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GUDMAP example
Hongsuda edited this page Jan 8, 2019
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1 revision
"tables": {
"Common.Gene": {
"annotations": {
"tag:isrd.isi.edu,2019:environments":{
"definitions": {
"columns": true,
"fkeys": true,
"sources": [
{
"Imaging_Data" : [
{ "inbound" : ["Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Gene_Association_Specimen_RID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Representative_Image_fkey" ] },
"RID"
],
"entity": true,
"markdown_name": "Imaging Data",
"aggregate": "array_d"
},
{
"Min_Stage" : [
{ "inbound" : ["Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Gene_Association_Specimen_RID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Stage_ID_fkey" ] },
"RID"
],
"entity": true,
"markdown_name": "Min Stage",
"aggregate": "array_d",
"display": {
"row_order" : [{"column": "Ordinal"}, "descending":true],
"page_size" : 1
}
},
{
"Max_Stage" : [
{ "inbound" : ["Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Gene_Association_Specimen_RID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Stage_ID_fkey" ] },
"RID"
],
"entity": true,
"markdown_name": "Max Stage",
"aggregate": "array_d",
"display": {
"row_order" : [{"column": "Ordinal"}, "descending":false],
"page_size" : 1
}
}
]
},
"active": {
"compact" : {
"columns": true, // all columns defined in the env?
"fkeys": true, // all fks defined in the env?
]
},
"compact" : {
"columns": true,
"fkeys": true,
"sourcekeys": [
"Imaging_Data", "Min_Stage", "Max_Stage"
]
}
}, //env
"tag:isrd.isi.edu,2016:visible-columns" : {
"compact" : [
"NCBI_Symbol",
[ "Common", "Gene_Species_fkey"],
"Description",
"Specimen_Expression_Data",
"Array_Data",
{
"sourcekey" : "Imaging_Data",
"required_sourcekeys" : ["Imaging_Data"]
"display" : {
"template_engine": "handlebars",
"markdown_pattern" : "{{#each Imaging_Data}} [:span:{{{this.values.Stage}}} :/span:{.pseudo-column-rowname-thumbnail-title}{height=75}](/chaise/record/#{{{$catalog.snapshot}}}/Gene_Expression:Specimen/RID={{{this.values.Specimen_RID}}}){.pseudo-column-rowname-thumbnail-link} {{/each}}",
"row_markdown_pattern" : "[:span:{{{Stage}}} :/span:{.pseudo-column-rowname-thumbnail-title}{height=75}](/chaise/record/#{{{$catalog.snapshot}}}/Gene_Expression:Specimen/RID={{{Specimen_RID}}}){.pseudo-column-rowname-thumbnail-link}"
"Page_Size" : 25,
"Row_Order" : [{"column": "Stage"}, {"descending": true}] // can't do this based on ordinal ranking
}
}
],
"compact/brief" : [
"NCBI_Symbol",
[ "Common", "Gene_Species_fkey"],
"External_Links",
"Description",
"Synonyms",
[ "Common", "Gene_Chromosome_fkey" ]
],
"detailed" : [
"NCBI_GeneID",
"NCBI_Symbol",
"MGI_Symbol",
[ "Common", "Gene_Species_fkey" ],
"External_Links",
"Description",
"Synonyms",
[ "Common", "Gene_Chromosome_fkey" ],
"Location",
"NCBI_Date"
],
"filter" : {
"and" : [
{
"source" : "NCBI_Symbol",
"hide_not_null_choice": true,
"hide_null_choice": true
},
{
"source" : "MGI_Symbol"
},
{
"source" : "Species",
"hide_not_null_choice": true,
"hide_null_choice": true
},
{
"source" : "Synonyms"
},
{ "source" : "Any_Data",
"choices": [true],
"hide_not_null_choice": true,
"hide_null_choice": true,
"markdown_name" : "Any Data"
},
{ "source" : "Imaging_Data",
"hide_not_null_choice": true,
"hide_null_choice": true,
"markdown_name" : "Imaging Data"
},
{ "source" : "Array_Data",
"hide_not_null_choice": true,
"hide_null_choice": true,
"markdown_name" : "Array Data"
},
{ "source" : "Specimen_Expression_Data",
"hide_not_null_choice": true,
"hide_null_choice": true,
"markdown_name" : "Scored Expression Data"
},
{
"markdown_name" : "Scored Expression Region",
"source" : [
{ "inbound" : ["Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Gene_Association_Specimen_RID_fkey" ] },
{ "inbound" : ["Gene_Expression", "Specimen_Expression_Specimen_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Expression_Region_fkey" ] },
"RID"
]
},
{
"markdown_name" : "Assay Type",
"source" : [
{ "inbound" : ["Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Specimen_Gene_Association_Specimen_RID_fkey" ] },
"Assay_Type"
]
},
{
"markdown_name" : "Anchor Gene Anatomy",
"ux_mode" : "choices",
"source" : [
{ "inbound" : ["Gene_Expression", "Anchor_Gene_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Anchor_Gene_Anatomy_fkey" ] },
"ID"
]
},
{
"markdown_name" : "Marker Gene Anatomy",
"ux_mode" : "choices",
"source" : [
{ "inbound" : ["Gene_Expression", "Marker_Gene_NCBI_GeneID_fkey" ] },
{ "outbound" : ["Gene_Expression", "Marker_Gene_Anatomy_fkey" ] },
"ID"
]
},
{
"markdown_name" : "Antibody Tests",
"ux_mode" : "choice",
"source" : [
{ "inbound" : ["Antibody", "Antibody_Tests_Related_Gene_fkey" ] },
"RID"
]
}
]
}
}
},
"tag:isrd.isi.edu,2016:visible-foreign-keys" : {
"*" : [
[ "Gene_Expression", "Specimen_Gene_Association_NCBI_GeneID_fkey" ],
{
"markdown_name" : "Array Data",
"ux_mode" : "check_presence",
"source" : [
{ "inbound" : ["Gene_Expression", "Array_Data_NCBI_GeneID_fkey" ] },
"RID"
]
"display" : {
"markdown_pattern" : ":::iframe [Microarray Data (full screen)](/deriva-webapps/heatmap/#2/Gene_Expression:Array_Data_view/NCBI_GeneID={{{NCBI_GeneID}}}){width=1230 height=800 link=/deriva-webapps/heatmap/#2/Gene_Expression:Array_Data_view/NCBI_GeneID={{{NCBI_GeneID}}}} \n:::",
"page_size" : 25
}
},
[ "Gene_Expression", "Allele_NCBI_GeneID_fkey" ],
[ "Gene_Expression", "Probe_NCBI_GeneID_fkey" ],
[ "Antibody", "Antibody_Tests_Related_Gene_fkey" ],
[ "", "Antibody_Gene_Association_NCBI_GeneID_fkey" ],
[ "Histological_Images", "HE_Slide_Gene_fkey" ],
[ "Immunofluorescence", "Slide_Gene_NCBI_GeneID_fkey" ],
[ "Cell_Line", "Mouse_Strain_NCBI_GeneID_fkey" ],
[ "Cell_Line", "Reporter_Cell_Line_Reporter_Gene_fkey" ],
[ "Cell_Line", "Reporter_cell_Line_NCBI_GeneID_fkey" ]
]
}
}
}