forked from cytoscape/cx2js-example
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathITCR Connectivity Map.cx
11 lines (11 loc) · 80.5 KB
/
ITCR Connectivity Map.cx
1
2
3
4
5
6
7
8
9
10
11
[{"numberVerification":[{"longNumber":281474976710655}]},{"metaData":[{"name":"cyVisualProperties","elementCount":6,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"nodes","elementCount":52,"idCounter":52,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"edges","elementCount":149,"idCounter":149,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"networkAttributes","elementCount":8,"idCounter":8,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"nodeAttributes","elementCount":127,"idCounter":127,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"edgeAttributes","elementCount":625,"idCounter":625,"version":"1.0","consistencyGroup":1,"properties":[]},{"name":"cartesianLayout","elementCount":52,"idCounter":53,"properties":[]},{"name":"cyTableColumn","elementCount":22,"idCounter":23,"properties":[]},{"name":"cyHiddenAttributes","elementCount":2,"idCounter":3,"properties":[]}]},
{"cyVisualProperties":[{"properties_of":"network","properties":{"NETWORK_ANNOTATION_SELECTION":"false","NETWORK_BACKGROUND_PAINT":"#FFFFFF","NETWORK_CENTER_X_LOCATION":"436.8355423734105","NETWORK_CENTER_Y_LOCATION":"-327.3485282681178","NETWORK_CENTER_Z_LOCATION":"0.0","NETWORK_DEPTH":"0.0","NETWORK_EDGE_SELECTION":"true","NETWORK_FORCE_HIGH_DETAIL":"false","NETWORK_HEIGHT":"380.0","NETWORK_NODE_LABEL_SELECTION":"false","NETWORK_NODE_SELECTION":"true","NETWORK_SCALE_FACTOR":"0.17498931497551828","NETWORK_SIZE":"550.0","NETWORK_WIDTH":"1032.0"}}, {"properties_of":"nodes:default","properties":{"COMPOUND_NODE_PADDING":"10.0","COMPOUND_NODE_SHAPE":"ROUND_RECTANGLE","NODE_BORDER_PAINT":"#666666","NODE_BORDER_STROKE":"SOLID","NODE_BORDER_TRANSPARENCY":"255","NODE_BORDER_WIDTH":"3.0","NODE_CUSTOMGRAPHICS_1":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_2":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_3":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_4":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_5":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_6":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_7":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_8":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_9":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_POSITION_1":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_2":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_3":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_4":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_5":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_6":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_7":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_8":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_9":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_SIZE_1":"50.0","NODE_CUSTOMGRAPHICS_SIZE_2":"50.0","NODE_CUSTOMGRAPHICS_SIZE_3":"50.0","NODE_CUSTOMGRAPHICS_SIZE_4":"50.0","NODE_CUSTOMGRAPHICS_SIZE_5":"50.0","NODE_CUSTOMGRAPHICS_SIZE_6":"50.0","NODE_CUSTOMGRAPHICS_SIZE_7":"50.0","NODE_CUSTOMGRAPHICS_SIZE_8":"50.0","NODE_CUSTOMGRAPHICS_SIZE_9":"50.0","NODE_CUSTOMPAINT_1":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_1, name=Node Custom Paint 1)","NODE_CUSTOMPAINT_2":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_2, name=Node Custom Paint 2)","NODE_CUSTOMPAINT_3":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_3, name=Node Custom Paint 3)","NODE_CUSTOMPAINT_4":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_4, name=Node Custom Paint 4)","NODE_CUSTOMPAINT_5":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_5, name=Node Custom Paint 5)","NODE_CUSTOMPAINT_6":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_6, name=Node Custom Paint 6)","NODE_CUSTOMPAINT_7":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_7, name=Node Custom Paint 7)","NODE_CUSTOMPAINT_8":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_8, name=Node Custom Paint 8)","NODE_CUSTOMPAINT_9":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_9, name=Node Custom Paint 9)","NODE_DEPTH":"0.0","NODE_FILL_COLOR":"#EFF0F2","NODE_HEIGHT":"110.0","NODE_LABEL_COLOR":"#000000","NODE_LABEL_FONT_FACE":"Dialog,plain,12","NODE_LABEL_FONT_SIZE":"20","NODE_LABEL_POSITION":"C,C,c,0.00,0.00","NODE_LABEL_TRANSPARENCY":"255","NODE_LABEL_WIDTH":"140.0","NODE_NESTED_NETWORK_IMAGE_VISIBLE":"true","NODE_PAINT":"#1E90FF","NODE_SELECTED":"false","NODE_SELECTED_PAINT":"#CC0033","NODE_SHAPE":"ELLIPSE","NODE_SIZE":"35.0","NODE_TRANSPARENCY":"200","NODE_VISIBLE":"true","NODE_WIDTH":"150.0","NODE_X_LOCATION":"0.0","NODE_Y_LOCATION":"0.0","NODE_Z_LOCATION":"0.0"},"dependencies":{"nodeCustomGraphicsSizeSync":"true","nodeSizeLocked":"false"},"mappings":{"NODE_HEIGHT":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=110.0,G=0=110.0,OV=0=0.0,L=1=330.0,E=1=330.0,G=1=450.0,OV=1=32.0"},"NODE_LABEL":{"type":"PASSTHROUGH","definition":"COL=name,T=string"},"NODE_LABEL_FONT_SIZE":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30,E=0=20,G=0=20,OV=0=0,L=1=60,E=1=60,G=1=1,OV=1=32"},"NODE_LABEL_WIDTH":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=140.0,G=0=140.0,OV=0=0.0,L=1=430.0,E=1=430.0,G=1=430.0,OV=1=32.0"},"NODE_WIDTH":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=150.00235145970396,G=0=150.00235145970396,OV=0=0.0,L=1=450.0,E=1=450.0,G=1=1.0,OV=1=32.0"}}}, {"properties_of":"edges:default","properties":{"EDGE_CURVED":"true","EDGE_LABEL_COLOR":"#000000","EDGE_LABEL_FONT_FACE":"Dialog,plain,10","EDGE_LABEL_FONT_SIZE":"10","EDGE_LABEL_TRANSPARENCY":"255","EDGE_LABEL_WIDTH":"200.0","EDGE_LINE_TYPE":"SOLID","EDGE_PAINT":"#323232","EDGE_SELECTED":"false","EDGE_SELECTED_PAINT":"#FFFF33","EDGE_SOURCE_ARROW_SELECTED_PAINT":"#FFFF00","EDGE_SOURCE_ARROW_SHAPE":"NONE","EDGE_SOURCE_ARROW_SIZE":"6.0","EDGE_SOURCE_ARROW_UNSELECTED_PAINT":"#000000","EDGE_STROKE_SELECTED_PAINT":"#CC0033","EDGE_STROKE_UNSELECTED_PAINT":"#848484","EDGE_TARGET_ARROW_SELECTED_PAINT":"#FFFF00","EDGE_TARGET_ARROW_SHAPE":"NONE","EDGE_TARGET_ARROW_SIZE":"6.0","EDGE_TARGET_ARROW_UNSELECTED_PAINT":"#000000","EDGE_TRANSPARENCY":"255","EDGE_UNSELECTED_PAINT":"#404040","EDGE_VISIBLE":"true","EDGE_WIDTH":"2.0"},"dependencies":{"arrowColorMatchesEdge":"true"},"mappings":{"EDGE_LINE_TYPE":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=SOLID,K=1=Proposed,V=1=EQUAL_DASH,K=2=Ongoing,V=2=SOLID"},"EDGE_STROKE_UNSELECTED_PAINT":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=#FF9900,K=1=Proposed,V=1=#666666,K=2=Ongoing,V=2=#009900"},"EDGE_UNSELECTED_PAINT":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=#FF6600,K=1=Proposed,V=1=#BDBDBD,K=2=Ongoing,V=2=#006699"},"EDGE_WIDTH":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=10.0,K=1=Proposed,V=1=3.0,K=2=Ongoing,V=2=7.0"}}}, {"properties_of":"network","properties":{"NETWORK_ANNOTATION_SELECTION":"false","NETWORK_BACKGROUND_PAINT":"#FFFFFF","NETWORK_CENTER_X_LOCATION":"436.8355423734105","NETWORK_CENTER_Y_LOCATION":"-327.3485282681178","NETWORK_CENTER_Z_LOCATION":"0.0","NETWORK_DEPTH":"0.0","NETWORK_EDGE_SELECTION":"true","NETWORK_FORCE_HIGH_DETAIL":"false","NETWORK_HEIGHT":"380.0","NETWORK_NODE_LABEL_SELECTION":"false","NETWORK_NODE_SELECTION":"true","NETWORK_SCALE_FACTOR":"0.17498931497551828","NETWORK_SIZE":"550.0","NETWORK_WIDTH":"1032.0"}}, {"properties_of":"nodes:default","properties":{"COMPOUND_NODE_PADDING":"10.0","COMPOUND_NODE_SHAPE":"ROUND_RECTANGLE","NODE_BORDER_PAINT":"#666666","NODE_BORDER_STROKE":"SOLID","NODE_BORDER_TRANSPARENCY":"255","NODE_BORDER_WIDTH":"3.0","NODE_CUSTOMGRAPHICS_1":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_2":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_3":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_4":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_5":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_6":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_7":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_8":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_9":"org.cytoscape.ding.customgraphics.NullCustomGraphics,0,[ Remove Graphics ],","NODE_CUSTOMGRAPHICS_POSITION_1":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_2":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_3":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_4":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_5":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_6":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_7":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_8":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_POSITION_9":"C,C,c,0.00,0.00","NODE_CUSTOMGRAPHICS_SIZE_1":"50.0","NODE_CUSTOMGRAPHICS_SIZE_2":"50.0","NODE_CUSTOMGRAPHICS_SIZE_3":"50.0","NODE_CUSTOMGRAPHICS_SIZE_4":"50.0","NODE_CUSTOMGRAPHICS_SIZE_5":"50.0","NODE_CUSTOMGRAPHICS_SIZE_6":"50.0","NODE_CUSTOMGRAPHICS_SIZE_7":"50.0","NODE_CUSTOMGRAPHICS_SIZE_8":"50.0","NODE_CUSTOMGRAPHICS_SIZE_9":"50.0","NODE_CUSTOMPAINT_1":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_1, name=Node