Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(8 intermediate revisions by one other user not shown)
Line 32: Line 32:
 
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
== April 2, 2020 ==
 
  
=== Community phenotype requests ===
+
== May 7, 2020 ==
* March 9-28
 
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 
* 361 annotations overall
 
* 48 papers requested received curation (2% response rate)
 
* 53 distinct papers overall (5 papers without request)
 
* 53 distinct persons overall
 
  
=== Community curation volunteers ===
+
=== Alliance COVID Page ===
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
+
* Available on stage
* 14 volunteers so far, all have been assigned a WBPerson ID
+
* Textpresso for Coronavirus up for testing
* Chris will set up a webinar tutorial in the coming week or two
 
  
=== AFP pipeline ===
+
=== SimpleMine at Alliance ===
* Will resend email requests to authors that haven't already responded
+
* Still some confusion about what it is
* May also send out for older papers
+
* Will try to help clarify on PI meeting on Friday
* May work with people to help
 
* Does the old AFP form still work? It should
 
* If someone has a link to the old form, they won't get one for the new form
 
* Maybe could set up an automatic redirect from the old form to the new form
 
* Received many submissions recently (>20% response rate)
 
  
=== Ontology Annotator ===
+
=== Development environment for Alliance work ===
* Need to work on Genotype OA dumper
+
* Raymond and Juancarlos have been working on
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
+
* Existing hardware is strained; set up virtual machine
* Ampersands (&) are also problematic for object names in the OA
+
* Still some technical issues
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 
** 16283  | [hlh-13::GFP;unc-119(+)]                                              | 2013-02-07 17:43:22.384819-08
 
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                          | 2019-08-14 08:44:49.91063-07
 
  
=== Use Slack More ===
+
=== Open Publishing Festival ===
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
+
* Later this month
 +
* Micropublications involved
 +
* Organized by the Collaborative Knowledge Foundation
 +
* Will involve publishers of books, journals, etc.
 +
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 +
* Open to all
  
 +
=== Genotype class ===
 +
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 +
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 +
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 +
* Would be good to be clear/transparent about which components were automatically inferred
  
== April 9, 2020 ==
+
=== WS277/278 ===
 
+
* Pipelines are pushed back by about 14 days/2 weeks
=== Volunteer curators ===
 
* Have sent out emails to schedule tutorials
 
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
 
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
 
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
 
 
 
===TAGC is virtual (4.22-25.2020)===
 
FYI in case you missed it
 
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
 
 
===summer students===
 
* Caltech SURF students (and other summer students worldwide) now are looking for projects
 
* Maybe they could curate for WormBase
 
* In addition to phenotype, they could curate:
 
** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
 
** Anatomy function, looking for novel info; opportunity to program/code
 
 
 
=== OA semicolon issue ===
 
* Juancarlos has fixed the issues on sandbox
 
* Curators should test on Mangolassi
 
 
 
=== Textmining/automation ===
 
* Daniela will discuss with Christina Zorn from Xenbase
 
* Will discuss SVM, AFP, Textpresso, etc.
 
 
 
=== Retracted WBPapers ===
 
* Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
 
* https://github.com/WormBase/website/issues/7637
 
* Can we systematically detect retractions? Yes
 
* What about finding papers that cite retractions? Maybe, but likely tricky
 
 
 
 
 
== April 16, 2020 ==
 
 
 
=== Community Phenotype Curation Tutorials ===
 
* Chris has run 6 tutorials, recorded 4
 
* MPG files saved on DropBox; ask Chris for access
 
* Plan to edit videos to make tutorial video to post on WB YouTube channel
 
 
 
=== Author First Pass ===
 
* May run a webinar and use Zoom to record
 
* May make a short tutorial video
 
* Jae: Is there documentation for terminology used in the form?
 
