WormBase-Caltech Weekly Calls

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

2020 Meetings




April 2, 2020

Community phenotype requests

  • 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

  • Tracking volunteers here
  • 14 volunteers so far, all have been assigned a WBPerson ID
  • Chris will set up a webinar tutorial in the coming week or two

AFP pipeline

  • Will resend email requests to authors that haven't already responded
  • May also send out for older papers
  • 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

  • Need to work on Genotype OA dumper
  • Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
  • Ampersands (&) are also problematic for object names in the OA
    • 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

  • Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication

April 9, 2020

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


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


  • 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?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?