Custom Paint 1)","NODE_CUSTOMPAINT_2":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_2, name=Node Custom Paint 2)","NODE_CUSTOMPAINT_3":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_3, name=Node Custom Paint 3)","NODE_CUSTOMPAINT_4":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_4, name=Node Custom Paint 4)","NODE_CUSTOMPAINT_5":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_5, name=Node Custom Paint 5)","NODE_CUSTOMPAINT_6":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_6, name=Node Custom Paint 6)","NODE_CUSTOMPAINT_7":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_7, name=Node Custom Paint 7)","NODE_CUSTOMPAINT_8":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_8, name=Node Custom Paint 8)","NODE_CUSTOMPAINT_9":"DefaultVisualizableVisualProperty(id=NODE_CUSTOMPAINT_9, name=Node Custom Paint 9)","NODE_DEPTH":"0.0","NODE_FILL_COLOR":"#EFF0F2","NODE_HEIGHT":"110.0","NODE_LABEL_COLOR":"#000000","NODE_LABEL_FONT_FACE":"Dialog,plain,12","NODE_LABEL_FONT_SIZE":"20","NODE_LABEL_POSITION":"C,C,c,0.00,0.00","NODE_LABEL_TRANSPARENCY":"255","NODE_LABEL_WIDTH":"140.0","NODE_NESTED_NETWORK_IMAGE_VISIBLE":"true","NODE_PAINT":"#1E90FF","NODE_SELECTED":"false","NODE_SELECTED_PAINT":"#CC0033","NODE_SHAPE":"ELLIPSE","NODE_SIZE":"35.0","NODE_TRANSPARENCY":"200","NODE_VISIBLE":"true","NODE_WIDTH":"150.0","NODE_X_LOCATION":"0.0","NODE_Y_LOCATION":"0.0","NODE_Z_LOCATION":"0.0"},"dependencies":{"nodeCustomGraphicsSizeSync":"true","nodeSizeLocked":"false"},"mappings":{"NODE_HEIGHT":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=110.0,G=0=110.0,OV=0=0.0,L=1=330.0,E=1=330.0,G=1=450.0,OV=1=32.0"},"NODE_LABEL":{"type":"PASSTHROUGH","definition":"COL=name,T=string"},"NODE_LABEL_FONT_SIZE":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30,E=0=20,G=0=20,OV=0=0,L=1=60,E=1=60,G=1=1,OV=1=32"},"NODE_LABEL_WIDTH":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=140.0,G=0=140.0,OV=0=0.0,L=1=430.0,E=1=430.0,G=1=430.0,OV=1=32.0"},"NODE_WIDTH":{"type":"CONTINUOUS","definition":"COL=Connectivity Score,T=integer,L=0=30.0,E=0=150.00235145970396,G=0=150.00235145970396,OV=0=0.0,L=1=450.0,E=1=450.0,G=1=1.0,OV=1=32.0"}}}, {"properties_of":"edges:default","properties":{"EDGE_CURVED":"true","EDGE_LABEL_COLOR":"#000000","EDGE_LABEL_FONT_FACE":"Dialog,plain,10","EDGE_LABEL_FONT_SIZE":"10","EDGE_LABEL_TRANSPARENCY":"255","EDGE_LABEL_WIDTH":"200.0","EDGE_LINE_TYPE":"SOLID","EDGE_PAINT":"#323232","EDGE_SELECTED":"false","EDGE_SELECTED_PAINT":"#FFFF33","EDGE_SOURCE_ARROW_SELECTED_PAINT":"#FFFF00","EDGE_SOURCE_ARROW_SHAPE":"NONE","EDGE_SOURCE_ARROW_SIZE":"6.0","EDGE_SOURCE_ARROW_UNSELECTED_PAINT":"#000000","EDGE_STROKE_SELECTED_PAINT":"#CC0033","EDGE_STROKE_UNSELECTED_PAINT":"#848484","EDGE_TARGET_ARROW_SELECTED_PAINT":"#FFFF00","EDGE_TARGET_ARROW_SHAPE":"NONE","EDGE_TARGET_ARROW_SIZE":"6.0","EDGE_TARGET_ARROW_UNSELECTED_PAINT":"#000000","EDGE_TRANSPARENCY":"255","EDGE_UNSELECTED_PAINT":"#404040","EDGE_VISIBLE":"true","EDGE_WIDTH":"2.0"},"dependencies":{"arrowColorMatchesEdge":"true"},"mappings":{"EDGE_LINE_TYPE":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=SOLID,K=1=Proposed,V=1=EQUAL_DASH,K=2=Ongoing,V=2=SOLID"},"EDGE_STROKE_UNSELECTED_PAINT":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=#FF9900,K=1=Proposed,V=1=#666666,K=2=Ongoing,V=2=#009900"},"EDGE_UNSELECTED_PAINT":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=#FF6600,K=1=Proposed,V=1=#BDBDBD,K=2=Ongoing,V=2=#006699"},"EDGE_WIDTH":{"type":"DISCRETE","definition":"COL=Status,T=string,K=0=Exists,V=0=10.0,K=1=Proposed,V=1=3.0,K=2=Ongoing,V=2=7.0"}}}]},
{"nodes":[{"@id":52,"n":"TumorDecon","r":"TumorDecon"}, {"@id":51,"n":"ML Package","r":"ML Package"}, {"@id":50,"n":"GSEA/MSigDB","r":"GSEA/MSigDB"}, {"@id":49,"n":"PiiP","r":"PiiP"}, {"@id":48,"n":"HistoQC","r":"HistoQC"}, {"@id":47,"n":"HemOnc"}, {"@id":46,"n":"DeepPhe"}, {"@id":45,"n":"DINC","r":"DINC"}, {"@id":44,"n":"Galaxy","r":"Galaxy"}, {"@id":43,"n":"CNVnator","r":"CNVnator"}, {"@id":42,"n":"CDGnet","r":"CDGnet"}, {"@id":41,"n":"LesionTracker","r":"LesionTracker"}, {"@id":40,"n":"PETCT-CoSeg","r":"PETCT-CoSeg"}, {"@id":39,"n":"CDSA","r":"CDSA"}, {"@id":38,"n":"UCSC Xena","r":"UCSC Xena"}, {"@id":37,"n":"NDEx","r":"NDEx"}, {"@id":36,"n":"FHIR ShEx","r":"FHIR ShEx"}, {"@id":35,"n":"CaPTK","r":"CaPTK"}, {"@id":34,"n":"TIES","r":"TIES"}, {"@id":33,"n":"OpenCDS","r":"OpenCDS"}, {"@id":32,"n":"QUIP","r":"QUIP"}, {"@id":30,"n":"GenePattern","r":"GenePattern"}, {"@id":29,"n":"dcmqi","r":"dcmqi"}, {"@id":28,"n":"Galaxy-P multi-omics","r":"Galaxy-P multi-omics"}, {"@id":27,"n":"cBioPortal","r":"cBioPortal"}, {"@id":26,"n":"TCIA","r":"TCIA"}, {"@id":25,"n":"3D Slicer","r":"3D Slicer"}, {"@id":24,"n":"Single Cell Genome Viewer","r":"Single Cell Genome Viewer"}, {"@id":23,"n":"IGV","r":"IGV"}, {"@id":22,"n":"Globus","r":"Globus"}, {"@id":21,"n":"Bioconductor","r":"Bioconductor"}, {"@id":20,"n":"THRIVE","r":"THRIVE"}, {"@id":19,"n":"Trinity","r":"Trinity"}, {"@id":18,"n":"JBrowse","r":"JBrowse"}, {"@id":17,"n":"OncoMX","r":"OncoMX"}, {"@id":16,"n":"TCPA","r":"TCPA"}, {"@id":15,"n":"BMEG","r":"BMEG"}, {"@id":14,"n":"OmniSearch","r":"OmniSearch"}, {"@id":13,"n":"CLAMP-Cancer","r":"CLAMP-Cancer"}, {"@id":12,"n":"SlicerDMRI","r":"SlicerDMRI"}, {"@id":11,"n":"EMERSE","r":"EMERSE"}, {"@id":10,"n":"DICOM ToolKit (DCMTK)","r":"DICOM ToolKit (DCMTK)"}, {"@id":9,"n":"OpenCRAVAT","r":"OpenCRAVAT"}, {"@id":8,"n":"GEMINI","r":"GEMINI"}, {"@id":7,"n":"NG-CHM","r":"NG-CHM"}, {"@id":6,"n":"PDX Finder","r":"PDX Finder"}, {"@id":5,"n":"RADIOMICS.io","r":"RADIOMICS.io"}, {"@id":4,"n":"C-BIBOP","r":"C-BIBOP"}, {"@id":3,"n":"SingleCellTK","r":"SingleCellTK"}, {"@id":2,"n":"CIViC","r":"CIViC"}, {"@id":1,"n":"AMARETTO","r":"AMARETTO"}, {"@id":0,"n":"XNAT","r":"XNAT"}]},
{"edges":[{"@id":155,"s":52,"t":50,"i":"Connected with"}, {"@id":154,"s":52,"t":38,"i":"Connected with"}, {"@id":153,"s":52,"t":27,"i":"Connected with"}, {"@id":135,"s":51,"t":48,"i":"Connected with with"}, {"@id":134,"s":50,"t":30,"i":"Connected with"}, {"@id":133,"s":50,"t":37,"i":"Connected with"}, {"@id":128,"s":49,"t":48,"i":"Connected with"}, {"@id":127,"s":47,"t":46,"i":"Connected with"}, {"@id":126,"s":47,"t":13,"i":"Connected with"}, {"@id":144,"s":46,"t":36,"i":"Connected with"}, {"@id":143,"s":46,"t":13,"i":"Connected with"}, {"@id":142,"s":46,"t":10,"i":"Connected with"}, {"@id":141,"s":46,"t":2,"i":"Connected with"}, {"@id":140,"s":46,"t":34,"i":"Connected with"}, {"@id":123,"s":45,"t":9,"i":"interacts with"}, {"@id":157,"s":44,"t":7,"i":"Connected with"}, {"@id":124,"s":44,"t":22,"i":"interacts with"}, {"@id":122,"s":44,"t":28,"i":"Connected with"}, {"@id":121,"s":44,"t":9,"i":"Connected with"}, {"@id":120,"s":44,"t":19,"i":"Connected with"}, {"@id":119,"s":43,"t":18,"i":"Connected with"}, {"@id":102,"s":42,"t":37,"i":"Connected with"}, {"@id":113,"s":41,"t":40,"i":"Connected with"}, {"@id":112,"s":41,"t":5,"i":"Connected with"}, {"@id":111,"s":41,"t":26,"i":"Connected with"}, {"@id":44,"s":41,"t":29,"i":"Connected with"}, {"@id":43,"s":41,"t":25,"i":"Connected with"}, {"@id":61,"s":40,"t":5,"i":"Connected with"}, {"@id":60,"s":40,"t":25,"i":"Connected with"}, {"@id":145,"s":39,"t":17,"i":"Connected with"}, {"@id":101,"s":39,"t":27,"i":"Connected with"}, {"@id":23,"s":39,"t":5,"i":"Connected with"}, {"@id":22,"s":39,"t":6,"i":"Connected with"}, {"@id":21,"s":39,"t":35,"i":"Connected with"}, {"@id":75,"s":38,"t":34,"i":"Connected with"}, {"@id":74,"s":38,"t":14,"i":"Connected with"}, {"@id":118,"s":37,"t":30,"i":"Connected with"}, {"@id":117,"s":37,"t":2,"i":"Connected with"}, {"@id":85,"s":37,"t":16,"i":"Connected with"}, {"@id":49,"s":37,"t":38,"i":"Connected with"}, {"@id":48,"s":37,"t":14,"i":"Connected with"}, {"@id":47,"s":37,"t":9,"i":"Connected with"}, {"@id":46,"s":37,"t":27,"i":"Connected with"}, {"@id":33,"s":36,"t":13,"i":"Connected with"}, {"@id":18,"s":35,"t":0,"i":"Connected with"}, {"@id":17,"s":35,"t":41,"i":"Connected with"}, {"@id":16,"s":35,"t":29,"i":"Connected with"}, {"@id":15,"s":35,"t":25,"i":"Connected with"}, {"@id":89,"s":34,"t":22,"i":"Connected with"}, {"@id":88,"s":34,"t":20,"i":"Connected with"}, {"@id":87,"s":34,"t":32,"i":"Connected with"}, {"@id":86,"s":34,"t":26,"i":"Connected with"}, {"@id":63,"s":32,"t":12,"i":"Connected with"}, {"@id":62,"s":32,"t":25,"i":"Connected