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
 
* avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
 
* "dumb" machine starts out with precision above 0.6
 
* G-value (Michael's invention); does not depend on distribution of sets
 
* Applied to various data types
 
* Analysis: 10-fold cross validation
 
** Randomly select 10% pos and neg (without replacement) and repeat until all papers sampled
 
* F-value changes over different p/n values; G-value does not (essentially flat)
 
* Area Under the Curve (AUC): probability that a random positive scores higher than random negative
 
* AUC values for many WB data types upper 80%'s into 90%'s
 
* Ranjana: How many papers for a good training set? Michael: we don't know yet
 
* Can't reproduce old training sets (for old SVM); provide Michael better training sets if you want improved SVM
 
* If SVM still not good enough, Michael will work on deep neural networks (Tensor Flow)
 
* Michael can provide training sets he has used recently
 
  
=== 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
 
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
 
* Definitions include meanings or words:
 
** "Variations in the ability"
 
** "aberrant"
 
** "defect"
 
** "defective"
 
** "defects"
 
** "deficiency"
 
** "deficient"
 
** "disrupted"
 
** "impaired"
 
** "incompetent"
 
** "ineffective"
 
** "perturbation that disrupts"
 
** Failure to execute the characteristic response = abnormal?
 
** abnormal
 
** abnormality leading to specific outcomes
 
** fail to exhibit the same taxis behavior = abnormal?
 
** failure
 
** failure OR delayed
 
** failure, slower OR late
 
** failure/abnormal
 
** reduced
 
** slower
 
  
=== Citace upload ===
+
=== WS275 Citace upload ===
** Tuesday, Sep 24th
+
* Maybe Nov 22 upload to Hinxton
 +
* CIT curators upload to Spica on Tues Nov 19
  
=== Strain to ID mapping ===
+
=== ?Genotype class ===
* Waiting on Hinxton to send strain ID mapping file?
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
* Hopefully we can all get that well before the upload deadline
+
* 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 ===
 +
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 +
 
 +
 
 +
== November 14, 2019 ==
 +
 
 +
=== TAGC meeting ===
 +
* 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 ===
 +
* Lightning talk topics?
 +
** Single cell RNA Seq (Eduardo)
 +
** SimpleMine? (Wen)
 +
** SObA? (Raymond); still working on multi-species SObA
 +
** Phenotype community curation?
 +
** Micropublications?
 +
** AFP?
 +
 
 +
=== Alliance general ===
 +
* Alliance needs a curation database
 +
** A curation working group was proposed
 +
** 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
 +
** First priority is to focus on automatically recognizable entities/features from papers

Latest revision as of 19:58, 14 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


November 14, 2019

TAGC meeting

  • 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

  • Lightning talk topics?
    • Single cell RNA Seq (Eduardo)
    • SimpleMine? (Wen)
    • SObA? (Raymond); still working on multi-species SObA
    • Phenotype community curation?
    • Micropublications?
    • AFP?

Alliance general

  • Alliance needs a curation database
    • A curation working group was proposed
    • 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
    • First priority is to focus on automatically recognizable entities/features from papers