Anatomy AND life stage .ace examples

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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.