WS236 Models.wrm

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* 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 modifications

?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

Mary Ann proposed a model but upon internal discussion it seemed that this might be better placed with Karen at Caltech.

* ?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


* ?Gene and Disease Ontology - Ranjana

Proposed and working through Ideas with Hinxton.

?Gene additions

?Gene
DB_info	Database	?Database	?Database_field	Text
Disease_info 	Human_experimental_model	?DO_term	XREF	Gene_by_biology	#Evidence	            
              	Human_potential_model		?DO_term	XREF	Gene_by_orthology	#Evidence
              	Human_disease_relevance	?Text	#Evidence

?DO_term - New class

?DO_term 
 Name  UNIQUE              ?Text
 Status UNIQUE              Valid
                               Obsolete
 Alternate_id                     ?Text
 Definition UNIQUE         ?Text
 Comment            Text
 Synonymn           ?Text Scope_modifier UNIQUE Broad
                                                Exact
                                                Narrow
                                                Related
 Relationship         Is_a_child  	?DO_term  XREF  Is_a_parent
                   	Is_a_parent ?DO_term  XREF  Is_a_child 
 DB_info           Database    ?Database  ?Database_field   Text              
 Replaced_by                   ?DO_term
 Subset                              Text                  
 Created_by                      Text
 Creation_date                  Text             
 Attribute_of	Gene_by_biology    ?Gene       XREF   DO_term 
                     	Gene_by_orthology  ?Gene       XREF   DO_term
                    Phenotype  ?Phenotype  XREF   DO_term
                    WBProcess  ?WBProcess  XREF   DO_term
                    Reference  ?Paper      XREF   DO_term 
 Index	Ancestor   ?DO_term   XREF Descendent      
         	Descendent ?DO_term   XREF Ancestor   
 Version UNIQUE Text      


Possible changes

1) further eradication of the species from the tags in favor of a ?Species tag in the model branch

2) Couple of issues with broken tag structures/Models

3) Data storage questions

  Created_by Text
  Version Text
  Subset Text
  Creation_date Text -> Creation_date DateType

4) Possible redundancy between Index and Parent/Child

5) Standardisation of Parent/Child as there are multiple ontologies in the schema, all doing things differently.