Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
== April 4, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
=== Paul's Biocuration Keynote ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
 
* Can someone send Paul the latest AFP form location and documentation
 
* Will also discuss the future of micropublications
 
  
=== IWM Swag ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Stickers vs. screen cloths
 
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
 
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
 
** As for design would be nice to have new design
 
** Gary had made cartoon for community curation (proposal might be offensive to some)
 
* Include water bottles for special contributors? In addition to shot glasses?
 
* Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
 
* Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
 
** We can ask Jessie if she can draw up a couple quick sketch ideas
 
  
=== Collaborators tool ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Juancarlos worked on a tool to extract WBPerson collaborators
 
* WB staff generally had ~100 collaborators, Paul S has 670
 
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
 
* Make modification to ACEDB model?
 
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
== April 11, 2019 ==
 
  
=== Canadian C. elegans meeting ===
+
== September 12, 2019 ==
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
 
* Karen may be able to go; she will contact Kimberly for any pertinent information
 
  
=== Feedback from small RNA meeting April 3-5, 2019 ===
+
=== Update on SVM pipeline ===
* Future meeting invitations and summer workshop?
+
* New SVM pipeline: more analysis and more parameter tuning
* Dustin Updike - in Maine - interested in running a summer workshop for students
+
* avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
** Maybe one or two week-long (5-10 days); unconfirmed
+
* For example shown, "dumb" machine starts out with precision above 0.6
** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
+
* G-value (Michael's invention); does not depend on distribution of sets
** Hopefully they can cover travel costs of WB curators
+
* Applied to various data types
** Dustin will get back to us about details as they emerge
+
* Analysis: 10-fold cross validation
* Julie Claycomb interested in having WB curator at Toronto's worm meeting
+
** 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
  
=== New SVM approach ===
+
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
* Michael will send around paper list with new and old results in the same file
+
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
* Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
+
* 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
* Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
+
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
* Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
+
* 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 workshop ===
+
=== Citace upload ===
* On Saturday of meeting
+
** Tuesday, Sep 24th
  
=== NIH workshop on Trustworthiness ===
+
=== Strain to ID mapping ===
* Chris attended on Monday and Tuesday
+
* Waiting on Hinxton to send strain ID mapping file?
* Not quite clear that there is or will be any mandate from funders; just encouragement
+
* Hopefully we can all get that well before the upload deadline
* FAIR data and TRUST-worthy repositories
+
* Will do global replacement at time of citace upload (at least for now)
** FAIR = Findable, Accessible, Interoperable, Reusable
 
** TRUST = Transparency, Responsibility, User community, Sustainability, Technology
 
* Chris will review briefly at next site-wide call
 
* Karen: This is something the data commons really wants
 
** Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
 
  
 +
=== New name server ===
 +
* When will this officially go live?
 +
* Will we now be able to request strain IDs through the server? Yes
  
== April 18, 2019 ==
+
=== 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
  
=== IWM swag ===
 
* Stickers, screen cloths?
 
* Jessie's design(s)?
 
  
=== Life stage and anatomy ontologies ===
+
== September 19, 2019 ==
* Each ontology now has an ODK GitHub repository (thanks Nico!):
+
 
** Anatomy ontology: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
+
=== Strains ===
** Life stage ontology: https://github.com/obophenotype/c-elegans-development-ontology
+
* Need to wait for new strain IDs from Hinxton before running dumping scripts
* We will perform a round of comparisons between the original OBO files and the ODK-generated OBO files
+
* Don't edit multi-ontology strain fields in OA for now!
* Will follow up with quality control fixes (e.g. duplicate or missing definitions)
+
* 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