Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
== September 12, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
  
=== Update on SVM pipeline ===
 
* New SVM pipeline: more analysis and more parameter tuning
 
  
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
+
== November 7, 2019 ==
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
+
 
* Have tried to create a logical definition pattern for these terms, but the vagueness of the meaning of "defective" and how it is distinct from "abnormal" has stalled the process
+
=== WS275 Citace upload ===
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
+
* Maybe Nov 22 upload to Hinxton
* Definitions include meanings or words:
+
* CIT curators upload to Spica on Tues Nov 19
** "aberrant"
+
 
** "defective"
+
=== ?Genotype class ===
** "defect"
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
** "defects"
+
* Several classes have a "Genotype" tag with text entry
** "deficiency"
+
** Strain
** "disrupted"
+
** 2_point_data
** "ineffective"
+
** Pos_neg_data
** "perturbation that disrupts"
+
** Multi_pt_data
** "variations in the ability"
+
** RNAi
** failure to execute the characteristic response = abnormal?
+
** Phenotype_info
** abnormal
+
** Mass_spec_experiment (no data as of WS273)
** abnormality leading to specific outcomes
+
** Condition
** fail to exhibit the same taxis behavior = abnormal?
+
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
** failure
+
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
** failure OR delayed
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** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
** failure/abnormal
+
** 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