Difference between revisions of "WS236 Models.wrm"

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(Created page with '__TOC__ === General housekeeping - ?Accession class === ?Accession class retirement phase 1 * Remove simple examples of: <pre> Database ?Database ?Database_field ?Accession …')
 
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__TOC__
 
__TOC__
  
=== General housekeeping - ?Accession class ===
+
=== * General housekeeping - ?Accession class ===
  
 
?Accession class retirement phase 1
 
?Accession class retirement phase 1
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This will significantly reduce the numbers of empty objects in the ?Accession class
 
This will significantly reduce the numbers of empty objects in the ?Accession class
  
=== Transposon gene reactivation - Paul ===
+
=== * Transposon gene reactivation - Paul ===
  
 
==== Poor nomenclature in ?Gene history and Event ====
 
==== Poor nomenclature in ?Gene history and Event ====
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</pre>
 
</pre>
  
=== Sequence collection - Kevin ===
+
=== * Sequence collection - Kevin ===
  
 
When we added the Assembly Sequence_collection to the ?Species class, we made it unique, in the assumption that there would only ever be one current assembly for each species.
 
When we added the Assembly Sequence_collection to the ?Species class, we made it unique, in the assumption that there would only ever be one current assembly for each species.
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Turns out we were wrong. So I therefore propose to remove the UNIQUE.  
 
Turns out we were wrong. So I therefore propose to remove the UNIQUE.  
  
=== Starin ===
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=== * Starin ===
  
 
==== ?Strain - Michael====
 
==== ?Strain - Michael====
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=== ?Drug_resistance ===
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=== * ?Drug_resistance ===
  
 
Poss handed partly to caltech...need update
 
Poss handed partly to caltech...need update
  
=== ?Variation and ?Feature mapping changes ===
+
=== * ?Variation and ?Feature mapping changes ===
  
 
This models update unifies the mapping of these 2 classes and provides a second (better) method for mapping genomic features which we will be using in the near future.
 
This models update unifies the mapping of these 2 classes and provides a second (better) method for mapping genomic features which we will be using in the near future.

Revision as of 14:20, 28 November 2012

* General housekeeping - ?Accession class

?Accession class retirement phase 1

  • Remove simple examples of:
Database ?Database ?Database_field ?Accession 

from the models file in favor of:

?Database_field Text

This will significantly reduce the numbers of empty objects in the ?Accession class

* Transposon gene reactivation - Paul

Poor nomenclature in ?Gene history and Event

Model changes to ?Gene and ?Transposon

I'd like to change tags in the ?Gene model and #Gene_history_action hash.

#Gene_history_action Event  Created
                            Killed
                            Made_into_transposon        // for CDSs that become Transposon CDSs - no longer count as Live Gene

#Gene_history_action Event  Created
                            Killed
                            Transposon_in_origin        // for genes that are identified as having CDSs/Proteins that are Transposon in origin

?Gene
History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
    Made_into_transposon

?Gene
History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
    Transposon_in_origin

As this was poorly thought out and is misleading (gets a high status position in the Overview widget which is good, but tag name has issues)

Gene::Transposon

I'd also like to make a connection between Gene and Transposon

?Gene
        Allele ?Variation XREF Gene #Evidence
    Corresponding_transposon ?Transposon XREF Gene #Evidence

?Transposon
    Corresponding_gene ?Gene XREF Corresponding_transposon #Evidence 

#Gene_history_action

I just spotted an additional change the the #Gene_history_action model that might be needed?

2 options.

1) Just need to remove the killed from the "Suppressed genes. A use case would be the Transposon_in_origin genes where the scripts would only used the "Transposon_in_origin tag in the History tag structure.

2) Talking with Mary Ann, even though this is overkill, it fills an omission whereby all tags in the #Gene_history_action can be represented as a rooted tag within the object and for consistency this should be added.

addition of:

#Gene_history_action Event Suppressed 

* Sequence collection - Kevin

When we added the Assembly Sequence_collection to the ?Species class, we made it unique, in the assumption that there would only ever be one current assembly for each species.

Turns out we were wrong. So I therefore propose to remove the UNIQUE.

* Starin

?Strain - Michael

I would like to propose removal of the unused tags:

Reference_strain - changes to the Sequence_collection class we would be able to identify a reference strain.
Males - has been superseded by the phenotype ontology

?Strain - Mary Ann

Sample_history

renamed to

Strain_history

M-A Felix wants this renamed and as of now it has only been used once and is not displayed on the site.

?Strain - Mary Ann

?Strain
     Isolation GPS UNIQUE Float UNIQUE Float #Position_confidence
           Elevation UNIQUE Unique Float #Position_confidence

#Position_confidence Exact
                     Approximate
                     Inferred_from_GPS


* ?Drug_resistance

Poss handed partly to caltech...need update

* ?Variation and ?Feature mapping changes

This models update unifies the mapping of these 2 classes and provides a second (better) method for mapping genomic features which we will be using in the near future.

?Variation
SMap 	S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Allele    //Data removed from the primary database
    	Sequence_details	Flanking_sequences UNIQUE Text UNIQUE Text  //No change
				Mapping_target UNIQUE ?Sequence //addition to store the Sequence the object should map to.
				Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int //data provided by paper/submitter/project

?Feature
SMap 	S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Allele    //Data removed from the primary database
    	Sequence_details	Flanking_sequences UNIQUE Text UNIQUE Text  //Removal of leading ?Sequence connection
				Mapping_target UNIQUE ?Sequence //addition to store the Sequence the object should map to.
				Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int //data provided by paper/submitter/project