Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
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= 2021 Meetings =
  
= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
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== September 2, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
 +
Needed for
 +
*AFP community curation
 +
*microPublication author tracking for all species
 +
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
 +
Problems:
 +
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
 +
*need to do this outside of Alliance
  
== November 7, 2019 ==
+
Action
 +
*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
=== WS275 Citace upload ===
+
Will do
* Maybe Nov 22 upload to Hinxton
+
*create biolink model based on current WB postgres/Caltech model
* CIT curators upload to Spica on Tues Nov 19
+
*Adam will add tables when we have them
  
=== ?Genotype class ===
+
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
 
* Several classes have a "Genotype" tag with text entry
 
** Strain
 
** 2_point_data
 
** Pos_neg_data
 
** Multi_pt_data
 
** RNAi
 
** Phenotype_info
 
** Mass_spec_experiment (no data as of WS273)
 
** Condition
 
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
** Reference to parent strain, like "Parent strain is AG359"
 
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
 
  
=== Gene comparison SObA ===
+
== September 16, 2021 ==
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
  
 +
1. CeNGEN enriched genes per cell type data targeted for WS283.
  
== November 14, 2019 ==
+
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
  
=== TAGC meeting ===
+
== September 23, 2021 ==
* The Allied Genetics Conference next April (2020) in/near Washington DC
 
* Abstract deadline is Dec 5th
 
* Alliance has a shared booth (3 adjacent booths)
 
* Micropublications will have a booth (Karen and Daniela will attend)
 
* Focus will be on highlighting the Alliance
 
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
 
  
=== Alliance all hands meeting ===
+
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
* Lightning talk topics?
+
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
** Single cell RNA Seq (Eduardo)
+
* Update the WB page on citing WormBase
** SimpleMine? (Wen)
 
** SObA? (Raymond); still working on multi-species SObA
 
** Phenotype community curation?
 
** Micropublications?
 
** AFP?
 
  
=== Alliance general ===
+
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
* Alliance needs a curation database
+
 
** A curation working group was proposed
+
3. Server room in Braun power down for no apparent reason. Reset.
** What needs to happen to get this going?
 
** Would include text mining tools/resources
 
** Would be good to have something like the curation status form
 
** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
 
** Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type
 
* Micropubs pushing data submission forms; might as well house them within the Alliance
 
* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
 
** Maybe MOD curators can manage configuration files to indicate what is relevant for their species
 

Latest revision as of 18:17, 23 September 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.