WS236 Models.wrm
Contents
* 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
* Species/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.
* Strain 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
Michael suggested a UNIQUE Fload after the Approximate tag to specify the estimated error range (+-360.0) but this might be overkill.
* ?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
Mapping
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.
It has been pointed out that 1bp features cannot infer strand solely based on the 2 stored co-ordinates so storing the source strand where available might be useful. As the majority of this data will be coming from gff, we will adopt the gff strand convention (+-.)
?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 UNIQUE Text #Evidence //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 UNIQUE Text #Evidence //data provided by paper/submitter/project
Gary W.
Would also like to add a Text description of the type of score followed by an #Evidence hash to the ?Feature model to follow Score
?Feature Score Float Text #Evidence
* ?Gene and Disease Ontology - Ranjana
Proposed and working through Ideas with Hinxton.
?Gene additions
?Gene
DB_info Database ?Database ?Database_field Text//for pointing to OMIM ortholog and disease
Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence
Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence
Disease_relevance ?Text ?Species #Evidence
?DO_term - New class
?DO_term
Name UNIQUE ?Text
Status UNIQUE Valid
Obsolete
Alternate_id ?Text
Definition UNIQUE ?Text
Comment Text
Synonymn Broad ?Text
Exact ?Text
Narrow ?Text
Related ?Text
Parent Is_a ?DO_term XREF Is
Child Is ?DO_term XREF Is_a
DB_info Database ?Database ?Database_field Text
Type GOLD
gram_negative_bacterial_infectious_disease //changed - for _ in tag names.
gram_positive_bacterial_infectious_disease
sexually_transmitted_infectious_disease
tick_borne_infectious_disease
zoonotic_infectious_disease
Attribute_of Gene_by_biology ?Gene XREF Experimental_model
Gene_by_orthology ?Gene XREF Potential_model
Phenotype ?Phenotype XREF DO_term
WBProcess ?WBProcess XREF DO_term
Reference ?Paper XREF DO_term
Version UNIQUE Text
Other class modifications because of XREF/References
?Phenotype DO_term ?DO_term #Evidence ?WBProcess DO_term ?DO_term #Evidence ?Paper DO_term ?DO_term #Evidence
Possible changes
Most previously mentioned have been resolved
1) Possible redundancy between Index and Parent/Child
Postponed tags:
Index Ancestor ?DO_term XREF Descendent
Descendent ?DO_term XREF Ancestor
* Condition Class - Wen
Change the temparature Int to a Float
Temperature Int Temperature Float
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