Difference between revisions of "WS236 Models.wrm"
(Created page with '__TOC__ === General housekeeping - ?Accession class === ?Accession class retirement phase 1 * Remove simple examples of: <pre> Database ?Database ?Database_field ?Accession …') |
|||
Line 1: | Line 1: | ||
__TOC__ | __TOC__ | ||
− | === General housekeeping - ?Accession class === | + | === * General housekeeping - ?Accession class === |
?Accession class retirement phase 1 | ?Accession class retirement phase 1 | ||
Line 19: | Line 19: | ||
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 ==== | ||
Line 76: | Line 76: | ||
</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. | ||
Line 82: | Line 82: | ||
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 === | + | === * Starin === |
==== ?Strain - Michael==== | ==== ?Strain - Michael==== | ||
Line 115: | Line 115: | ||
− | === ?Drug_resistance === | + | === * ?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
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
* 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