Life Stage

Life_Stage Data Model

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?Life_stage   Name UNIQUE Text   //added by Daniela 120509
              Contains Cell ?Cell XREF Life_stage
                   Cell_group ?Cell_group XREF Life_stage
                   Anatomy_term ?Anatomy_term XREF Life_stage
                   Sub_stage ?Life_stage XREF Contained_in
              Contained_in ?Life_stage XREF Sub_stage            // changed for Wen 010516
              Preceded_by ?Life_stage XREF Followed_by
              Followed_by ?Life_stage XREF Preceded_by
              Expr_pattern ?Expr_pattern XREF Life_stage
              Remark	?Text #Evidence               
               Definition ?Text // added for Wen [020607 krb]
               Other_name ?Text // added for Wen [020607 krb]
               Reference ?Paper XREF Life_stage 
               Curated_by UNIQUE Text // added for Sylvia [010928 krb]
              
            

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Life_Stage

Originally Life_stage objects were stored as names. In May 2012 Caltech decided to switch Life_stage objects from names to IDs. In order to do that we need a model change to store the original name (see model).

All data types that were using Life_stage had to be modified and dumped into Ids instead of names

• Phenotype -Karen
• Process -Karen
• RNAi -Chris
• gene regulation -Xiaodong
• gene expression -Daniela
• Anatomy_term -Raymond
• Expression Cluster -Wen
• Condition -Wen & Gary W
• Strain -Mary Ann

Life_Stage tags

tags used in Life_stage extracted from the Life_Stage. ace dump that I got from Wen on May 9th 2012

• Definition
• Anatomy_term
• Reference
• Other_name
• Expr_pattern
• Contained_in -> Change data into IDs
• Cell_group
• Sub_stage -> Change data into IDs
• Cell
• Followed_by -> Change data into IDs
• Remark -> goid: WBls could be deleted because will be redundant with IDs
• Preceded_by -> Change data into IDs

Action items

Modify the .ace dump as follows

1) Object should be replaced with ID instead of name using the mapping table

2) the following tags should be replaced with ID instead of name

• Contained_in
• Followed_by
• Precede_by
• Sub_stage

3) The lines containing Remark "goid: WBls:#######" should be deleted

Mapping table is here http://tazendra.caltech.edu/~azurebrd/var/work/lifestage