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 ===
+
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
* 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 ===
 
* 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 ===
+
== December 5, 2019 ==
** Tuesday, Sep 24th
 
  
=== Strain to ID mapping ===
+
=== New interaction Venn diagram tool ===
* Waiting on Hinxton to send strain ID mapping file?
+
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
* Hopefully we can all get that well before the upload deadline
+
* 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

Latest revision as of 21:08, 5 December 2019

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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