with"}, {"@id":116,"s":30,"t":23,"i":"Connected with"}, {"@id":115,"s":30,"t":21,"i":"Connected with"}, {"@id":39,"s":30,"t":19,"i":"Connected with"}, {"@id":38,"s":30,"t":7,"i":"Connected with"}, {"@id":37,"s":30,"t":9,"i":"Connected with"}, {"@id":36,"s":30,"t":1,"i":"Connected with"}, {"@id":151,"s":28,"t":19,"i":"Connected with"}, {"@id":150,"s":28,"t":37,"i":"Connected with"}, {"@id":35,"s":28,"t":23,"i":"Connected with"}, {"@id":34,"s":28,"t":9,"i":"Connected with"}, {"@id":99,"s":27,"t":23,"i":"Connected with"}, {"@id":20,"s":27,"t":38,"i":"Connected with"}, {"@id":19,"s":27,"t":6,"i":"Connected with"}, {"@id":103,"s":26,"t":29,"i":"Connected with"}, {"@id":1,"s":25,"t":26,"i":"Connected with"}, {"@id":0,"s":25,"t":5,"i":"Connected with"}, {"@id":100,"s":23,"t":9,"i":"Connected with"}, {"@id":42,"s":23,"t":14,"i":"Connected with"}, {"@id":98,"s":22,"t":19,"i":"Connected with"}, {"@id":97,"s":22,"t":23,"i":"Connected with"}, {"@id":96,"s":22,"t":2,"i":"Connected with"}, {"@id":95,"s":22,"t":28,"i":"Connected with"}, {"@id":94,"s":22,"t":9,"i":"Connected with"}, {"@id":93,"s":22,"t":26,"i":"Connected with"}, {"@id":114,"s":21,"t":1,"i":"Connected with"}, {"@id":7,"s":21,"t":37,"i":"Connected with"}, {"@id":5,"s":21,"t":14,"i":"Connected with"}, {"@id":4,"s":21,"t":23,"i":"Connected with"}, {"@id":3,"s":21,"t":2,"i":"Connected with"}, {"@id":2,"s":21,"t":27,"i":"Connected with"}, {"@id":70,"s":20,"t":0,"i":"Connected with"}, {"@id":69,"s":20,"t":41,"i":"Connected with"}, {"@id":72,"s":19,"t":23,"i":"Connected with"}, {"@id":71,"s":19,"t":2,"i":"Connected with"}, {"@id":129,"s":18,"t":45,"i":"Connected with"}, {"@id":125,"s":18,"t":9,"i":"interacts with"}, {"@id":104,"s":18,"t":2,"i":"Connected with"}, {"@id":149,"s":17,"t":42,"i":"Connected with"}, {"@id":148,"s":17,"t":47,"i":"Connected with"}, {"@id":147,"s":17,"t":27,"i":"Connected with"}, {"@id":146,"s":17,"t":6,"i":"Connected with"}, {"@id":41,"s":17,"t":2,"i":"Connected with"}, {"@id":131,"s":16,"t":17,"i":"Connected with"}, {"@id":130,"s":16,"t":45,"i":"Connected with"}, {"@id":68,"s":16,"t":38,"i":"Connected with"}, {"@id":9,"s":15,"t":0,"i":"Connected with"}, {"@id":8,"s":15,"t":37,"i":"Connected with"}, {"@id":27,"s":13,"t":34,"i":"Connected with"}, {"@id":26,"s":13,"t":14,"i":"Connected with"}, {"@id":67,"s":12,"t":0,"i":"Connected with"}, {"@id":66,"s":12,"t":25,"i":"Connected with"}, {"@id":90,"s":11,"t":33,"i":"Connected with"}, {"@id":32,"s":10,"t":29,"i":"Connected with"}, {"@id":31,"s":10,"t":25,"i":"Connected with"}, {"@id":45,"s":9,"t":15,"i":"Connected with"}, {"@id":29,"s":9,"t":38,"i":"Connected with"}, {"@id":28,"s":9,"t":19,"i":"Connected with"}, {"@id":106,"s":8,"t":2,"i":"Connected with"}, {"@id":156,"s":7,"t":37,"i":"Connected with"}, {"@id":136,"s":7,"t":19,"i":"Connected with"}, {"@id":57,"s":7,"t":16,"i":"Connected with"}, {"@id":56,"s":7,"t":5,"i":"Connected with"}, {"@id":55,"s":7,"t":9,"i":"Connected with"}, {"@id":53,"s":7,"t":2,"i":"Connected with"}, {"@id":52,"s":7,"t":39,"i":"Connected with"}, {"@id":51,"s":7,"t":27,"i":"Connected with"}, {"@id":50,"s":7,"t":4,"i":"Connected with"}, {"@id":59,"s":6,"t":9,"i":"Connected with"}, {"@id":58,"s":6,"t":2,"i":"Connected with"}, {"@id":65,"s":5,"t":29,"i":"Connected with"}, {"@id":64,"s":5,"t":35,"i":"Connected with"}, {"@id":14,"s":4,"t":26,"i":"Connected with"}, {"@id":13,"s":4,"t":41,"i":"Connected with"}, {"@id":12,"s":4,"t":29,"i":"Connected with"}, {"@id":11,"s":4,"t":35,"i":"Connected with"}, {"@id":10,"s":4,"t":25,"i":"Connected with"}, {"@id":132,"s":3,"t":17,"i":"Connected with"}, {"@id":110,"s":3,"t":21,"i":"Connected with"}, {"@id":109,"s":3,"t":30,"i":"Connected with"}, {"@id":108,"s":3,"t":27,"i":"Connected with"}, {"@id":107,"s":3,"t":24,"i":"Connected with"}, {"@id":152,"s":2,"t":47,"i":"Connected with"}, {"@id":84,"s":2,"t":13,"i":"Connected with"}, {"@id":83,"s":2,"t":14,"i":"Connected with"}, {"@id":82,"s":2,"t":34,"i":"Connected with"}, {"@id":81,"s":2,"t":27,"i":"Connected with"}, {"@id":25,"s":2,"t":9,"i":"Connected with"}, {"@id":24,"s":2,"t":23,"i":"Connected with"}, {"@id":139,"s":1,"t":19,"i":"Connected with"}, {"@id":138,"s":1,"t":37,"i":"Connected with"}, {"@id":137,"s":1,"t":7,"i":"Connected with"}, {"@id":80,"s":0,"t":41,"i":"Connected with"}, {"@id":79,"s":0,"t":10,"i":"Connected with"}, {"@id":78,"s":0,"t":29,"i":"Connected with"}, {"@id":76,"s":0,"t":25,"i":"Connected with"}]},
{"networkAttributes":[{"n":"rightsHolder","v":"aaa"}, {"n":"author","v":"Rudolf T. Pillich, PhD"}, {"n":"rights","v":"Waiver-No rights reserved (CC0)"}, {"n":"name","v":"ITCR Connectivity Map"}, {"n":"description","v":"<h5>This network shows the interactions between projects funded under the <a href=\"https://itcr.cancer.gov/\" target=\"\" style=\"font-weight: bold;\">Informatics Technology for Cancer Research</a><b> </b>(ITCR) program and the bioinformatic tools they create. Edges in the graph can be selected to show information about tools integration,the status of the collaboration and "Evidence" of its output.</h5><pre><b>Edge Color legend</b><br/>Orange solid: Existing connections<br/>Blue solid: Ongoing connections<br/>Grey dashed: Proposed connections<br/>Selected items: Dark red</pre><p></p>"}, {"n":"networkType","v":"Connectivity Map"}, {"n":"version","v":"07-May-2020"}, {"n":"labels","v":"NIH, NCI, ITCR"}]},
{"nodeAttributes":[{"po":52,"n":"Resource Website","v":"https://sites.google.com/site/leilishahriyari/tumordecon"}, {"po":52,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":52,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":51,"n":"Resource Website","v":"https://cancertech.cs.washington.edu/"}, {"po":51,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":51,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":50,"n":"Resource Website","v":"http://gsea-msigdb.org"}, {"po":50,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":50,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":49,"n":"Resource Website","v":"http://pathiip.org"}, {"po":49,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":49,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":48,"n":"Resource Website","v":"https://github.com/choosehappy/HistoQC"}, {"po":48,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":48,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":47,"n":"Resource Website","v":"https://hemonc.org/wiki/Ontology"}, {"po":47,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":47,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":46,"n":"Resource Website","v":"https://github.com/DeepPhe/DeepPhe-Release"}, {"po":46,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":46,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":45,"n":"Resource Website","v":"http://dinc.kavrakilab.org/"}, {"po":45,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":45,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":44,"n":"Resource Website","v":"https://galaxyproject.org/"}, {"po":44,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":44,"n":"Connectivity Score","v":"15","d":"integer"}, {"po":43,"n":"Resource Website","v":"https://github.com/abyzovlab/CNVnator"}, {"po":43,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":43,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":42,"n":"Resource Website","v":"http://epiviz.cbcb.umd.edu/shiny/CDGnet/"}, {"po":42,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":42,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":41,"n":"Connectivity Score","v":"14","d":"integer"}, {"po":41,"n":"Connectivity Score","v":"14","d":"integer"}, {"po":40,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":40,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":39,"n":"Resource Website","v":"https://cancer.digitalslidearchive.org/"}, {"po":39,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":39,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":38,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":38,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":37,"n":"Resource Website","v":"http://www.ndexbio.org"}, {"po":37,"n":"Connectivity Score","v":"14","d":"integer"}, {"po":37,"n":"Connectivity Score","v":"14","d":"integer"}, {"po":36,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":36,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":35,"n":"Connectivity Score","v":"2","d":"integer"}, {"po":35,"n":"Connectivity Score","v":"2","d":"integer"}, {"po":34,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":34,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":33,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":33,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":32,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":32,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":30,"n":"Resource