WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
November 1, 2018
Community phenotype requests
- Sent out 1,000 request emails for community submissions of phenotypes on October 18 and October 20
- As before, request focuses on a single paper, but we've now added extra papers at bottom of email message
- We've also added a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes
- 21 emails bounced
- 56 papers received annotations, 44 from direct requests, 12 not directly requested
- 9 of 12 not directly requested were appended requests to email message
- 277 annotations submitted (raw) via the form (some more submitted as Excel spreadsheets)
- 247 allele/transgene phenotype annotations
- 30 RNAi phenotype annotations
- 48 distinct community curators
SPELL
- Todd working on a spell.wormbase.org site for doing worm SPELL analyses
- Should be faster, more stable
Predicted protein-protein interactions
- Jae has requested data set
- Total data set 20GB (how much is C. elegans?)
- Haven't heard back from author recently
- How much do we want this data? Should reach out a couple more times (once every ~two weeks)
November 8, 2018
Author First Pass
- Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
- Raymond, Ranjana, Gary, Jae and Karen ok to have a monthly digest. Chris, Wen no email
- Will check in with Gary W and see if he wants to be notified for RNAseq data flagging
- Should ask April what she wants to do
- Shall we add in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
- Yes, Add site and time of action
- How would we like to handle Methods papers? These may have reagents and some bona fide experimental results, but are not our 'typical' experimental papers. Possibly add a new 'methods' flag?
- Worth flagging methods papers. Will send methods papers to authors for 6 months and then evaluate how useful it is
- Do we need to still maintain the cfp form? If we can keep the data tables and still see the flags in the curation status form, do we need the cfp form?
- The CFP form can be retired
- Add back in the AFP from ‘this is a review paper, I am not curating this’
Expression Pattern Model
- there would be value in having a separate ?Expr_annotation class, like we did for ?GO_annotation. It might look something like this (details not completely thought through):
Class ?Expr_annotation Life_stage ?Life_stage XREF Expr_pattern #Qualifier Not_in_Life_stage ?Life_stage #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier Not_in_Anatomy_term ?Anatomy_term #Qualifier GO_CC ?GO_term XREF Expr_pattern GO_BP ?GO_term XREF Expr_pattern Cell ?Cell Cell_group ?Cell_group #Qualifer Certain Partial Uncertain
An Expr_pattern can then have a list of ?Expr_annotations, each grouping together all properties of a single observation.
Daniela will work on a model for an ?Expression_annotation class. The change can be gradual. We can Add the ?Expression_annotation class and still dump anatomy, life stage and GO in the old tags. Down the line those tags will be deprecated and fully replaced by the ?Expression_annotation tags
?Cell and ?Cell group could go away