Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Discussion of what features are commonly used in the Caltech paper editor or otherwise wrt papers | *Discussion of what features are commonly used in the Caltech paper editor or otherwise wrt papers | ||
*Discussion of what features are commonly used in the curation status form | *Discussion of what features are commonly used in the curation status form | ||
+ | |||
+ | = May 12, 2022 = | ||
+ | |||
+ | ==Subcellular localization field== | ||
+ | * WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples. | ||
+ | “miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.” | ||
+ | |||
+ | * Other MODs do not make such distinction. | ||
+ | * Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the ExpressionExperimentStatement in LinkML. | ||
+ | |||
+ | <pre> | ||
+ | ExpressionExperimentStatement: | ||
+ | |||
+ | is_a: EntityStatement | ||
+ | |||
+ | description: >- | ||
+ | |||
+ | Free-text describing some aspect(s) of a gene's expression, particularly | ||
+ | |||
+ | nuanced information that is not readily captured in annotations. | ||
+ | |||
+ | This statement's scope is limited to the associated ExpressionExperiment. | ||
+ | |||
+ | notes: >- | ||
+ | |||
+ | Inherits: statement_subject, statement_type, statement_text, references. | ||
+ | |||
+ | Not sure if/how to use the statement_type slot - seems redundant. | ||
+ | |||
+ | slot_usage: | ||
+ | |||
+ | statement_subject: | ||
+ | |||
+ | range: ExpressionExperiment | ||
+ | </pre> |
Revision as of 17:13, 12 May 2022
Previous Years
2022 Meetings
March 10, 2022
Update on Biocyc linking from WormBase (Kimberly)
Wormicloud for Alliance (Valerio/Jae)
Wormicloud Improvement (Jae)
Apologies: Stavros (attending ISB 1st UK-Local Biocuration Conference)
April 28, 2022
WormBase
- WB grant report
Alliance Migration
- Discussion of what features are commonly used in the Caltech paper editor or otherwise wrt papers
- Discussion of what features are commonly used in the curation status form
May 12, 2022
Subcellular localization field
- WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.
“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”
- Other MODs do not make such distinction.
- Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the ExpressionExperimentStatement in LinkML.
ExpressionExperimentStatement: is_a: EntityStatement description: >- Free-text describing some aspect(s) of a gene's expression, particularly nuanced information that is not readily captured in annotations. This statement's scope is limited to the associated ExpressionExperiment. notes: >- Inherits: statement_subject, statement_type, statement_text, references. Not sure if/how to use the statement_type slot - seems redundant. slot_usage: statement_subject: range: ExpressionExperiment