Difference between revisions of "WS246 Models.wrm"
From WormBaseWiki
Jump to navigationJump to search (Added as these are linked in the release notes.) |
|||
| (2 intermediate revisions by the same user not shown) | |||
| Line 2: | Line 2: | ||
| − | * This cycle we see | + | * This cycle we see 6 model changes effecting 7 classes: |
1) Automated_descriptions in the ?Gene class | 1) Automated_descriptions in the ?Gene class | ||
| Line 10: | Line 10: | ||
These descriptions will be based on data already curated in WormBase. Currently these data are: | These descriptions will be based on data already curated in WormBase. Currently these data are: | ||
Orthology/Homology and the GO annotations for Process, Function and Cell component. | Orthology/Homology and the GO annotations for Process, Function and Cell component. | ||
| + | |||
| + | Automated_description ?Text #Evidence // Ranjana [140917 pad] | ||
2) Roll back ?Multi_counts and ?Transgene to WS244 models | 2) Roll back ?Multi_counts and ?Transgene to WS244 models | ||
| Line 51: | Line 53: | ||
7) Minor cosmetic changes - mistakes in header and addition/removal of white space. | 7) Minor cosmetic changes - mistakes in header and addition/removal of white space. | ||
| − | |||
== Full diff file == | == Full diff file == | ||
Latest revision as of 15:51, 18 September 2014
Model changes for WS246
- This cycle we see 6 model changes effecting 7 classes:
1) Automated_descriptions in the ?Gene class
Caltech are going to be adding ~3000 automated descriptions for genes where there is no manually curated concise description. These descriptions will be based on data already curated in WormBase. Currently these data are: Orthology/Homology and the GO annotations for Process, Function and Cell component.
Automated_description ?Text #Evidence // Ranjana [140917 pad]
2) Roll back ?Multi_counts and ?Transgene to WS244 models
?Multi_counts model
Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts
?Transgene model
Mapping_data Multi_point ?Multi_pt_data
3) ?Sequence collection - ability to connect to multiple strains
?Sequence collection
Strain ?Strain
What has prompted this proposal is learning this: Taken from WBPaper00044268: "Even though the two sequenced D. immitis came from independent isolates from different continents, they showed low genetic differentiation, allowing the raw sequencing data from both nematodes to be co-assembled."
4) ?Pseudogene - Additional attributes
?Pseudogene
Attributes SubType UNIQUE processed_pseudogene #Evidence
unprocessed_pseudogene #Evidence
5) ?Expr_pattern - additional Cis-regulatory_element Type
?Expr_pattern
Type Cis-regulatory_element Text
6) #Qualifier - Additions to combine life stage with anatomy term in expression pattern annotation.
#Qualifier
Anatomy_term ?Anatomy_term //combines life stage with anatomy term in expr pattern annotation
Life_stage ?Life_stage //combines life stage with anatomy term in expr pattern annotation
7) Minor cosmetic changes - mistakes in header and addition/removal of white space.
Full diff file
Index: models.wrm =================================================================== RCS file: /nfs/ensembl/cvsroot/wormbase/wspec/models.wrm,v retrieving revision 1.409 diff -r1.409 models.wrm 6c6 < // Explination about class/objectcount limits --- > // Explanation about class/object count limits 17c17 < // Last edited on: $Date: 2014-07-17 08:51:10 $ --- > // Last edited on: $Date: 2014-09-17 08:41:37 $ 314a315 > Automated_description ?Text #Evidence // Ranjana [140917 pad] 506d506 < Unaffiliated_construct ?Construct 535a536 > Unaffiliated_construct ?Construct 949a951,952 > Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts > 1401c1404 < Strain UNIQUE ?Strain --- > Strain ?Strain 1549c1552,1554 < Fragment #Evidence --- > Fragment #Evidence > SubType UNIQUE processed_pseudogene #Evidence > unprocessed_pseudogene #Evidence 2061a2067 > Cis-regulatory_element Text 2087,2088c2093,2096 < Uncertain Text //For faint or variable expression < Partial Text //For expression of unidentified cell in a cell group --- > Uncertain Text //For faint or variable expression > Partial Text //For expression of unidentified cell in a cell group > Anatomy_term ?Anatomy_term //combines life stage with anatomy term in expr pattern annotation > Life_stage ?Life_stage //combines life stage with anatomy term in expr pattern annotation 2458a2467 > Mapping_data Multi_point ?Multi_pt_data
