Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(53 intermediate revisions by 4 users not shown)
Line 37: Line 37:
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== July 11th, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
=== Alliance all hands meeting ===
 
* Raymond: would be interested in discussing ontologies and their usage in the Alliance
 
** Phenotype, anatomy ontologies, GO, etc.
 
** Ontology browsers, SObA
 
  
=== IWM workshop ===
+
== September 12, 2019 ==
* Videos ready for upload
 
* Wen and Raymond now have access to outreach@wormbase.org account; will upload videos
 
  
=== Protocol videos ===
+
=== Update on SVM pipeline ===
* Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
+
* New SVM pipeline: more analysis and more parameter tuning
* Can make each video a Video Weblog so people can make comments, etc.
+
* 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
  
== July 25, 2019 ==
+
=== Citace upload ===
 +
** Tuesday, Sep 24th
  
=== Anatomy ontology ===
+
=== Strain to ID mapping ===
* Raymond added back some deprecated cell group terms as obsolete terms
+
* 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)
  
=== Life stage ontology ===
+
=== New name server ===
* Who will take charge of it? Raymond or Chris?
+
* When will this officially go live?
* OBO-to-ACE script is working
+
* Will we now be able to request strain IDs through the server? Yes
* OBO is working (?) in SObA and WOBr
 
* Chris will take over life stage ontology; Daniela & Raymond will send Chris location of OBO-to-ACE script
 
* Chris will send release OBO to Raymond to test WOBr and SObA
 
  
=== Anatomy term acronyms ===
+
=== SObA Graphs ===
* Some anatomy terms: can the name be changed?
+
* New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
** e.g. "DTC" is main label for "distal tip cell"
+
* 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
** e.g. "HMC" is main label for "head mesodermal cell"
+
* Diff tool: Raymond and Juancarlos created a prototype diff tool (for comparing two genes, for example)
** e.g. "gon herm dtca" is main label for "anterior distal tip cell"
+
** Paul: compared two genes that should be very similar, but there are a lot of differences; may reflect annotation coverage rather than biology
* Karen: would be good to still point out a "public name" or "common name"
 
** Chris: we may need to select a specific OWL annotation property to dump into OBO so our scripts can recognize them and populate ACEDB/Datomic; will look into; may require model change
 
  
=== Author first pass ===
+
 
* Paul: spent about 30-40 minutes doing author first pass for a micropublication
+
== September 19, 2019 ==
* Entities need to be listed 10+ times (fixed threshold) to be recognized, but micropubs won't usually have this many occurrences of terms
+
 
* Need a better way to report allele details; curation of alleles can happen at Caltech or Hinxton; need to discuss
+
=== Strains ===
* Google summer of code: add to schedule so we can post requests/openings
+
* Need to wait for new strain IDs from Hinxton before running dumping scripts
* Karen: Could implement something like Apollo? Talk to Nathan?
+
* Don't edit multi-ontology strain fields in OA for now!
* How can we optimize micropub author first pass?
+
* Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
* Need to minimize/eliminate redundant curation effort
+
* "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
* Curation forms could hide fields that have already been curated; OR, show existing curated data to form users
+
 
* Paul: Can we have submission form build a report to send to user, but possibly not store locally?
+
=== Alliance literature curation ===
** Karen: May be counter to the intent of micropublication where we want authors to submit data in parallel to submission/publication process
+
* Working group will be formed soon
* Eventually there shouldn't be any author first pass for micropublications
+
* Will work out general common pipelines for literature curation
* For now we will exclude micropublications from AFP
+
 
* Can NIH funded groups be pressured to submit data? We need the pipeline to operate smoothly (and properly) before making a requirement
+
=== 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