Website","v":"http://genepattern.org"}, {"po":30,"n":"Connectivity Score","v":"19","d":"integer"}, {"po":30,"n":"Connectivity Score","v":"20","d":"integer"}, {"po":29,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":29,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":28,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":28,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":27,"n":"Connectivity Score","v":"11","d":"integer"}, {"po":27,"n":"Connectivity Score","v":"11","d":"integer"}, {"po":26,"n":"Connectivity Score","v":"10","d":"integer"}, {"po":26,"n":"Connectivity Score","v":"10","d":"integer"}, {"po":25,"n":"Connectivity Score","v":"22","d":"integer"}, {"po":25,"n":"Connectivity Score","v":"22","d":"integer"}, {"po":24,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":24,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":23,"n":"Connectivity Score","v":"15","d":"integer"}, {"po":23,"n":"Connectivity Score","v":"15","d":"integer"}, {"po":22,"n":"Resource Website","v":"https://www.globus.org"}, {"po":22,"n":"Connectivity Score","v":"15","d":"integer"}, {"po":22,"n":"Connectivity Score","v":"15","d":"integer"}, {"po":21,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":21,"n":"Connectivity Score","v":"12","d":"integer"}, {"po":20,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":20,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":19,"n":"Resource Website","v":"https://github.com/NCIP/Trinity_CTAT/wiki"}, {"po":19,"n":"Connectivity Score","v":"16","d":"integer"}, {"po":19,"n":"Connectivity Score","v":"16","d":"integer"}, {"po":18,"n":"Resource Website","v":"https://jbrowse.org"}, {"po":18,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":18,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":17,"n":"Resource Website","v":"https://www.oncomx.org/"}, {"po":17,"n":"Connectivity Score","v":"17","d":"integer"}, {"po":17,"n":"Connectivity Score","v":"17","d":"integer"}, {"po":16,"n":"Resource Website","v":"https://tcpaportal.org/tcpa/my_protein.html"}, {"po":16,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":16,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":15,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":15,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":14,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":14,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":13,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":13,"n":"Connectivity Score","v":"0","d":"integer"}, {"po":12,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":12,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":11,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":11,"n":"Connectivity Score","v":"1","d":"integer"}, {"po":10,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":10,"n":"Connectivity Score","v":"7","d":"integer"}, {"po":9,"n":"Resource Website","v":"https://opencravat.org"}, {"po":9,"n":"Connectivity Score","v":"27","d":"integer"}, {"po":9,"n":"Connectivity Score","v":"27","d":"integer"}, {"po":8,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":8,"n":"Connectivity Score","v":"3","d":"integer"}, {"po":7,"n":"Resource Website","v":"http://www.ngchm.net/"}, {"po":7,"n":"Connectivity Score","v":"19","d":"integer"}, {"po":7,"n":"Connectivity Score","v":"23","d":"integer"}, {"po":6,"n":"Resource Website","v":"http://www.pdxfinder.org"}, {"po":6,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":6,"n":"Connectivity Score","v":"5","d":"integer"}, {"po":5,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":5,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":4,"n":"Connectivity Score","v":"8","d":"integer"}, {"po":4,"n":"Connectivity Score","v":"8","d":"integer"}, {"po":3,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":3,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":2,"n":"Connectivity Score","v":"29","d":"integer"}, {"po":2,"n":"Connectivity Score","v":"29","d":"integer"}, {"po":1,"n":"Resource Website","v":"http://portals.broadinstitute.org/pochetlab/amaretto.html"}, {"po":1,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":1,"n":"Connectivity Score","v":"6","d":"integer"}, {"po":0,"n":"Connectivity Score","v":"4","d":"integer"}, {"po":0,"n":"Connectivity Score","v":"4","d":"integer"}]},
{"edgeAttributes":[{"po":155,"n":"Status","v":"Ongoing"}, {"po":155,"n":"Suggested By","v":"Leili Shahriyari"}, {"po":155,"n":"name","v":"TumorDecon (Connected with) GSEA/MSigDB"}, {"po":155,"n":"Why?","v":"Tumors consist of many different cell types, including various immune cells, fibroblasts and epithelial cells, and each tumor has its own unique variation of immune cells resulting in different responses to the same treatments. TumorDecon software includes several deconvolution methods and signature matrixes of various cell types. The input of this software is the gene expression profile of the tumor, and the output is the relative number of each cell type"}, {"po":154,"n":"Status","v":"Ongoing"}, {"po":154,"n":"Suggested By","v":"Leili Shahriyari"}, {"po":154,"n":"name","v":"TumorDecon (Connected with) UCSC Xena"}, {"po":154,"n":"Why?","v":"Tumors consist of many different cell types, including various immune cells, fibroblasts and epithelial cells, and each tumor has its own unique variation of immune cells resulting in different responses to the same treatments. TumorDecon software includes several deconvolution methods and signature matrixes of various cell types. The input of this software is the gene expression profile of the tumor, and the output is the relative number of each cell type"}, {"po":153,"n":"Status","v":"Ongoing"}, {"po":153,"n":"Suggested By","v":"Leili Shahriyari"}, {"po":153,"n":"name","v":"TumorDecon (Connected with) cBioPortal"}, {"po":153,"n":"Why?","v":"Tumors consist of many different cell types, including various immune cells, fibroblasts and epithelial cells, and each tumor has its own unique variation of immune cells resulting in different responses to the same treatments. TumorDecon software includes several deconvolution methods and signature matrixes of various cell types. The input of this software is the gene expression profile of the tumor, and the output is the relative number of each cell type"}, {"po":135,"n":"Status","v":"Proposed"}, {"po":135,"n":"Suggested By","v":"Linda Shapiro, Anant Madabhushi, Andrew Janowczyk"}, {"po":135,"n":"name","v":"ML Package (Connected with with) HistoQC"}, {"po":135,"n":"Why?","v":"HistoQC will supply quality control information and image metrics to the ML Package, enabling more robust performance of their downstream analytical tools and pipelines."}, {"po":134,"n":"Status","v":"Exists"}, {"po":134,"n":"Suggested By","v":"Helga Thorsvaldottir"}, {"po":134,"n":"name","v":"GSEA/MSigDB (Connected with) GenePattern"}, {"po":134,"n":"Evidence","v":"GSEA is one of the analyses included with GenePattern"}, {"po":133,"n":"Status","v":"Ongoing"}, {"po":133,"n":"Suggested By","v":"Dexter Pratt"}, {"po":133,"n":"name","v":"GSEA/MSigDB (Connected with) NDEx"}, {"po":133,"n":"Why?","v":"The NDEx and MSigDB projects are collaborating to integrate their two resources, enabling NDEx users to find gene sets relevant to their networks and vice versa, for MSigDB users to find networks relevant to their gene sets."}, {"po":128,"n":"Status","v":"Proposed"}, {"po":128,"n":"Suggested By","v":"Andrew Janowczyk, Anant Madabhushi"}, {"po":128,"n":"name","v":"PiiP (Connected with) HistoQC"}, {"po":128,"n":"Why?","v":"HistoQC will supply quality control information and image metrics to the PiiP project, enabling more robust performance of Piip's analytical tools and pipelines"}, {"po":127,"n":"Status","v":"Exists"}, {"po":127,"n":"Suggested By","v":"Jeremy Warner"}, {"po":127,"n":"name","v":"HemOnc (Connected with) DeepPhe"}, {"po":127,"n":"Evidence","v":"https://github.com/DeepPhe/DeepPhe-Release/blob/master/LICENSE"}, {"po":127,"n":"Why?","v":"To add to the existing ontologies and enable identification of chemotherapy regimens."}, {"po":126,"n":"Status","v":"Proposed"}, {"po":126,"n":"Suggested By","v":"Jeremy Warner"}, {"po":126,"n":"name","v":"HemOnc (Connected with) CLAMP-Cancer"}, {"po":126,"n":"Why?","v":"To add to the existing ontologies and enable identification of chemotherapy regimens."