Difference between revisions of "WS247 Models.wrm"
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== GO_annotation class - Kimberly ==
== GO_annotation class - Kimberly ==
Revision as of 16:14, 4 December 2014
- 1 Analysis class - Gary
- 2 #Address hash - Cecilia
- 3 GO_annotation class - Kimberly
- 4 Feature - M.A.
- 5 Tag additions for connecting ?Picture to ?WBProcess (Topic)
- 6 Unique -> UNIQUE housekeeping change
- 7 Expr_patter - Daniela
- 8 Expr_patter 2 - Daniela
- 9 Wen has two model proposals for WS247:
- 10 ?Position_Matrix - Xiaodong
- 11 For Discussion - Nomenclature_history tag - Kimberly
Analysis class - Gary
Add Independent_variable for storing the condition of interest so that it is easy to find out what are the experimental variables that are being varied in an experiment
#Address hash - Cecilia
Remove UNIQUE so that multiple affiliations can be stored along with a single address??
#Address Institution UNIQUE Text
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)
?Picture Depict WBProcess ?WBProcess XREF Picture
?WBProcess Picture ?Picture #Evidence
?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
Regulation Regulated_by_gene ?Gene // Wen WS228 Regulated_by_treatment Text // Wen WS228 Regulated_by_molecule ?Molecule // Wen WS228
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.
?Position_Matrix - Xiaodong
I would like to propose a model change for ?Position_matrix:
?Position_Matrix Description ?Text #Evidence Brief_id UNIQUE ?Text // Addition Xiaodong Type UNIQUE Frequency Weight Background_model Text UNIQUE Float Site_values Text UNIQUE Float REPEAT Threshold Float Consensus Text #Evidence Associated_feature ?Feature XREF Associated_with_Position_Matrix #Evidence Sites_used UNIQUE Int Derived_from_matrix ?Position_Matrix Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence Transcription_factor UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3 Remark ?Text #Evidence
I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs.
For Discussion - Nomenclature_history tag - Kimberly
- 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.
@Pdavis I guess this is formalising what has been stored as a remark in the ?Gene objects. M.A. is probably the best person to advise on this and will also be able to contribute/promote lots of remarks into this field if we go ahead with it.