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.
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