}, {"po":144,"n":"Status","v":"Ongoing"}, {"po":144,"n":"Suggested By","v":"Guergana Savova and Guoqioan Jiang"}, {"po":144,"n":"name","v":"DeepPhe (Connected with) FHIR ShEx"}, {"po":144,"n":"Why?","v":"To integrate FHIR-based data model validation in DeepPhe"}, {"po":143,"n":"Status","v":"Proposed"}, {"po":143,"n":"Suggested By","v":"Guergana Savova and Hua Xu"}, {"po":143,"n":"name","v":"DeepPhe (Connected with) CLAMP-Cancer"}, {"po":143,"n":"Why?","v":"To take advantage of the NLP components in each tool"}, {"po":142,"n":"Status","v":"Ongoing"}, {"po":142,"n":"Suggested By","v":"Guergana Savova and Andrey Fedorov"}, {"po":142,"n":"name","v":"DeepPhe (Connected with) DICOM ToolKit (DCMTK)"}, {"po":142,"n":"Why?","v":"To integrate DeepPhe extraction from radiology reports"}, {"po":141,"n":"Status","v":"Ongoing"}, {"po":141,"n":"Suggested By","v":"Guergana Savova and Obi Griffith"}, {"po":141,"n":"name","v":"DeepPhe (Connected with) CIViC"}, {"po":141,"n":"Why?","v":"To incorporate CIViC's knowledge base for clinical interpretations of mutations related to cancer in DeepPhe"}, {"po":140,"n":"Status","v":"Proposed"}, {"po":140,"n":"Suggested By","v":"Guergana Savova and Michael Becich"}, {"po":140,"n":"name","v":"DeepPhe (Connected with) TIES"}, {"po":140,"n":"Why?","v":"To take advantage of the NLP components in each tool"}, {"po":123,"n":"Status","v":"Proposed"}, {"po":123,"n":"Suggested By","v":"Dinler Antunes/Kavraki Lab"}, {"po":123,"n":"name","v":"DINC (interacts with) CRAVAT"}, {"po":123,"n":"Why?","v":"CRAVAT allows to analyze gene mutations, providing annotations and visualization resources to locate and characterize new mutations in the context of previously described variants. One of the visualization tools available in CRAVAT is MuPIT, a 3D structure viewer that shows the position of the mutation in the structure of the affected protein (in the cases a structure is available on the Protein Data Bank). Many mutations are located in known binding sites for drugs and peptidomimetic inhibitors, and the user might wonder how these mutations would affect the binding of these ligands of interest. DINC is a parallelized meta-docking tool that can quickly predict the binding mode of a receptor-ligand complex, providing an estimated biding affinity. A connection between CRAVAT and DINC, or more specifically, between MuPIT and DINC, could allow the user of CRAVAT to not only visualize the location of the mutations of interest, but also to trigger docking jobs on DINC to compare the binding of a drug of interest to the mutated protein versus the wild-type, for instance. Or to compare the impact of different mutations on the binding of a given inhibitor. Or to screen different inhibitors and find the one that is more likely to bind to the mutated protein. We can also discuss interactions on the reverse direction. After submitting a regular docking job to DINC, the user could be given the option to search on CRAVAT if the predicted binding residues are known sites of mutation, and maybe select other variants that would be of interest for his docking experiment."}, {"po":157,"n":"Status","v":"Exists"}, {"po":157,"n":"Suggested By","v":"Bradley Broom"}, {"po":157,"n":"name","v":"Galaxy (Connected with) NG-CHM"}, {"po":157,"n":"Evidence","v":"https://www.ncbi.nlm.nih.gov/pubmed/29092932"}, {"po":157,"n":"Why?","v":"To enable NG-CHMs to be created within a Galaxy workflow"}, {"po":124,"n":"Status","v":"Exists"}, {"po":124,"n":"Suggested By","v":"Brigitte Raumann"}, {"po":124,"n":"name","v":"Galaxy (interacts with) Globus"}, {"po":124,"n":"Evidence","v":"https://www.globusgenomics.org/genomics/"}, {"po":124,"n":"Why?","v":"Globus Genomic is an genomics analysis platform that integrates the data management provided by Globus, an extensible analysis environment provided by Galaxy, and compute and storage capabilities powered by Amazon Web Services."}, {"po":122,"n":"Status","v":"Exists"}, {"po":122,"n":"Suggested By","v":"Jeremy Goecks"}, {"po":122,"n":"name","v":"Galaxy (Connected with) Galaxy-P multi-omics"}, {"po":122,"n":"Evidence","v":"http://galaxyp.org"}, {"po":122,"n":"Why?","v":"Galaxy-P multi-omics builds on the Galaxy platform"}, {"po":121,"n":"Status","v":"Exists"}, {"po":121,"n":"Suggested By","v":"Jeremy Goecks"}, {"po":121,"n":"name","v":"Galaxy (Connected with) CRAVAT"}, {"po":121,"n":"Evidence","v":"https://toolshed.g2.bx.psu.edu"}, {"po":121,"n":"Why?","v":"CRAVAT can be run in Galaxy"}, {"po":120,"n":"Status","v":"Exists"}, {"po":120,"n":"Suggested By","v":"Jeremy Goecks"}, {"po":120,"n":"name","v":"Galaxy (Connected with) Trinity"}, {"po":120,"n":"Evidence","v":"https://toolshed.g2.bx.psu.edu"}, {"po":120,"n":"Why?","v":"Trinity tools can be run in Galaxy"}, {"po":119,"n":"Status","v":"Proposed"}, {"po":119,"n":"Suggested By","v":"Alexej Abyzov"}, {"po":119,"n":"name","v":"CNVnator (Connected with) JBrowse"}, {"po":119,"n":"Why?","v":"To visualize CNV in the context of other data; on-the-fly segmentation."}, {"po":102,"n":"Status","v":"Ongoing"}, {"po":102,"n":"Suggested By","v":"Rudi Pillich, Dexter Pratt, Simina Boca"}, {"po":102,"n":"name","v":"CDGnet (Connected with) NDEx"}, {"po":102,"n":"Evidence","v":"http://ndexbio.org/#/user/f3b50e1f-b855-11e8-9520-0ac135e8bacf"}, {"po":102,"n":"Why?","v":"Integrate networks developed in CDGnet with those in NDEx, perform normalization and standardization"}, {"po":113,"n":"Status","v":"Proposed"}, {"po":113,"n":"Suggested By","v":"Gordon Harris"}, {"po":113,"n":"name","v":"LesionTracker (Connected with) PETCT-CoSeg"}, {"po":113,"n":"Why?","v":"Integrate PETCT-CoSeg segmentation algorithms into LesionTracker client-side packages or wrap as server-side services"}, {"po":112,"n":"Status","v":"Proposed"}, {"po":112,"n":"Suggested By","v":"Gordon Harris"}, {"po":112,"n":"name","v":"LesionTracker (Connected with) RADIOMICS.io"}, {"po":112,"n":"Why?","v":"Integrate Radiomics feature calculators into LesionTracker client-side packages"}, {"po":111,"n":"Status","v":"Exists"}, {"po":111,"n":"Suggested By","v":"Gordon Harris"}, {"po":111,"n":"name","v":"LesionTracker (Connected with) TCIA"}, {"po":111,"n":"Evidence","v":"www.crowds-cure.org"}, {"po":111,"n":"Why?","v":"Deploy LesionTracker-based web viewer to view / crowdsource annotations on TCIA datasets"}, {"po":44,"n":"Status","v":"Exists"}, {"po":44,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":44,"n":"name","v":"LesionTracker (Connected with) dcmqi"}, {"po":44,"n":"Why?","v":"Provide capability to use LesionTracker to visualize image analysis results converted into standardized DICOM representation using dcmci."}, {"po":43,"n":"Status","v":"Exists"}, {"po":43,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":43,"n":"name","v":"LesionTracker (Connected with) 3D Slicer"}, {"po":43,"n":"Evidence","v":"https://dicom4qi.readthedocs.io/en/latest/"}, {"po":43,"n":"Why?","v":"Integrate analysis tools implemented in 3D Slicer server-side with the visualization and annotation tools implemented in OHIF LesionTracker"}, {"po":61,"n":"Status","v":"Proposed"}, {"po":61,"n":"Suggested By","v":"Xiaodong Wu"}, {"po":61,"n":"name","v":"PETCT-CoSeg (Connected with) RADIOMICS.io"}, {"po":61,"n":"Why?","v":"Integrate to the radiomics tools to facilate the use of both PET and CT"}, {"po":60,"n":"Status","v":"Exists"}, {"po":60,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":60,"n":"name","v":"PETCT-CoSeg (Connected with) 3D Slicer"}, {"po":60,"n":"Why?","v":"Collection of 3D Slicer extensions for quantitative analysis of PET-CT data"}, {"po":145,"n":"Status","v":"Ongoing"}, {"po":145,"n":"Suggested By","v":"Raja Mazumder"}, {"po":145,"n":"name","v":"CDSA (interacts with) OncoMX"}, {"po":145,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":145,"n":"Why?","v":"Cross referencing digital imaging data from TCGA cancers using gene symbols"}, {"po":101,"n":"Status","v":"Exists"}, {"po":101,"n":"Suggested By","v":"JJ Gao"}, {"po":101,"n":"name","v":"CDSA (Connected with) cBioPortal"}, {"po":101,"n":"Why?","v":"Visualize TCGA cancer slides in the cBioPortal using CDSA"}, {"po":23,"n":"Status","v":"Proposed"}, {"po":23,"n":"Suggested By","v":"Gutman/Cooper"}, {"po":23,"n":"name","v":"CDSA (Connected with) RADIOMICS.io"}, {"po":23,"n":"Why?","v":"Common python image feature set"}, {"po":22,"n":"Status","v":"Proposed"}, {"po":22,"n":"Suggested By","v":"Gutman/Cooper"}, {"po":22,"n":"name","v":"CDSA (Connected with) PDX Finder"}, {"po":22,"n":"Why?","v":"Mouse phenotype histology portal"}, {"po":21,"n":"Status","v":"Proposed"}, {"po":21,"n":"Suggested By","v":"Gutman/Cooper"}, {"po":21,"n":"name","v":"CDSA (Connected with) CaPTK"}, {"po":21,"n":"Why?","v":"Common python image feature set"}, {"po":75,"n":"Status","v":"Ongoing"}, {"po":75,"n":"Suggested By","v":"Juli Klemm"}, {"po":75,"n":"name","v":"UCSC Xena (Connected with) TIES"}, {"po":75,"n":"Why?","v":"Integrate TIES's NLP-based clinical data search with the Xena browser allowing Xena users to use clinical report text to search for samples and genomic results."