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]]
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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
  
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= 2018 Meetings =
+
= 2019 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
[[WormBase-Caltech_Weekly_Calls_October_2018|October]]
 
  
 +
== September 12, 2019 ==
  
== November 1, 2018 ==
+
=== 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
  
=== Community phenotype requests ===
+
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
* Sent out 1,000 request emails for community submissions of phenotypes on October 18 and October 20
+
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
* As before, request focuses on a single paper, but we've now added extra papers at bottom of email message
+
* 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
* We've also added a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes
+
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
* 21 emails bounced
+
* Definitions include meanings or words:
* 56 papers received annotations, 44 from direct requests, 12 not directly requested
+
** "Variations in the ability"
* 9 of 12 not directly requested were appended requests to email message
+
** "aberrant"
* 277 annotations submitted (raw) via the form (some more submitted as Excel spreadsheets)
+
** "defect"
** 247 allele/transgene phenotype annotations
+
** "defective"
** 30 RNAi phenotype annotations
+
** "defects"
* 48 distinct community curators
+
** "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
  
=== SPELL ===
+
=== Citace upload ===
* Todd working on a spell.wormbase.org site for doing worm SPELL analyses
+
** Tuesday, Sep 24th
* Should be faster, more stable
 
  
=== Predicted protein-protein interactions ===
+
=== Strain to ID mapping ===
* Jae has requested data set
+
* Waiting on Hinxton to send strain ID mapping file?
* Total data set 20GB (how much is C. elegans?)
+
* Hopefully we can all get that well before the upload deadline
* Haven't heard back from author recently
+
* Will do global replacement at time of citace upload (at least for now)
* How much do we want this data? Should reach out a couple more times (once every ~two weeks)
 
  
 +
=== New name server ===
 +
* When will this officially go live?
 +
* Will we now be able to request strain IDs through the server? Yes
  
== November 8, 2018 ==
+
=== 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
  
=== Author First Pass ===
 
* Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
 
** Raymond, Ranjana, Gary, Jae and Karen ok to have a monthly digest. Chris, Wen no email
 
** Will check in with Gary W and see if he wants to be notified for RNAseq data flagging
 
** Should ask April what she wants to do
 
* Shall we add  in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
 
** Yes, Add site and time of action
 
* How would we like to handle Methods papers?  These may have reagents and some bona fide experimental results, but are not our 'typical' experimental papers.  Possibly add a new 'methods' flag?
 
** Worth flagging methods papers. Will send methods papers to authors for 6 months and then evaluate how useful it is
 
* Do we need to still maintain the cfp form?  If we can keep the data tables and still see the flags in the curation status form, do we need the cfp form? http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi
 
** The CFP form can be retired
 
* Add back in the AFP from ‘this is a review paper, I am not flagging this’
 
  
=== Expression Pattern Model ===
+
== September 19, 2019 ==
  
* there would be value in having a separate ?Expr_annotation class, like we did for ?GO_annotation. It might look something like this (details not completely thought through):
+
=== Strains ===
     
+
* Need to wait for new strain IDs from Hinxton before running dumping scripts
<pre>     
+
* Don't edit multi-ontology strain fields in OA for now!
Class ?Expr_annotation
+
* Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
  Life_stage ?Life_stage XREF Expr_pattern #Qualifier
+
* "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
  Not_in_Life_stage ?Life_stage #Qualifier
 
  Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
 
  Not_in_Anatomy_term ?Anatomy_term #Qualifier
 
  GO_CC ?GO_term XREF Expr_pattern
 
  GO_BP ?GO_term XREF Expr_pattern
 
  Cell ?Cell
 
  Cell_group ?Cell_group
 
  
#Qualifer Certain
+
=== Alliance literature curation ===
          Partial
+
* Working group will be formed soon
          Uncertain
+
* Will work out general common pipelines for literature curation
</pre>
 
An Expr_pattern can then have a list of ?Expr_annotations, each grouping together all properties of a single observation.
 
  
Daniela will work on a model for an ?Expression_annotation class.
+
=== SObA Graph relations ===
The change can be gradual. We can Add the ?Expression_annotation class and still dump anatomy, life stage and GO in the old tags. Down the line those tags will be deprecated and fully replaced by the ?Expression_annotation tags
+
* 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"
  
?Cell and ?Cell group could go away
+
=== Author First Pass ===
 
+
* Putting together paper for AFP
 
+
* Reviewing all user input for paper
== November 15, 2018 ==
+
* Asking individual curators to check input
 
 
=== SPELL ===
 
* New WormBase release linked to the new SPELL website (https://spell.wormbase.org)
 
* Will watch for a few days
 
* Maybe should make an announcement for our users (for those that have it bookmarked)
 
 
 
=== Broken Disease links ===
 
* On WB Disease page, disease term links are broken
 
* Caltech (Raymond & Juancarlos) will fix
 
* https://github.com/WormBase/website/issues/6734
 
 
 
=== WOBr disease data ===
 
* WOBr currently looking at stale disease data; needs to be updated
 
* We also want to accommodate strain disease models; will take some work to get it into WOBr
 
* Ranjana will work with Raymond
 
 
 
=== RNAi targeting of non-coding genes ===
 
* WBPaper00053279 has example of RNAi knockdown of let-7 miRNA
 
* Authors report using 99bp dsRNA targeting the pri-miRNA
 
* Maybe survey RNAi labs to see if this is likely real, makes sense?
 
* If it's real, we need to update RNAi mapping pipeline to include non-coding gene targets
 
 
 
=== OBO to OWL transitions ===
 
* New GitHub repository for phenotype ontology
 
* OBO format becoming defunct; OBO Edit not being maintained
 
* We likely need to move from OBO to OWL
 
* Now we have .owl and .obo files (obo generated from owl)
 
* Can we (do we need to) update Postgres and query tools to use OWL files instead of OBO?
 
* We can try a pilot on phenotype OWL file to see how much effort would be required for transition
 
 
 
=== Protege tutorial ===
 
* Chris went to Stanford Protege tutorial
 
* Chris can give local WB tutorial on Protege, maybe in January
 
* Chris will send around documentation and tutorial docs
 
 
 
=== Updating phenotype ontology links ===
 
* The original Worm Phenotype Ontology paper points to this URL: http://caltech.wormbase.org/cvsweb/PhenOnt/
 
* That gets sent to Tazendra: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi
 
* Need to update where the PURL is retrieving the ontology from (will do with Nico in next week or two)
 
* May want to try to check logs for who is accessing the older file so that we can notify relevant parties of the change
 
* Once that is settled, we may want to have the Caltech URL redirect to the GitHub repository:
 
** https://github.com/obophenotype/c-elegans-phenotype-ontology
 
* Will break scripts if people are programmatically accessing the Caltech or Tazendra URLs
 

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