Difference between revisions of "WS247 Models.wrm"
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== For Discussion - Nomenclature_history tag== | == For Discussion - Nomenclature_history tag== | ||
− | Addition of a Nomenclature_history tag as part of the Structured_description grouping tag. | + | *Addition of a Nomenclature_history tag as part of the Structured_description grouping tag. |
− | This tag would provide some additional textual information about gene names and changes in order to clarify better some of the naming issues. | + | *This tag would provide some additional textual information about gene names and changes in order to clarify better some of the naming issues. |
− | Entries could be very simple: | + | *Entries could be very simple: |
− | umps-1 was originally identified in screens for radiation-sensitive mutant animals and thus originally named rad-6. | + | **umps-1 was originally identified in screens for radiation-sensitive mutant animals and thus originally named rad-6. |
− | Or more detailed: | + | *Or more detailed: |
− | gene x was originally named 'xxx-1'. This gene name is now retired because of .... and the current name assigned based on sequence similarity to the human ortholog. | + | **gene x was originally named 'xxx-1'. This gene name is now retired because of .... and the current name assigned based on sequence similarity to the human ortholog. |
Revision as of 16:32, 13 November 2014
Contents
GO_annotation class - Kimberly
Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.
Feature - M.A.
Can we remove Annotation and Defined_by_author
Tag additions for connecting ?Picture to ?WBProcess (Topic)
Add:
?Picture Depict WBProcess ?WBProcess XREF Picture
and change:
?WBProcess Picture ?Picture #Evidence
to:
?WBProcess Picture ?Picture XREF WBProcess #Evidence
Unique -> UNIQUE housekeeping change
Corresponding_transgene Unique ?Transgene XREF Corresponding_variation
Expr_patter - Daniela
I would like to add
Microarray_results ?Microarray_results XREF Expr_Pattern
to the Expr_pattern class
between Expression_cluster ?Expression_cluster XREF Expr_pattern and Pattern ?Text
this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings
Expr_patter 2 - Daniela
I would also like to add a Species tag in the Expr_pattern class
Species UNIQUE ?Species
Wen has two model proposals for WS247:
1. Can we move Microarray_results tag from under "Experimental_info" to under "Molecular_info"?
This tag used to store microarray data, but now it is only used to specify probe names corresponding to this gene. It is better staying under super tag "Molecular_info". This model change should not affect database build or website display.
2. Under ?Expression_cluster model
Please change:
Regulation Regulated_by_gene ?Gene // Wen WS228 Regulated_by_treatment Text // Wen WS228 Regulated_by_molecule ?Molecule // Wen WS228
into
Regulation Regulated_by_gene ?Gene XREF Regulate_expr_cluster Regulated_by_treatment Text Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster
Corresponding XREF already exist in ?Gene and ?Molecule class, the XREFs in Expression_cluster were probably forgotten when I proposed them for WS228.
For Discussion - Nomenclature_history tag
- Addition of a Nomenclature_history tag as part of the Structured_description grouping tag.
- This tag would provide some additional textual information about gene names and changes in order to clarify better some of the naming issues.
- Entries could be very simple:
- umps-1 was originally identified in screens for radiation-sensitive mutant animals and thus originally named rad-6.
- Or more detailed:
- gene x was originally named 'xxx-1'. This gene name is now retired because of .... and the current name assigned based on sequence similarity to the human ortholog.