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"

Adding new terms

In WS230 the following terms were used in Citace Minus but were not present in the obo file:

L1 Larva Male L2 Larva male L3 Larva male

the last term generated was L4 Larva male:

[Term]
id: WBls:0000073
name: L4 larva male
def: "The fourth stage larva male. At 25 Centigrade\, it ranges 40-49.5 hours after fertilization\, 26-35.5 hours after hatch." [wb:wjc]
is_a: WBls:0000038 ! L4 larva

I could have added the following but Raymond suggested to leave the sex distinction out of the ontology. We are therefore NOT adding these new terms. Checked in the Life stage WS230 dump -> no data associated with these terms, we could delete them from the obo file and modify citace minus accordingly. Waiting for Wen's feedback -> OK. I deleted the 3 L1 Larva Male L2 Larva male L3 Larva male terms from Citace Minus