}, {"po":74,"n":"Status","v":"Proposed"}, {"po":74,"n":"Suggested By","v":"Jingshan Huang"}, {"po":74,"n":"name","v":"UCSC Xena (Connected with) OmniSearch"}, {"po":74,"n":"Why?","v":"TCGA and GTEx data provided by Xena Data Store"}, {"po":118,"n":"Status","v":"Ongoing"}, {"po":118,"n":"Suggested By","v":"Dexter Pratt, Michael Reich"}, {"po":118,"n":"name","v":"NDEx (Connected with) GenePattern"}, {"po":118,"n":"Why?","v":"To enable enrichment analysis on NDEx networks using MSig DB signature gene lists and Gene Pattern Notebooks. We have implemented connectivity allowing users of GenePattern Notebook to query NDEx, retrieve resulting networks, and write networks back to NDEx, from within a notebook."}, {"po":117,"n":"Status","v":"Exists"}, {"po":117,"n":"Suggested By","v":"Rudi Pillich"}, {"po":117,"n":"name","v":"NDEx (Connected with) CIViC"}, {"po":117,"n":"Evidence","v":"http://www.ndexbio.org/#/user/77520e6b-816b-11e8-a4bf-0ac135e8bacf"}, {"po":117,"n":"Why?","v":"To integrate publication and distribution via NDEx in the CIViC data release process"}, {"po":85,"n":"Status","v":"Ongoing"}, {"po":85,"n":"Suggested By","v":"Rudi Pillich"}, {"po":85,"n":"name","v":"NDEx (Connected with) TCPA"}, {"po":85,"n":"Why?","v":"Enable integration of TCPA protein co-expression network outputs with existing reference networks (PPI, drug-target interaction, gene-pathway or gene-disease association, etc.) through the development of a network normalization schema."}, {"po":49,"n":"Status","v":"Proposed"}, {"po":49,"n":"Suggested By","v":"Jingchun Zhu"}, {"po":49,"n":"name","v":"NDEx (Connected with) UCSC Xena"}, {"po":49,"n":"Why?","v":"Display genomics data in the context of biological pathways"}, {"po":48,"n":"Status","v":"Proposed"}, {"po":48,"n":"Suggested By","v":"Jingshan Huang"}, {"po":48,"n":"name","v":"NDEx (Connected with) OmniSearch"}, {"po":48,"n":"Why?","v":"Identified candidate networks for ncRNAs under investigation"}, {"po":47,"n":"Status","v":"Exists"}, {"po":47,"n":"Suggested By","v":"Dexter Pratt"}, {"po":47,"n":"name","v":"NDEx (Connected with) CRAVAT"}, {"po":47,"n":"Why?","v":"NDEx has been incorporated into the CRAVAT application as a source of networks for pathway enrichment analysis of variants."}, {"po":46,"n":"Status","v":"Proposed"}, {"po":46,"n":"Suggested By","v":"Dexter Pratt"}, {"po":46,"n":"name","v":"NDEx (Connected with) cBioPortal"}, {"po":46,"n":"Why?","v":"Annotate network nodes with alteration data from cBioPortal"}, {"po":33,"n":"Status","v":"Proposed"}, {"po":33,"n":"Suggested By","v":"Guoqian Jiang"}, {"po":33,"n":"name","v":"FHIR ShEx (Connected with) CLAMP-Cancer"}, {"po":33,"n":"Why?","v":"Integrating FHIR-based data model validation into the CLAMP pipeline"}, {"po":18,"n":"Status","v":"Proposed"}, {"po":18,"n":"Suggested By","v":"Christos Davatzikos"}, {"po":18,"n":"name","v":"CaPTK (Connected with) XNAT"}, {"po":18,"n":"Why?","v":"Integrate CaPTk pipelines into XNAT workflows"}, {"po":17,"n":"Status","v":"Proposed"}, {"po":17,"n":"Suggested By","v":"Christos Davatzikos"}, {"po":17,"n":"name","v":"CaPTK (Connected with) LesionTracker"}, {"po":17,"n":"Why?","v":"Integrate segmentation and radiomic features of CaPTk into LesionTracker"}, {"po":16,"n":"Status","v":"Ongoing"}, {"po":16,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":16,"n":"name","v":"CaPTK (Connected with) dcmqi"}, {"po":16,"n":"Why?","v":"Conversion of the analysis results into structured and standardized format"}, {"po":15,"n":"Status","v":"Ongoing"}, {"po":15,"n":"Suggested By","v":"Christos Davatzikos"}, {"po":15,"n":"name","v":"CaPTK (Connected with) 3D Slicer"}, {"po":15,"n":"Why?","v":"Make CaPTk functionality available as Slicer Plugin"}, {"po":89,"n":"Status","v":"Exists"}, {"po":89,"n":"Suggested By","v":"Michael J. Becich"}, {"po":89,"n":"name","v":"TIES (Connected with) Globus"}, {"po":89,"n":"Why?","v":"Move from Globus Toolkit to Globus Auth for federated ID management"}, {"po":88,"n":"Status","v":"Proposed"}, {"po":88,"n":"Suggested By","v":"Michael J. Becich"}, {"po":88,"n":"name","v":"TIES (Connected with) THRIVE"}, {"po":88,"n":"Why?","v":"Automated spatial annotation of histopathoogic images for cancer research image discovery"}, {"po":87,"n":"Status","v":"Proposed"}, {"po":87,"n":"Suggested By","v":"Michael J. Becich"}, {"po":87,"n":"name","v":"TIES (Connected with) QUIP"}, {"po":87,"n":"Why?","v":"Automated cell level annotation of histopathoogic images for cancer research image discovery"}, {"po":86,"n":"Status","v":"Proposed"}, {"po":86,"n":"Suggested By","v":"Michael J. Becich"}, {"po":86,"n":"name","v":"TIES (Connected with) TCIA"}, {"po":86,"n":"Why?","v":"Enable histopathologic images to be shared along with radiology images for cancer research"}, {"po":63,"n":"Status","v":"Proposed"}, {"po":63,"n":"Suggested By","v":"Lauren O'Donnell"}, {"po":63,"n":"name","v":"QUIP (Connected with) SlicerDMRI"}, {"po":63,"n":"Why?","v":"Evaluate dMRI microstructure measures vs stereotactic samples from neurosurgery"}, {"po":62,"n":"Status","v":"Ongoing"}, {"po":62,"n":"Suggested By","v":"Joel Saltz"}, {"po":62,"n":"name","v":"QUIP (Connected with) 3D Slicer"}, {"po":62,"n":"Why?","v":"Pathology ground truth, 3D Pathology segmentation"}, {"po":116,"n":"Status","v":"Exists"}, {"po":116,"n":"Suggested By","v":"Michael Reich"}, {"po":116,"n":"name","v":"GenePattern (Connected with) IGV"}, {"po":116,"n":"Why?","v":"Visualize the results of RNA-seq, sequence variation, or epigenetic analyses"}, {"po":115,"n":"Status","v":"Exists"}, {"po":115,"n":"Suggested By","v":"Michael Reich"}, {"po":115,"n":"name","v":"GenePattern (Connected with) Bioconductor"}, {"po":115,"n":"Why?","v":"Access genomic analyses within a non-programming interface"}, {"po":39,"n":"Status","v":"Exists"}, {"po":39,"n":"Suggested By","v":"Michael Reich"}, {"po":39,"n":"name","v":"GenePattern (Connected with) Trinity"}, {"po":39,"n":"Why?","v":"Perform de novo transcriptome reconstruction as part of an analysis workflow"}, {"po":38,"n":"Status","v":"Ongoing"}, {"po":38,"n":"Suggested By","v":"Michael Reich"}, {"po":38,"n":"name","v":"GenePattern (Connected with) NG-CHM"}, {"po":38,"n":"Why?","v":"Enable sophisticated visualization and manipulation of heatmaps as steps within online analytical notebooks"}, {"po":37,"n":"Status","v":"Exists"}, {"po":37,"n":"Suggested By","v":"Michael Reich"}, {"po":37,"n":"name","v":"GenePattern (Connected with) OpenCRAVAT"}, {"po":37,"n":"Evidence","v":"https://genepattern.github.io/OpenCRAVAT/"}, {"po":37,"n":"Why?","v":"Embed 3D visualizations within interactive genomics analysis notebooks"}, {"po":36,"n":"Status","v":"Exists"}, {"po":36,"n":"Suggested By","v":"Nathalie Pochet, Michael Reich"}, {"po":36,"n":"name","v":"GenePattern (Connected with) AMARETTO"}, {"po":36,"n":"Evidence","v":"https://notebook.genepattern.org/services/sharing/notebooks/334/preview/"}, {"po":36,"n":"Why?","v":"Analytic modules in GenePattern to infer & benchmark regulatory networks (virus-induced cancer). We have created a GenePattern module and notebook implementing the AMARETTO multi-omics analysis method and are in the process of distributing it publicly"}, {"po":151,"n":"Status","v":"Proposed"}, {"po":151,"n":"Suggested By","v":"Tim Griffin"}, {"po":151,"n":"name","v":"Galaxy-P multi-omics (Connected with) Trinity"}, {"po":151,"n":"Why?","v":"Seeking to integrate non-reference based assembly methods of RNA-Seq data to increase depth of proteogenomic identification of protein sequence variants from cancer samples"}, {"po":150,"n":"Status","v":"Proposed"}, {"po":150,"n":"Suggested By","v":"Tim Griffin"}, {"po":150,"n":"name","v":"Galaxy-P multi-omics (Connected with) NDEx"}, {"po":150,"n":"Why?","v":"Seeking to extend visualization tools for identified protein sequence variants to directly query NDEx and display known networks for these proteins"}, {"po":35,"n":"Status","v":"Exists"}, {"po":35,"n":"Suggested By","v":"Tim Griffin / Pratik Jagtap"}, {"po":35,"n":"name","v":"Galaxy-P multi-omics (Connected with) IGV"}, {"po":35,"n":"Why?","v":"For visualization of known and novel proteoform-specific peptides on the genome"}, {"po":34,"n":"Status","v":"Exists"}, {"po":34,"n":"Suggested By","v":"Tim Griffin / Pratik Jagtap"}, {"po":34,"n":"name","v":"Galaxy-P multi-omics (Connected with) CRAVAT"}, {"po":34,"n":"Why?","v":"Single variant annotation page. Single variant query"}, {"po":99,"n":"Status","v":"Ongoing"}, {"po":99,"n":"Suggested By","v":"Helga Thorvaldsdottir"}, {"po":99,"n":"name","v":"cBioPortal (Connected with) IGV"}, {"po":99,"n":"Why?","v":"View genomic data in igv.js embedded in the cBioPortal"}, {"po":20,"n":"Status","v":"Proposed"}, {"po":20,"n":"Suggested By","v":"JJ Gao"}, {"po":20,"n":"name","v":"cBioPortal (Connected with) UCSC Xena"}, {"po":20,"n":"Why?","v":"Co-develop