Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* May be best to leave the format as is
 
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
  
== June 13, 2019 ==
+
== November 7, 2019 ==
  
=== IWM ===
+
=== WS275 Citace upload ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* Maybe Nov 22 upload to Hinxton
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* CIT curators upload to Spica on Tues Nov 19
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
 
* Workshop
+
=== ?Genotype class ===
** Presenters: it may be best to present as use cases rather than a research project
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
** Chris will cover SimpleMine for Wen
+
* Several classes have a "Genotype" tag with text entry
** Chris: won't do live demo; only screenshots, maybe some video
+
** Strain
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
+
** 2_point_data
* Paul's talk
+
** Pos_neg_data
** Cover Alliance
+
** Multi_pt_data
** New features?
+
** RNAi
*** SObA (for new data)
+
** Phenotype_info
*** Complete for protein-protein interactions
+
** Mass_spec_experiment (no data as of WS273)
*** RNASeq tools
+
** Condition
** Phenotype community curation
+
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
** Author First Pass
+
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
** Micropublication
+
** 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 ===
 +
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph

Latest revision as of 17:58, 7 November 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 7, 2019

WS275 Citace upload

  • Maybe Nov 22 upload to Hinxton
  • CIT curators upload to Spica on Tues Nov 19

?Genotype class

  • 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