WS246 Models.wrm

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Model changes for WS246

  • This cycle we see 6 model changes in 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