Difference between revisions of "WormBase-Caltech Weekly Calls"

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== July 6, 2017 ==
=== Noctua ===
* Use for all literature curation in future?
* We would need to see how it could be used for all data types
* We would also want a full-time developer working on Noctua; maybe bring Juancarlos into the project
=== SPELL ===
* SPELL related data - how to deal with?
** Data: recalculated, mapping, results dependent on SPELL
** Analysis (clustering tool): clunky, freezes w/limited resources
* Wen will work with Juancarlos to generate a SimpleMine-like tool for downloading data sets
* Wen has to remove log files to make space on machine
* ~360 data sets
* Current virtual machine has 10G memory; is becoming limiting
* SPELL has lots of dependencies; difficult to account for them all when building SPELL
* Would be good if we could setup a new (larger) virtual machine to run SPELL; how much time/resources do we want to spend on it?
=== Micropublications ===
* Poster at Zebrafish meeting pointing to micropublications
* Microarray micropublications? Unpublished results
* Can make links to GEO submissions
* Daniela and Karen can draw up a mock publication to look at as a template
=== Community Curation ===
* Considering sending requests to only one person, first author when have info
* This should allow for more emails to be sent out per week, and more submissions, even if we maintain the 16% response rate
* Chris will work with Juancarlos once he's back from vacation
* What's next data type? Interactions? Site of action? Anatomy?
* What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed
* Can send requests to lab heads to fill in phenotype info for alleles from their lab
=== Linking ===
* Will human genes link to AGR human gene pages? Gene Cards? HGNC?
== July 13, 2017 ==
=== Allele attribute assignment ===
* Some attributes of alleles are currently only assigned in the context of a phenotype annotation
* Many times these attributes are reported independently of a phenotype experiment
* It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation
* As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this:
Null  ?Phenotype_experiment
* This would allow us to always point to a ?Phenotype_experiment object as a container of evidence, but if we don't always have a ?Phenotype_experiment object to point to then maybe a better approach is just to reference the paper like this:
Null  ?Paper
* This would require a separate curation pipeline from phenotype to capture these attributes; will discuss more with Mary Ann when she's back from vacation
* We discussed and came up with a couple of potential solutions:
* First:
Variation_effect  Null  ?Text  #Evidence
* Second:
Variation_effect  Null  ?Paper  #Evidence
* The first solution allows to put in a free text remark, potentially referencing a phenotype or some detail, with the #Evidence hash allowing reference to a paper or a person_evidence
* The second solution requires reference to a ?Paper object, which would require a reworking of all person evidence/personal communication to become ?Paper objects, with an #Evidence hash to capture remarks
=== Phenotype form submission requests ===
* Originally we sent email requests independently of Author First Pass pipeline emails
* Now a link to phenotype form is being included in Author First Pass emails, and we're putting a hold on all new email requests to corresponding author for one month
* I (Chris) am considering returning to original approach of sending requests independently of AFP (and focusing on first authors), to see if we can get response rate up at all
=== New WormBase Caltech server ===
* We're getting a new server, to consolidate different computers and their services
* Let Raymond know if you have an idea for another (extra) use of the server
* Will likely re-use altair.caltech.edu
* 96 GB memory, ~6 TB hard drive
=== SPELL ===
* SPELL could go on new server
* Moved from current virtual machine to KVM
* Could expand memory and CPU
== July 20, 2017 ==
=== Variation effect assignment ===
* We had discussed last week having either of two models in the ?Variation class
* First:
?Variation  Variation_effect  Null  ?Text  #Evidence
* Second:
?Variation  Variation_effect  Null  ?Paper  #Evidence
* The first option can keep things as they are and can allow a remark in the ?Text entry, with paper or person evidence coming from the #Evidence hash
* The second option likely requires that we consider person evidence/communication as ?Paper objects
* Many entries in the Phenotype OA coming from Jonathan Hodgkin are from the C. elegans I and II books
** Would be good to create ?Paper objects for C. elegans I and II and reference them accordingly
*** Already exist:
**** C. elegans II WBPaper00004071
**** C. elegans I  WBPaper00004052
* Probably best to go with
?Variation  Variation_effect  Null  ?Text  #Evidence
* Going forward we can encourage people to micropublish if they want to submit personal communication
=== Blog posts for WormMine ===
* Not quite ready; Chris will contact Ranjana about it when ready
=== WormMine templates ===
* Todd had encouraged development of template queries
* Older templates are still difficult to access and edit, but new queries going forward are OK
=== New Server ===
* New WormBase server (@ Catlech) is online
* Let Raymond know if anyone has uses for the server
* Anything that needs to be running 24-7 (e.g. services) can be considered
=== Supplement for AGR ===
* Proposing tuning up of orthology calls
* Paul S. wants to get Gene Orienteer back up, and have RNASeq analysis pipeline
* Pull in WormNet data (predicted interactions)
== July 27, 2017 ==
=== AGR GO Slim ===
*Discussion of new AGR GO slim and representation of C. elegans genes
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
*Key to graphs
**Red = AGR slim
**Orange = C. elegans orphans
**Multi-colors = Other organism orphans, as well

Revision as of 14:23, 10 August 2017

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August 3, 2017

WB grant

  • Progress (maintenance stuff) can be written as of last grant cycle
  • Current projects and report the steady state

CRISPR alleles

  • Some authors not reporting CRISPR alleles with standard nomenclature
  • Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
  • Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
    • RNAi mapping pipeline not setup to handle this
    • Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
    • Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene

Ontology Browser

  • Has been less stable lately; Raymond has needed to restart machine
  • Being served from Dell server (in Braun building)