Difference between revisions of ".ace examples"

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Expr_pattern : "Expr123XXX"
 
Expr_pattern : "Expr123XXX"
Anatomy_term "WBbt:0003955" "WBls:0000002" "GO:0000???" "GO:0000???"
+
Anatomy_term "WBbt:0003955" "WBls:000000?" "GO:0000???" "GO:0000???"
  
 
an alternative would be to associate life stages through the anatomy  
 
an alternative would be to associate life stages through the anatomy  
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Expr_pattern : "Expr123XXX"
 
Expr_pattern : "Expr123XXX"
Detected_in "WBbt:0003955" "WBls:0000002"
+
Detected_in "WBbt:0003955" "WBls:000000?" "GO:0000???" "GO:0000???"
Detected_in "WBbt:0005772" "WBls:0000002"
+
Detected_in "WBbt:0005772" "WBls:000000?" "GO:0000???" "GO:0000???"
  
 
</pre>
 
</pre>

Revision as of 12:26, 5 May 2014

Scenario 1: 1 or more Anatomy_term and NO life stage, no GO_cc, no GO_bp


All objects that have no life stage could map to all stages Ce -WBls:0000002 (we recently removed C elegans development after C mungall's suggestion)
- would be better 'any stage' or even better map to the life_stages in which a cell/tissue exists -see below. 
Shall we consider to reinstate C elegans development? 
That would be more appropriate for cases in which no anatomy, no life stage info are given but only subcellular localization -see below scenario #5
 
examples:

1) expressed in ALA will dump as

Expr_pattern : "Expr123XXX"
Anatomy_term	"WBbt:0003955" "WBls:000000?" "GO:0000???" "GO:0000???"

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. the .ace will look like

Detected_in	"WBbt:0003955" "WBls:0000003" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000018" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000019" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000020" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000016" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000017" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000004" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000015" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000014" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000021" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0003955" "WBls:0000013" "GO:0000???" "GO:0000???"

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"
Detected_in	"WBbt:0003955" "WBls:000000?" "GO:0000???" "GO:0000???"
Detected_in	"WBbt:0005772" "WBls:000000?" "GO:0000???" "GO:0000???"

Scenario 2: one Anatomy_term and one or multiple life stages

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"
Detected_in	"WBbt:0003955" "WBls:0000003"
Detected_in	"WBbt:0003955" "WBls:0000018"
Detected_in	"WBbt:0003955" "WBls:0000019"
Detected_in	"WBbt:0003955" "WBls:0000020"
Detected_in	"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: multiple Anatomy_terms and multiple life stages

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: no Anatomy_term and one or multiple life stages

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"
Detected_in	"WBbt:0007833" "WBls:0000024"
Detected_in	"WBbt:0007833" "WBls:0000038"

Example: WBPaper00042278

mir-265 expressed in embryo, l1, l2, l3, l4, adult

Expr_pattern : "Expr10791"
Detected in "WBbt:0007833" "WBls:0000003"
Detected in "WBbt:0007833" "WBls:0000024"
Detected in "WBbt:0007833" "WBls:0000027"
Detected in "WBbt:0007833" "WBls:0000035"
Detected in "WBbt:0007833" "WBls:0000038"
Detected in "WBbt:0007833" "WBls:0000041"

Stage specific expression, check objects labeled 'Temporal description' in the remarks.


Scenario 5: 1 or more GO cellular component and NO life stage nor anatomy


Example
WBPaper00038084

Expr11212

GFP::PKN-1 colocalized with alpha-actinin and UNC-89, indicating localization at dense bodies and M lines.

Expr_pattern : "Expr11212"
Detected in "WBbt:0007833" "WBls:000000x" "GO:0031430"
Detected in "WBbt:0007833" "WBls:000000x" "GO:0097433"

Back to Expression pattern remodel