Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
(291 intermediate revisions by 8 users not shown)
Line 16: Line 16:
  
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
  
Line 21: Line 23:
  
  
= 2018 Meetings =
+
= 2019 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
[[WormBase-Caltech_Weekly_Calls_October_2018|October]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_November_2018|November]]
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
== December 6, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
=== SObA for disease (& other ontology?) annotations ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Next Alliance all-hands call in February, present SObA for Skunkworks (innovation talks)?
 
* SObA top-slicing (summary view) gets tricky; Raymond looking into better solutions, if available
 
* SObA summary could be redundant with ribbon? SObA would provide dynamic, trimmed nodes
 
  
=== Worm phenotype ontology ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Meeting today at 12pm Pacific, 3pm Eastern
 
* In process of adding back obsolete terms to the ontology
 
* Question about "has_obo_namespace" attribute; not required for ODK process; used by WB pipelines?
 
  
=== ISB Meeting, Cambridge, UK, April 2019 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Abstracts from WB?
 
** New Author First Pass - Daniela, Valerio, Kimberly, et al.
 
** Automated gene descriptions - Ranjana, gene description working group
 
  
=== GO expression data using Uberon anatomy terms ===
 
* Some GO curators curating C. elegans expression annotations (from synapse annotation project) to Uberon anatomy terms, not WBbt terms
 
* Kimberly will look into enforcing Noctua editor to use C. elegans anatomy ontology when creating C. elegans annotations
 
* Can possibly perform automated mapping if appropriate cross-references exist
 
* Kimberly has already found annotations to inappropriate Uberon terms
 
  
 +
== September 12, 2019 ==
  
== December 13, 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
  
=== Protege Tutorial ===
+
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
+
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
* Please fill out poll if you are interested in attending
+
* 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
* Resources available
+
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
** here (right-click and Save As): https://www.dropbox.com/s/6fygtby4x6d2t0r/ProtegeShortCourse.zip?dl=0
+
* Definitions include meanings or words:
** and here: https://protege.stanford.edu/shortcourse/201810/resources.html
+
** "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
  
=== Updates to Gene Regulation OA ===
+
=== Citace upload ===
* Removed two unused fields/tables: Trans-regulator Seq and Trans-regulated Seq
+
** Tuesday, Sep 24th
* (In progress) Now a single field for anatomy, life stage, and subcellular localization (SCL) (as opposed to a set of each for each type of regulation result)
 
* May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a result type
 
  
=== Micropublication workshop IWM 2019 ===
+
=== Strain to ID mapping ===
* Micropublication group will apply for a workshop
+
* Waiting on Hinxton to send strain ID mapping file?
* If they get it they will need a tiny (~5 min) slot in the general WB
+
* Hopefully we can all get that well before the upload deadline
 +
* Will do global replacement at time of citace upload (at least for now)
  
=== RNAi uniquely_mapped tags ===
+
=== New name server ===
* User pointed out that an RNAi object in WormMine was not flagged as "Uniquely mapped"
+
* When will this officially go live?
* Turns out that the current RNAi mapping pipeline does not add a "Uniquely_mapped" tag
+
* Will we now be able to request strain IDs through the server? Yes
* All existing tags are coming from older RNAi objects in CitaceMinus
 
* Chris working on .ACE file to delete all of these tags from CitaceMinus
 
* Chris will upload the .ACE file to citpub@spica in the Data_for_midbuild directory for Wen
 
  
=== Worm wiring & Worm Atlas ===
+
=== SObA Graphs ===
* Todd and Raymond meeting this afternoon
+
* New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
* Chris will join
+
* 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
* 2pm Pacific time
+
* 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
  
=== WS270 upload ===
 
* Jan 11th upload to Hinxton
 
* Tuesday, January 8th citace upload 10am
 
  
=== Alliance grant renewal ===
+
== September 19, 2019 ==
* Send Paul drafts for working group updates before next Thursday Dec 20, just to give him a heads up on content
 
* Paul currently working off All-Hands meeting presentations
 
  
=== Alliance vs. MODs efficiencies ===
+
=== Strains ===
* Compare user pipelines for getting info like:
+
* Need to wait for new strain IDs from Hinxton before running dumping scripts
** for a human disease gene, what are the phenotypes in model organisms?
+
* Don't edit multi-ontology strain fields in OA for now!
* What are the best work products of the Alliance so far?
+
* Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
** Expression ribbon
+
* "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
** Orthology
 
** Molecular interactions? Good to have nicer interface, consolidation of data; no automated comparative tools yet, but can get equivalent results with some clicking
 
** How to best measure impact?
 
  
=== Noctua imports ===
+
=== Alliance literature curation ===
* Can we export/duplicate a Noctua model to apply to a different gene?
+
* Working group will be formed soon
* Can export in GPAD or GAF
+
* Will work out general common pipelines for literature curation
* Want to seed Noctua models with MOD data; efficient, large scale import
 
  
== December 20, 2018 ==
+
=== 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"
  
=== Authors, Papers, Meeting Abstracts ===
+
=== Author First Pass ===
*Authors on older (i.e. 2000) meeting abstracts don't always have associated WBPerson objects
+
* Putting together paper for AFP
**Anything we can/should do about this?
+
* Reviewing all user input for paper
*Author on some older abstracts are also listed First Name Last Name as opposed to Last Name, First Name
+
* Asking individual curators to check input
**This results in display errors
 
**Any way to fix this via script?
 
*Can meeting abstracts be added to TPC?
 

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