Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
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[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
[[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]]
 +
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[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== February 7, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
=== Automation of curation ===
 
* For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into data types
 
* MGI and WB curate by datatype, so may have an easier time
 
* All MODS still need paper triage
 
  
=== IWM workshop ===
+
== September 12, 2019 ==
* Ranjana replied to Julie about a consolidated WormBase workshop; hasn't heard back
 
  
=== Site-specific outreach ===
+
=== Update on SVM pipeline ===
* Wen has been invited to small RNA meeting in Mexico in April; may go if they offer to pay (waiting to hear back)
+
* 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
  
=== SObA ===
+
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
* Raymond and Juancarlos have worked out a way to display top-slicing of the ontology (trimming to higher level nodes)
+
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
* Needs a bit more clean up; will send around a URL when ready
+
* 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
  
== February 21, 2019 ==
+
=== 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)
  
=== SObA ===
+
=== New name server ===
 +
* When will this officially go live?
 +
* Will we now be able to request strain IDs through the server? Yes
  
* SObA GO graph, with top slicing function. You can try it here <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi> by entering the name of your favorite gene.
+
=== 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
  
* specific genes, from simple to complex
 
let-4 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-4%20(Caenorhabditis%20elegans,%20WB:WBGene00002282,%20-,%20C44H4.2,%20sym-5)>
 
  
let-60 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-60%20(Caenorhabditis%20elegans,%20WB:WBGene00002335,%20-,%20ZK792.6,%20lin-34)>
+
== September 19, 2019 ==
  
daf-2 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=daf-2%20(Caenorhabditis%20elegans,%20WB:WBGene00000898,%20-,%20Y55D5A.5)>
+
=== 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
  
* Looks good
+
=== Alliance literature curation ===
* Some confusion with filled circle legend (half red and half blue) for slim terms; maybe make two separate circles, one red, one blue and possibly indicate each as direct/indirect, respectively
+
* Working group will be formed soon
* May be good to make graph depth options more obvious; we can move it up to the top of the legend, maybe also display all graph depths by default so a user can see them and select one
+
* Will work out general common pipelines for literature curation
* Would it be possible to force display of any AGR/Alliance slim terms on the path from an annotation node to root (not all pertinent slim terms are currently displaying due to the trimming algorithms in place); might be possible but would probably significantly interfere with the current trimming and display algorithm
 
  
=== Moving away from dependency on OBO format files ===
+
=== SObA Graph relations ===
* Nico, an ontology developer with the Monarch group, has some suggestions for how we can move away from dependency on OBO files
+
* Currently only integrating over "is a", "part of" and "regulates"
* Planning to have a meeting on Monday (Feb 25) at 9am Pacific, 12pm Eastern, 5pm UK to discuss
+
* Maybe we could provide users an option to specify which relations to include, or maybe just exclude "regulates"
* How are we handling OBO for GO? GO OBO is parsed into ACE format
 
* This should be a group-wide discussion as we have many OBO dependencies
 
* There are several OBO-to-ACE conversion scripts we use
 
* What is the trend in the ontology field? Seems to be that OBO will become deprecated and OWL will supersede it
 
* We will try to reschedule to Tuesday (same time) to include more people
 
  
=== Phenotype request mass emails ===
+
=== Author First Pass ===
* 1,820 emails gone out this week (since Monday) for 1,820 papers (957 still in queue; need to wait for Google limit to expire)
+
* Putting together paper for AFP
* Have received 217 direct annotations for 49 papers (45 requested papers) from 47 distinct community curators
+
* Reviewing all user input for paper
** 158 to Phenotype OA
+
* Asking individual curators to check input
** 59 to RNAi OA
 
* Have received 5 submissions via email (4 worksheets)
 
** 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
 
** 4 phenotype submissions, 4 curators, 93 phenotype annotations
 
* 57 papers flagged as not having phenotypes
 
* Total: 310 phenotype annotations from 51 community curators for 53 papers
 

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