Javascript lib for survival analysis"}, {"po":19,"n":"Status","v":"Proposed"}, {"po":19,"n":"Suggested By","v":"JJ Gao"}, {"po":19,"n":"name","v":"cBioPortal (Connected with) PDX Finder"}, {"po":19,"n":"Why?","v":"Cross-linking the PDX samples in the two resources"}, {"po":103,"n":"Status","v":"Exists"}, {"po":103,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":103,"n":"name","v":"TCIA (Connected with) dcmqi"}, {"po":103,"n":"Why?","v":"Conversion of the analysis results into structured and standardized format"}, {"po":1,"n":"Status","v":"Ongoing"}, {"po":1,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":1,"n":"name","v":"3D Slicer (Connected with) TCIA"}, {"po":1,"n":"Why?","v":"Use 3D Slicer as an interface to access TCIA-hosted data"}, {"po":0,"n":"Status","v":"Exists"}, {"po":0,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":0,"n":"name","v":"3D Slicer (Connected with) RADIOMICS.io"}, {"po":0,"n":"Why?","v":"Interactive interface to the command-line/batch processing tools"}, {"po":100,"n":"Status","v":"Ongoing"}, {"po":100,"n":"Suggested By","v":"Helga Thorvaldsdottir"}, {"po":100,"n":"name","v":"IGV (Connected with) CRAVAT"}, {"po":100,"n":"Why?","v":"Add to IGV the ability to directly link to the analysis and annotation capabilities of CRAVAT and the visualization capabilities of MuPIT"}, {"po":42,"n":"Status","v":"Proposed"}, {"po":42,"n":"Suggested By","v":"Jingshan Huang"}, {"po":42,"n":"name","v":"IGV (Connected with) OmniSearch"}, {"po":42,"n":"Why?","v":"IGV genomics viewer for OmniSearch search and analysis results"}, {"po":98,"n":"Status","v":"Exists"}, {"po":98,"n":"Suggested By","v":"Ravi Madduri"}, {"po":98,"n":"name","v":"Globus (Connected with) Trinity"}, {"po":98,"n":"Evidence","v":"https://dev.globusgenomics.org"}, {"po":98,"n":"Why?","v":"Integration of Trinity with Globus Genomics"}, {"po":97,"n":"Status","v":"Exists"}, {"po":97,"n":"Suggested By","v":"Ravi Madduri"}, {"po":97,"n":"name","v":"Globus (Connected with) IGV"}, {"po":97,"n":"Evidence","v":"https://dev.globusgenomics.org"}, {"po":97,"n":"Why?","v":"Integration of IGV and Globus Genomics"}, {"po":96,"n":"Status","v":"Proposed"}, {"po":96,"n":"Suggested By","v":"Ravi Madduri"}, {"po":96,"n":"name","v":"Globus (Connected with) CIViC"}, {"po":96,"n":"Why?","v":"Integrate CIViC with Globus Genomcis"}, {"po":95,"n":"Status","v":"Exists"}, {"po":95,"n":"Suggested By","v":"Ravi Madduri"}, {"po":95,"n":"name","v":"Globus (Connected with) Galaxy-P multi-omics"}, {"po":95,"n":"Evidence","v":"https://dev.globusgenomics.org"}, {"po":95,"n":"Why?","v":"Integrate Galaxy-P tools with Globus Genomics"}, {"po":94,"n":"Status","v":"Proposed"}, {"po":94,"n":"Suggested By","v":"Ravi Madduri"}, {"po":94,"n":"name","v":"Globus (Connected with) CRAVAT"}, {"po":94,"n":"Why?","v":"Integrate CRAVAT with Globus Genomics"}, {"po":93,"n":"Status","v":"Proposed"}, {"po":93,"n":"Suggested By","v":"Ian Foster"}, {"po":93,"n":"name","v":"Globus (Connected with) TCIA"}, {"po":93,"n":"Why?","v":"Use Globus to access TCIA hosted data"}, {"po":114,"n":"Status","v":"Exists"}, {"po":114,"n":"Suggested By","v":"Nathalie Pochet, Vincent Carey"}, {"po":114,"n":"name","v":"Bioconductor (Connected with) AMARETTO"}, {"po":114,"n":"Evidence","v":"https://www.bioconductor.org/packages/release/bioc/html/AMARETTO.html"}, {"po":114,"n":"Why?","v":"Integrative statistical learning using ontology and network methods in cancer genomics"}, {"po":7,"n":"Status","v":"Exists"}, {"po":7,"n":"Suggested By","v":"Rudi Pillich"}, {"po":7,"n":"name","v":"Bioconductor (Connected with) NDEx"}, {"po":7,"n":"Evidence","v":"http://bioconductor.org/packages/release/bioc/html/ndexr.html"}, {"po":7,"n":"Why?","v":"R client available as a Bioconductor package for programmatic access to the NDEx REST API"}, {"po":5,"n":"Status","v":"Proposed"}, {"po":5,"n":"Suggested By","v":"Jingshan Huang"}, {"po":5,"n":"name","v":"Bioconductor (Connected with) OmniSearch"}, {"po":5,"n":"Why?","v":"A new set of cancer genomic analysis tasks that can be readily integrated with existing Bioconductor tools"}, {"po":4,"n":"Status","v":"Proposed"}, {"po":4,"n":"Suggested By","v":"mtmrogan"}, {"po":4,"n":"name","v":"Bioconductor (Connected with) IGV"}, {"po":4,"n":"Why?","v":"Visualize (and update) computed results, like epivizr"}, {"po":3,"n":"Status","v":"Proposed"}, {"po":3,"n":"Suggested By","v":"mtmorgan"}, {"po":3,"n":"name","v":"Bioconductor (Connected with) CIViC"}, {"po":3,"n":"Why?","v":"Place statistically supported results into biological context"}, {"po":2,"n":"Status","v":"Proposed"}, {"po":2,"n":"Suggested By","v":"JJ Gao"}, {"po":2,"n":"name","v":"Bioconductor (Connected with) cBioPortal"}, {"po":2,"n":"Why?","v":"Bioconductor Package of loading genomics and clinical data from the cBioPortal API"}, {"po":70,"n":"Status","v":"Proposed"}, {"po":70,"n":"Suggested By","v":"Brion Sarachan"}, {"po":70,"n":"name","v":"THRIVE (Connected with) XNAT"}, {"po":70,"n":"Why?","v":"Workflow to curate pathology image submissions"}, {"po":69,"n":"Status","v":"Ongoing"}, {"po":69,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":69,"n":"name","v":"THRIVE (Connected with) LesionTracker"}, {"po":69,"n":"Why?","v":"Cornerstone is used for visualizing multiplexed data"}, {"po":72,"n":"Status","v":"Ongoing"}, {"po":72,"n":"Suggested By","v":"Brian Haas / James Robinson"}, {"po":72,"n":"name","v":"Trinity (Connected with) IGV"}, {"po":72,"n":"Why?","v":"Visualize ab initio-assembled transcriptomes, read alignments, sequence variants, and fusions"}, {"po":71,"n":"Status","v":"Proposed"}, {"po":71,"n":"Suggested By","v":"Brian Haas"}, {"po":71,"n":"name","v":"Trinity (Connected with) CIViC"}, {"po":71,"n":"Why?","v":"inferring significance of rna-seq based fusions & mutations, also curating fusions in literature"}, {"po":129,"n":"Status","v":"Proposed"}, {"po":129,"n":"Suggested By","v":"Dinler Antunes"}, {"po":129,"n":"name","v":"JBrowse (Connected with) DINC"}, {"po":129,"n":"Why?","v":"The JBrowse is a Cancer Genome Browser with the primary goal of viewing genomic context of SVs (and simpler variants), along with genome-situated evidence such as RNAseq reads. In spite of being DNA-oriented, current efforts on JBrowse 2 are aiming on the \"protein space\", including plans for building a mini-protein browser. In addition, there are plans for a JBrowse protein viewer. DINC is a parallelized meta-docking tool to predict binding modes of a receptor-ligand complexes and providing structure-based biding affinities. We are working to expand the scope and functionalities of this tool, in order to make DINC a reference tool for structural analysis in cancer research. For that, it would be useful to have connections with the protein visualization tool inside JBrowse, which in turn will be connected to other ITCR resources, such as the Clinical Interpretation of Variants in Cancer (CIViC). We want to investigate ways to facilitate the connection between (i) searching and visualizing protein mutations on JBrowse and (ii) submitting selected mutations to docking jobs on DINC (e.g., virtual screening of available drugs to evaluate the impact of different mutations on drug resistance)."}, {"po":125,"n":"Status","v":"Ongoing"}, {"po":125,"n":"Suggested By","v":"CRAVAT Team"}, {"po":125,"n":"name","v":"JBrowse (interacts with) CRAVAT"}, {"po":125,"n":"Why?","v":"JBrowse is well suited to be a visualization widget in the OpenCRAVAT store, where users who submit mutations to CRAVAT for interpretation and prioritization can explore those mutations in the context of JBrowse multi-track views of the genome."