Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
== March 7, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
=== IWM workshop ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* Still haven't heard back from organizers yet
 
  
=== IWM swag ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Think of ideas for the meeting
 
  
=== Upload ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Local upload to Spica is Tuesday, March 12th, 10am Pacific
 
  
=== Trustworthy data repositories workshop ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Chris will go to NIH, April 8 and 9
 
* To discuss trustworthiness standards for data repositories
 
  
  
==March 21, 2019==
+
== September 12, 2019 ==
  
===IWM 2019 workshop===
+
=== Update on SVM pipeline ===
Topic/Speaker
+
* New SVM pipeline: more analysis and more parameter tuning
*Start with gene page, that's when you have a single gene --Kimberly
+
* avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
*Then go on to data mining, for multiple genes--SimpleMine, WormMine, Parasite BioMart etc  --Wen and Chris
+
* For example shown, "dumb" machine starts out with precision above 0.6
*Then you can also visualize data with these tools-WoBR, SoBA, etc
+
* G-value (Michael's invention); does not depend on distribution of sets
*If you are interested in other species, find cross-species data at the Alliance --Ranjana
+
* Applied to various data types
*Help us curate your data!  End with community curation-New Author First pass form, community curation forms--Daniela
+
* 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
  
I think we have a good flow here, can keep thinking about this.  Ranjana will shorten abstract and submit final list first week of April.
+
=== 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 2019 swag ideas===
+
=== Citace upload ===
*WormBase sticker
+
** Tuesday, Sep 24th
**Micropub folks have done stickers, in Paul's office, take a look
 
**Daniela will look into this, pricing and time
 
*Gary's ideas:
 
**Screen cleaning cloths with community curation theme on them, he will send around the picture
 
**Water bottles for the top community curators
 
**Fidget spinners, with the WB picture in the middle
 
**Gary will talk to Daniel to see if he can help with finding sellers/prices
 
  
We could do them all , a mixture, depending on the budget, need to ask Paul S. what the budget is for IWM swag
+
=== 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
  
==March 28, 2019==
 
  
===Textpresso Central vs Old Textpresso site===
+
== September 19, 2019 ==
*A search for "SimpleMine" got 1 paper in TPC, 5 papers in the old site.
 
*A search for "alg-5" in TPC got 6 hits but the first two were redundant. The result missed pmid29927939 that was found by the old site.
 
*A search for allele "ev673" in TPC returns no results, but expected paper (PMID:24004945 / WBPaper00044133) returned in old site.
 
  
=== Protein-protein interactions up-to-date ===
+
=== Strains ===
* We should post an announcement to the community
+
* Need to wait for new strain IDs from Hinxton before running dumping scripts
* Could ask for feedback if any authors are aware of anything missing
+
* 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
  
=== Micropublication tutorials ===
+
=== Alliance literature curation ===
* Can Wen mention (at small RNA meeting) that micropub representatives can do site visits to discuss micropubs?
+
* 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