Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
== May 2, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
=== SObA for all ontologies ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
* SObA graph search for all ontologies
 
* Juancarlos and Raymond looking for feedback; let them know
 
* Would be good to make it clear to users what the edges/arrows mean; what relations are included for inference? Can we include blurb in the legend?
 
** Raymond: thinking of putting blurb on a separate documentation page
 
* Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted so we'd need to look at Tazendra logs to see who (and how many people) are using the tool (cannot rule out bots etc.)
 
  
=== IWM swag - screen cloth ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Need to finalize design
 
* Put Dick & Jane cartoon in one corner, tools in another corner, WB logo, Alliance logo
 
* Daniel can take care of ordering and printing, but needs someone to choose the design
 
  
=== Phenotype ontology patternization ===
 
* Chris working on patternizing phenotype terms to standardize logical definitions for classes of terms
 
* This is part of the ongoing effort to align phenotype ontologies across the organisms
 
* Paul S: It's important for community submitted phenotypes (and the use of the form) to make sure the ontology makes sense and is readily browsable
 
* Does "dumpy" mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community?
 
* Does someone annotate to Egl or vulvaless?
 
* How do we help community curators decide the correct term?
 
* Could we develop a smart annotation aid/tool/helper? Use images, examples, etc.
 
  
 +
== September 12, 2019 ==
  
== May 9, 2019 ==
+
=== Update on SVM pipeline ===
=== SObA for all ontologies ===
+
* New SVM pipeline: more analysis and more parameter tuning
* Revised version http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
+
* avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
* Changed legend labelling, added linkouts
+
* For example shown, "dumb" machine starts out with precision above 0.6
* To implement on Gene pages. One vs. Five widgets?
+
* G-value (Michael's invention); does not depend on distribution of sets
* Would be good to provide documentation on what the inferences mean; can we provide an indication of what relations a particular SObA edge could be comprised of?
+
* Applied to various data types
* Let's release to the website, but gather feedback from (naive) users to see what documentation we needv
+
* 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
 +
 
 +
 
 +
== September 19, 2019 ==
 +
 
 +
=== Strains ===
 +
* Need to wait for new strain IDs from Hinxton before running dumping scripts
 +
* Don't edit multi-ontology strain fields in OA for now!
 +
* Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
 +
* "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
 +
 
 +
=== Alliance literature curation ===
 +
* Working group will be formed soon
 +
* Will work out general common pipelines for literature curation
 +
 
 +
=== SObA Graph relations ===
 +
* Currently only integrating over "is a", "part of" and "regulates"
 +
* Maybe we could provide users an option to specify which relations to include, or maybe just exclude "regulates"
 +
 
 +
=== Author First Pass ===
 +
* Putting together paper for AFP
 +
* Reviewing all user input for paper
 +
* Asking individual curators to check input

Revision as of 16:39, 19 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


September 19, 2019

Strains

  • Need to wait for new strain IDs from Hinxton before running dumping scripts
  • Don't edit multi-ontology strain fields in OA for now!
  • Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
  • "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now

Alliance literature curation

  • Working group will be formed soon
  • Will work out general common pipelines for literature curation

SObA Graph relations

  • Currently only integrating over "is a", "part of" and "regulates"
  • Maybe we could provide users an option to specify which relations to include, or maybe just exclude "regulates"

Author First Pass

  • Putting together paper for AFP
  • Reviewing all user input for paper
  • Asking individual curators to check input