Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(435 intermediate revisions by 9 users not shown)
Line 16: Line 16:
  
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
  
Line 21: Line 23:
  
  
= 2018 Meetings =
+
= 2019 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
[[WormBase-Caltech_Weekly_Calls_October_2018|October]]
+
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
  
 +
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
  
== November 1, 2018 ==
 
  
=== Community phenotype requests ===
+
== December 5, 2019 ==
* Sent out 1,000 request emails for community submissions of phenotypes on October 18 and October 20
 
* As before, request focuses on a single paper, but we've now added extra papers at bottom of email message
 
* We've also added a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes
 
* 21 emails bounced
 
* 56 papers received annotations, 44 from direct requests, 12 not directly requested
 
* 9 of 12 not directly requested were appended requests to email message
 
* 277 annotations submitted (raw) via the form (some more submitted as Excel spreadsheets)
 
** 247 allele/transgene phenotype annotations
 
** 30 RNAi phenotype annotations
 
* 48 distinct community curators
 
  
=== SPELL ===
+
=== New interaction Venn diagram tool ===
* Todd working on a spell.wormbase.org site for doing worm SPELL analyses
+
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
* Should be faster, more stable
+
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
 +
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
 +
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 +
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 +
* Request: could there be a toggle to include/exclude high-throughput interactions?
 +
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 +
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 +
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
  
=== Predicted protein-protein interactions ===
+
=== New round of phenotype requests ===
* Jae has requested data set
+
* GMail really throttling email sending
* Total data set 20GB (how much is C. elegans?)
+
* Chris will reach out to Google/GMail to see if we can:
* Haven't heard back from author recently
+
** A) get a clear explanation about what their restrictions are and how they work and
* How much do we want this data? Should reach out a couple more times (once every ~two weeks)
+
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
  
== November 1, 2018 ==
+
=== Aligning interaction data with GO and GO-CAM ===
 +
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
 +
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
 +
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 +
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 +
* Chris and Kimberly will meet to discuss further
  
=== Author First Pass ===
+
=== Short SObA talk at Alliance meeting ===
* Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
+
* Raymond prepared to give short talk on SObA to the Alliance group
* Shall we add  in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
 
  
=== Expression Pattern Model ===
+
=== Single cell data visualization tool ===
 +
* Eduardo will present to Paul's lab meeting tomorrow
 +
* Will discuss at Alliance expression working group pre-meeting

Latest revision as of 21:08, 5 December 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2019 Meetings

January

February

March

April

May

June

July

August

September

October

November


December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting