Difference between revisions of "Anatomy AND life stage .ace examples"
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Revision as of 12:50, 25 April 2014
Anatomy AND Life_stage
Scenario 1: All objects that have no life stage should map to all stages Ce -WBls:0000002 (we recently removed C elegans development after C mungall's suggestion) examples: 1) expressed in ALA will dump as Expr_pattern : "Expr123XXX" Anatomy_term "WBbt:0003955" "WBls:0000002" an alternative would be to associate life stages through the anatomy For instance the ALA anatomy term has 11 life stages appended in the tree view. Would that be an option? the .ace will look like Anatomy_term "WBbt:0003955" "WBls:0000003" Anatomy_term "WBbt:0003955" "WBls:0000018" Anatomy_term "WBbt:0003955" "WBls:0000019" Anatomy_term "WBbt:0003955" "WBls:0000020" Anatomy_term "WBbt:0003955" "WBls:0000016" Anatomy_term "WBbt:0003955" "WBls:0000017" Anatomy_term "WBbt:0003955" "WBls:0000004" Anatomy_term "WBbt:0003955" "WBls:0000015" Anatomy_term "WBbt:0003955" "WBls:0000014" Anatomy_term "WBbt:0003955" "WBls:0000021" Anatomy_term "WBbt:0003955" "WBls:0000013" or do we leave the more detailed description for the cases in which authors *specifically* determined the stage? 2) Expressed in ALA and intestine will dump as Expr_pattern : "Expr123XXX" Anatomy_term "WBbt:0003955" "WBls:0000002" Anatomy_term "WBbt:0005772" "WBls:0000002" Scenario 2: all objects that have one tissue/cell and multiple life stages should dump multiple lines with Tissue1 -> LS1 Tissue1 -> LS2 Tissue1 -> LS3 Tissue1 -> LS4 Tissue1 -> LS5 Expr_pattern : "Expr123XXX" Anatomy_term "WBbt:0003955" "WBls:0000003" Anatomy_term "WBbt:0003955" "WBls:0000018" Anatomy_term "WBbt:0003955" "WBls:0000019" Anatomy_term "WBbt:0003955" "WBls:0000020" Anatomy_term "WBbt:0003955" "WBls:0000016" on the site -gene page. expression widget, expression table http://www.wormbase.org/species/c_elegans/gene/WBGene00002992?query=lin-3#01f3--10 the anatomy term should be displayed only once and the life stages should all be displayed on the gene expression page, in the details widget http://www.wormbase.org/species/all/expr_pattern/Expr9352#021--10 we could build a table Expressed in ALA L1 larva L2 larva adult …… Scenario 3: all objects that have multiple tissue/cell and multiple life stages should dump multiple lines. All those objects should be manually assessed in order to determine if Tissue-> LS relationship can be established Tissue1 -> LS1 Tissue1 -> LS2 Tissue1 -> LS3 Tissue1 -> LS4 Tissue 2 -> LS2 Tissue 2 -> LS7 on the site -gene page. expression widget, expression table http://www.wormbase.org/species/c_elegans/gene/WBGene00002992?query=lin-3#01f3--10 the anatomy term should be displayed only once and the life stages should all be displayed with no redundancy (i.e. if in 2 tissues expression is observed in L2, L2 should appear only once) on the gene expression page, in the details widget http://www.wormbase.org/species/all/expr_pattern/Expr9352#021--10 we could build a table Expressed in ALA L1 larva L2 larva adult …… intestine adult Scenario 4: If the description of expression of a gene is only pointing to a life stage the (e.g. rt-pcr) the annotation should be made to organism, life stage e.g. egl-1 was expressed in L1 and L4 Expr_pattern : "Expr123XXX" Anatomy_term "WBbt:0007833" "WBls:0000024" Anatomy_term "WBbt:0007833" "WBls:0000038"
For future recording of stage specific expression, check objects labeled 'Temporal description' in the remarks.