- 1 * General housekeeping - ?Accession class
- 2 * Transposon gene reactivation - Paul
- 3 * Sequence collection - Kevin
- 4 * Starin modifications
- 5 * ?Drug_resistance
- 6 * ?Variation and ?Feature mapping changes
- 7 * ?Gene and Disease Ontology - Ranjana
* 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:
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)
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
I just spotted an additional change the the #Gene_history_action model that might be needed?
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.
#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
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
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 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
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.