Life Stage

Life_Stage Data Model

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?Life_stage   Public_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

.ace file to modify located here: /home/acedb/draciti/Life_stage and is named Life_stageWS230.ace

Modify the .ace dump as follows

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

2) A new tag called Public_name should be added and should contain the name that was previously the object name

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

• Contained_in
• Followed_by
• Precede_by
• Sub_stage

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

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

script at : /home/acedb/draciti/Life_stage/parse.pl output goes to script. Errors from lack of mappings are in the file. current output in file "out"