WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
Previous Years
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
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)
SURF program
- 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)