be one.
Paul: we will be replacing postgres with Alliance eventually - only for papers, people, and laboratory
what about other curation data?
Juancarlos - curation data will continue to go to postgres. paper, person, and laboratory are easier to get into the alliance as it is not completely modeled in acedb anyway.
Paul: we can't replace the WB build with Alliance effort...yet
Kevin: part of the builg, transitive connections created (ex.promoter annotation linked back to the gene) are lightweight process, which can be uncoupled from the build, and can be implemented at the Alliance. Heavy duty stuff will be a bit more effort.


ParaSite up for renewal, discussion underway about joining the Alliance or not, open question, but leaning towards continuing with ENSEMBL.
Paul: would be good at some point to be able to add phenotype annotation to parasites
Karen: Where does worm parasite-human disease data go?
Raymond: we do not have cross-species interactions, so not really anywhere at the moment, ask Ranjana about infectious disease data.
Lincoln: NIAID look at one off project funding from different NIH institutes
Paul: be nimble.

Upcoming webinars

No more webinars.
no webinar for Todd's session, people have to right the helpdesk- todd will record a version without his image