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 ===
 
* 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 ===
+
== September 12, 2019 ==
* 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
 
  
 +
=== 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)
 +
* For example shown, "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
  
== June 13, 2019 ==
+
=== 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
  
=== IWM ===
+
=== Citace upload ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
** Tuesday, Sep 24th
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
 
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
=== Strain to ID mapping ===
* Workshop
+
* Waiting on Hinxton to send strain ID mapping file?
** Presenters: it may be best to present as use cases rather than a research project
+
* Hopefully we can all get that well before the upload deadline
** Chris will cover SimpleMine for Wen
+
* Will do global replacement at time of citace upload (at least for now)
** Chris: won't do live demo; only screenshots, maybe some video
+
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
+
=== New name server ===
* Paul's talk
+
* When will this officially go live?
** Cover Alliance
+
* Will we now be able to request strain IDs through the server? Yes
** New features?
+
 
*** SObA (for new data)
+
=== SObA Graphs ===
*** Complete for protein-protein interactions
+
* New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
*** RNASeq tools
+
* A lot of whitespace padding above and below graph; maybe trim? trimming vertically would ultimately limit the view pane when user wants to zoom in, so we should leave as is for now
** Phenotype community curation
+
* Diff tool: Raymond and Juancarlos created a prototype diff tool (for comparing two genes, for example)
** Author First Pass
+
** Paul: compared two genes that should be very similar, but there are a lot of differences; may reflect annotation coverage rather than biology
** Micropublication
 

Latest revision as of 21:07, 12 September 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 12, 2019

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)
  • For example shown, "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

    • Tuesday, Sep 24th

Strain to ID mapping

  • Waiting on Hinxton to send strain ID mapping file?
  • Hopefully we can all get that well before the upload deadline
  • Will do global replacement at time of citace upload (at least for now)

New name server

  • When will this officially go live?
  • Will we now be able to request strain IDs through the server? Yes

SObA Graphs

  • New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
  • A lot of whitespace padding above and below graph; maybe trim? trimming vertically would ultimately limit the view pane when user wants to zoom in, so we should leave as is for now
  • Diff tool: Raymond and Juancarlos created a prototype diff tool (for comparing two genes, for example)
    • Paul: compared two genes that should be very similar, but there are a lot of differences; may reflect annotation coverage rather than biology