Difference between revisions of "WormBase-Caltech Weekly Calls"

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=== Entity markup ===
 
=== Entity markup ===
* In silico entity linking project needs link checking
+
* InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
* There is a brief summary table outlining the link URLs and predicted quality
+
* There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
* Could Cecilia check links?
+
* Could Cecilia check links?  
 
* New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
 
* New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
* Eventually markup should be job of authors during the process of writing. Need an authoring tool
+
* Eventually markup should be job of authors during the process of writing. Need an authoring tool - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not
  
 
=== Sequence features ===
 
=== Sequence features ===

Revision as of 19:35, 10 August 2017

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

January

February

March

April

May

June

July


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)


August 10, 2017

WormBase grant

  • Neuronal wiring with Scott Emmons? Maybe not for this round
  • Transcription regulatory networks? Is a priority
  • Paul will assemble existing parts and send around for review

Entity markup

  • InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
  • There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
  • Could Cecilia check links?
  • New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
  • Eventually markup should be job of authors during the process of writing. Need an authoring tool - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not

Sequence features

  • Should we have a standard human readable names for sequence features?
  • Should we consolidate several features associated with the same gene when displaying in network views?
  • Is there an automated way to give them public names?
  • Maybe name automatically, but then allow manual overwriting
  • Use gene name when experimentally demonstrated connection
  • Needs to be automated, rule-based
  • Could name based on neighboring gene(s)

Person lineage graph

  • Running off of Datomic

Docker container system

  • Potentially very useful for WB web services

Consider content for NAR paper

  • Send ideas to Raymond

Micropublications

  • Input for the WB grant?
  • Could discuss microreviews

Concise descriptions

  • Automated descriptions good for genes with little info
  • Human-written descriptions good for genes with lots of info; don't change too frequently
  • Some have suggested including protein domain info