Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
  
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= 2018 Meetings =
+
= 2019 Meetings =
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 +
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
== September 12, 2019 ==
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
=== Citace upload ===
 +
** Tuesday, Sep 24th
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
=== 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)
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
=== New name server ===
 +
* When will this officially go live?
 +
* Will we now be able to request strain IDs through the server? Yes
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
 
  
 +
== September 19, 2019 ==
  
== September 6, 2018 ==
+
=== 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
  
=== Genotype class ===
+
=== Alliance literature curation ===
* Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
+
* Working group will be formed soon
**  https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
+
* Will work out general common pipelines for literature curation
* Would be good for people to look at so we can discuss next time
 
* Would also be good to have Kevin H take a look and provide feedback
 
  
=== Citace Upload ===
+
=== SObA Graph relations ===
* Send citace files to Wen by Sept 18, 10am Pacific
+
* 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"
  
=== Automated gene descriptions ===
+
=== Author First Pass ===
* Group making improvements
+
* Putting together paper for AFP
* Added disease, protein domains
+
* Reviewing all user input for paper
** When direct experimental evidence for disease relevance, will say "gene has been used to study"
+
* Asking individual curators to check input
* When minimal data (information-poor genes), we can refer to human ortholog and data stored for that human gene in Alliance
 
* Continue to receive feedback from users; include enrichment information, etc.
 
* Now have good trimming algorithms to retain important info without flooding a description with too many granular terms
 
* Will not store automated descriptions in Postgres
 
* Wen will modify SimpleMine scripts to accommodate change
 
* Would be good to write a paper on automated concise descriptions
 
* Came up at GO meeting/hackathon: Translating GO-CAM models into concise descriptions?
 
** Should be doable; just need to develop code when we're ready to do that
 

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