Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Expression Pattern Model === | === 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): | ||
+ | |||
+ | <pre> | ||
+ | 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 | ||
+ | </pre> | ||
+ | An Expr_pattern can then have a list of ?Expr_annotations, each grouping together all properties of a single observation. |
Revision as of 20:03, 7 November 2018
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 1, 2018
Author First Pass
- Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
- Shall we add in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
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.