 
 
=== Zoom accounts ===
 
* People can try to use Caltech Zoom account
 
 
 
 
 
== April 23, 2020 ==
 
 
 
=== Community Phenotype Curation Tutorials ===
 
* Chris has finished first round of tutorials; 8 tutorials, 6 video recordings
 
* There are ~8 new volunteers; will setup tutorials for them soon
 
 
 
=== ECO code implementation ===
 
* ?ECO_term to replace ?GO_code in ACEDB models
 
* GAF files with three-letter codes can still be generated by mapping
 
 
 
=== Simplemine for Alliance ===
 
* Wen has presented proposal to Search group
 
* Plan is to have a link to the Alliance Simplemine prototype from the Alliance web page
 
 
 
=== Venn diagram tool ===
 
* Conceived by Jae, implemented by Sibyl
 
* Currently used for interactions data
 
* Could use for other data types like phenotype (e.g. comparing RNAi vs. allele phenotype)
 
* Could also use for Expression data, e.g. comparing results from different methods
 
* Could maybe use for disease data
 
 
 
=== AFP tutorial ===
 
* Daniela, Kimberly, Valerio will run through the AFP form with Nikita from Gupta lab tomorrow
 
* May record in the future to make a tutorial video
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
 
 
=== Expression markers ===
 
* SURF student projects: Identifying good expression markers? Maybe, but may require more curation experience
 
* Wen looked at expression cluster data; hard to find good, very specific (i.e. neuron) markers
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
* Already have an "Expression markers" widget on anatomy term pages
 
* Could combinations of genes (e.g. cGal) act as markers?
 
 
 
== April 30, 2020 ==
 
 
 
=== Adding ?ECO_term class for WS278 ===
 
* Proposed[https://wiki.wormbase.org/index.php/Evidence_Code_Ontology#.3FECO_term_Model ?ECO_term model]
 
** How are the Parent/Child and Ancestor/Descendant tags used in WB for ontology classes?  Do we still need them in .ace files?
 
*Confirm proposed changes to class models that will use this tag:
 
** ?GO_annotation
 
** ?Phenotype
 
** ?Disease_model_annotation
 
 
 
=== Ontology term models in WB ===
 
* Discuss using ?RO_term values in our WB ontology term models
 
* Currently relations between ontology terms are captured with text that is sometimes inconsistent for the same concept, e.g. is_a
 
* Where possible, should be use ?RO_term to express the relations between ontology terms in our WB models?
 
* Impact on web display?
 
 
 
===Entries in the new Genotype OA===
 
*21 genotype entries created in the Genotype OA required for disease curation
 
*Few more to come, and at some point need to work on the dumper, in order to submit for WS278
 
*The use of the Genotype class across disease related classes waiting on approval of proposed models, will need dumper changes as well; hopefully we have enough time to get all this done for WS278
 
 
 
===ZOOM for tutorial===
 
 
 
* High Definition (1440p)
 
* Caltech account works well
 
 
 
===New AFP version===
 
* Planned to be released in June
 
* We need to improve datatype definitions. Please take a look at the current form here: http://textpressocentral.org:5000
 
* Frequency of automated alerts on new submissions for specific datatypes will change monthly to weekly
 

Revision as of 17:15, 7 May 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April


May 7, 2020

Alliance COVID Page

  • Available on stage
  • Textpresso for Coronavirus up for testing

SimpleMine at Alliance

  • Still some confusion about what it is
  • Will try to help clarify on PI meeting on Friday

Development environment for Alliance work

  • Raymond and Juancarlos have been working on
  • Existing hardware is strained; set up virtual machine
  • Still some technical issues

Open Publishing Festival

  • Later this month
  • Micropublications involved
  • Organized by the Collaborative Knowledge Foundation
  • Will involve publishers of books, journals, etc.
  • Will have a MOD-focused event, would be good to have WB curators participate/attend
  • Open to all

Genotype class

  • Ranjana finished populating the Genotype OA with genotypes needed for disease curation
  • Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
  • There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
  • Would be good to be clear/transparent about which components were automatically inferred

WS277/278

  • Pipelines are pushed back by about 14 days/2 weeks