}, {"po":104,"n":"Status","v":"Exists"}, {"po":104,"n":"Suggested By","v":"Ian Holmes"}, {"po":104,"n":"name","v":"JBrowse (Connected with) CIViC"}, {"po":104,"n":"Evidence","v":"https://github.com/elsiklab/myvariantviewer"}, {"po":104,"n":"Why?","v":"View CIViC variants as annotation track in the context of JBrowse cancer data bundle"}, {"po":149,"n":"Status","v":"Exists"}, {"po":149,"n":"Suggested By","v":"Raja Mazumder"}, {"po":149,"n":"name","v":"OncoMX (interacts with) CDGnet"}, {"po":149,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":149,"n":"Why?","v":"To visualize FDA-approved and EDRN biomarkers with gene expression data"}, {"po":148,"n":"Status","v":"Exists"}, {"po":148,"n":"Suggested By","v":"Raja Mazumder"}, {"po":148,"n":"name","v":"OncoMX (interacts with) HemOnc"}, {"po":148,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":148,"n":"Why?","v":"Cross-reference hematological information and tumors by gene symbols in the context of biomarkers"}, {"po":147,"n":"Status","v":"Proposed"}, {"po":147,"n":"Suggested By","v":"Raja Mazumder"}, {"po":147,"n":"name","v":"OncoMX (interacts with) cBioPortal"}, {"po":147,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":147,"n":"Why?","v":"Cross-reference cancer meta data with corresponding biomarkers using gene symbols"}, {"po":146,"n":"Status","v":"Ongoing"}, {"po":146,"n":"Suggested By","v":"Raja Mazumder"}, {"po":146,"n":"name","v":"OncoMX (interacts with) PDX Finder"}, {"po":146,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":146,"n":"Why?","v":"Cross-reference mutation data and clinical metadata using gene symbols"}, {"po":41,"n":"Status","v":"Exists"}, {"po":41,"n":"Suggested By","v":"Mazumder/Crichton"}, {"po":41,"n":"name","v":"OncoMX (Connected with) CIViC"}, {"po":41,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":41,"n":"Why?","v":"Providing complimentary biomarker information"}, {"po":131,"n":"Status","v":"Exists"}, {"po":131,"n":"Suggested By","v":"Mazumder/Chricton"}, {"po":131,"n":"name","v":"TCPA (Connected with) OncoMX"}, {"po":131,"n":"Evidence","v":"https://oncomx.org/faq?fq=/static/docs/UpdatedREADME.1.0.12.txt"}, {"po":131,"n":"Why?","v":"Visualize gene symbols and protein markers with coresponding biomarker metadata"}, {"po":130,"n":"Status","v":"Proposed"}, {"po":130,"n":"Suggested By","v":"Dinler Antunes"}, {"po":130,"n":"name","v":"TCPA (Connected with) DINC"}, {"po":130,"n":"Why?","v":"DINC is a parallelized meta-docking tool to predict binding modes of a receptor-ligand complexes and providing structure-based biding affinities.We are working to expand the scope and functionalities of this tool, in order to make DINC a reference tool for structural analysis in cancer research. For that, it would be useful to have connections with reference tumor-mutation databases such as TCPA. We want to investigate ways to facilitate the connection between (i) searching a mutation of interest on TCPA and (ii) submitting it to a docking job on DINC (e.g., virtual screening of available drugs to evaluate the impact of the selected mutation on drug resistance)."}, {"po":68,"n":"Status","v":"Proposed"}, {"po":68,"n":"Suggested By","v":"Mary Goldman"}, {"po":68,"n":"name","v":"TCPA (Connected with) UCSC Xena"}, {"po":68,"n":"Why?","v":"Add RPPA data for CCLE data (RNAseq and CNV) already in Xena"}, {"po":9,"n":"Status","v":"Proposed"}, {"po":9,"n":"Suggested By","v":"Juli Klemm"}, {"po":9,"n":"name","v":"BMEG (Connected with) XNAT"}, {"po":9,"n":"Why?","v":"Connect radiomics data with other biomedical evidence"}, {"po":8,"n":"Status","v":"Proposed"}, {"po":8,"n":"Suggested By","v":"Josh Stuart"}, {"po":8,"n":"name","v":"BMEG (Connected with) NDEx"}, {"po":8,"n":"Why?","v":"Ingest network models into evidence graph"}, {"po":27,"n":"Status","v":"Proposed"}, {"po":27,"n":"Suggested By","v":"Hua Xu"}, {"po":27,"n":"name","v":"CLAMP-Cancer (Connected with) TIES"}, {"po":27,"n":"Why?","v":"Use CLAMP NLP modules for TIES"}, {"po":26,"n":"Status","v":"Proposed"}, {"po":26,"n":"Suggested By","v":"Hua Xu"}, {"po":26,"n":"name","v":"CLAMP-Cancer (Connected with) OmniSearch"}, {"po":26,"n":"Why?","v":"Use CLAMP to develop literature mining pipelines"}, {"po":67,"n":"Status","v":"Proposed"}, {"po":67,"n":"Suggested By","v":"Lauren O'Donnell"}, {"po":67,"n":"name","v":"SlicerDMRI (Connected with) XNAT"}, {"po":67,"n":"Why?","v":"Enable DICOM tractography in XNAT"}, {"po":66,"n":"Status","v":"Exists"}, {"po":66,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":66,"n":"name","v":"SlicerDMRI (Connected with) 3D Slicer"}, {"po":66,"n":"Why?","v":"3D Slicer is the interactive platform, where SlicerDMRI is a problem-specific solution"}, {"po":90,"n":"Status","v":"Ongoing"}, {"po":90,"n":"Suggested By","v":"Guilherme Del Fiol"}, {"po":90,"n":"name","v":"EMERSE (Connected with) OpenCDS"}, {"po":90,"n":"Why?","v":"Identify assertions of cancer family history within unstructured EHR clinical reports"}, {"po":32,"n":"Status","v":"Exists"}, {"po":32,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":32,"n":"name","v":"DICOM ToolKit (DCMTK) (Connected with) dcmqi"}, {"po":32,"n":"Why?","v":"dcmqi provides a set of abstractions to simplify data conversion of specific types of DICOM objects, is based on DCMTK"}, {"po":31,"n":"Status","v":"Exists"}, {"po":31,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":31,"n":"name","v":"DICOM ToolKit (DCMTK) (Connected with) 3D Slicer"}, {"po":31,"n":"Why?","v":"DCMTK is a library that implements low-level API for working with DICOM data"}, {"po":45,"n":"Status","v":"Proposed"}, {"po":45,"n":"Suggested By","v":"Ryan Spangler"}, {"po":45,"n":"name","v":"CRAVAT (Connected with) BMEG"}, {"po":45,"n":"Why?","v":"Incorporate 3D variant visualization into BMEG browser's variants page"}, {"po":29,"n":"Status","v":"Exists"}, {"po":29,"n":"Suggested By","v":"Jingchun Zhu"}, {"po":29,"n":"name","v":"CRAVAT (Connected with) UCSC Xena"}, {"po":29,"n":"Why?","v":"Dynamic annotate mutations"}, {"po":28,"n":"Status","v":"Exists"}, {"po":28,"n":"Suggested By","v":"Brian Haas"}, {"po":28,"n":"name","v":"OpenCRAVAT (Connected with) Trinity"}, {"po":28,"n":"Evidence","v":"https://github.com/KarchinLab/open-cravat/wiki."}, {"po":28,"n":"Why?","v":"Variant annotation - 3D structure with variants"}, {"po":106,"n":"Status","v":"Exists"}, {"po":106,"n":"Suggested By","v":"Aaron Quinkan"}, {"po":106,"n":"name","v":"GEMINI (Connected with) CIViC"}, {"po":106,"n":"Why?","v":"Prioritize clinically relevant genes and mutations"}, {"po":156,"n":"Status","v":"Ongoing"}, {"po":156,"n":"Suggested By","v":"Bradley Broom"}, {"po":156,"n":"name","v":"NG-CHM (Connected with) NDEx"}, {"po":156,"n":"Evidence","v":"http://tcga.ngchm.net"}, {"po":156,"n":"Why?","v":"To provide pathway and interaction retrieval for a set of genes extracted from a heat map"}, {"po":136,"n":"Status","v":"Exists"}, {"po":136,"n":"Suggested By","v":"Brian Haas"}, {"po":136,"n":"name","v":"NG-CHM (Connected with) Trinity"}, {"po":136,"n":"Evidence","v":"https://github.com/broadinstitute/infercnv/wiki/Next-Generation-Clustered-Heat-Map"}, {"po":136,"n":"Why?","v":"To allow interactive navigation of copy number alterations inferred from single cell transcriptome data as detected by our Trinity CTAT tool called inferCNV."}, {"po":57,"n":"Status","v":"Exists"}, {"po":57,"n":"Suggested By","v":"Juli Klemm"}, {"po":57,"n":"name","v":"NG-CHM (Connected with) TCPA"}, {"po":57,"n":"Why?","v":"Visualization of RPPA data"}, {"po":56,"n":"Status","v":"Proposed"}, {"po":56,"n":"Suggested By","v":"Juli Klemm"}, {"po":56,"n":"name","v":"NG-CHM (Connected with) RADIOMICS.io"}, {"po":56,"n":"Why?","v":"Visualize radiomics data with clustered heat maps"}, {"po":55,"n":"Status","v":"Exists"}, {"po":55,"n":"Suggested By","v":"Bradley Broom"}, {"po":55,"n":"name","v":"NG-CHM (Connected with) CRAVAT"}, {"po":55,"n":"Why?","v":"View structure of genes included in a heat map"}, {"po":53,"n":"Status","v":"Exists"}, {"po":53,"n":"Suggested By","v":"Bradley Broom"}, {"po":53,"n":"name","v":"NG-CHM (Connected with) CIViC"}, {"po":53,"n":"Why?","v":"Link to CIViC gene record pages from heatmap gene labels"}, {"po":52,"n":"Status","v":"Exists"}, {"po":52,"n":"Suggested By","v":"Bradley Broom"}, {"po":52,"n":"name","v":"NG-CHM (Connected with) CDSA"}, {"po":52,"n":"Why?","v":"Visualize TCGA slide of sample included in heat map"}, {"po":51,"n":"Status","v":"Exists"}, {"po":51,"n":"Suggested By","v":"Bradley Broom"}, {"po":51,"n":"name","v":"NG-CHM (Connected with) cBioPortal"}, {"po":51,"n":"Why?","v":"Link to cBioPortal from selected samples in NG-CHM"}, {"po":50,"n":"Status","v":"Proposed"}, {"po":50,"n":"Suggested By","v":"Jayashree Kalpathy-Cramer"}, {"po":50,"n":"name","v":"NG-CHM (Connected with) C-BIBOP"}, {"po":50,"n":"Why?","v":"Visualization for radiomics challenges and to develop feature ontology"}, {"po":59,"n":"Status","v":"Ongoing"}, {"po":59,"n":"Suggested By","v":"Carol Bult"}, {"po":59,"n":"name","v":"PDX Finder (Connected with) OpenCRAVAT"}, {"po":59,"n":"Why?","v":"To visualize mutations in context of 3D structures and assess significance"}, {"po":58,"n":"Status","v":"Exists"}, {"po":58,"n":"name","v":"PDX Finder (Connected with) CIViC"}, {"po":58,"n":"Evidence","v":"http://www.pdxfinder.org/data/pdx/JAX/TM01130#variation"}, {"po":58,"n":"Why?","v":"Provide PDX model/sample variants to CIViC"}, {"po":65,"n":"Status","v":"Ongoing"}, {"po":65,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":65,"n":"name","v":"RADIOMICS.io (Connected with) dcmqi"}, {"po":65,"n":"Why?","v":"dcmqi can be used to store the radiomics features in a structured and standardized format"}, {"po":64,"n":"Status","v":"Proposed"}, {"po":64,"n":"Suggested By","v":"Christos Davatzikos"}, {"po":64,"n":"name","v":"RADIOMICS.io (Connected with) CaPTK"}, {"po":64,"n":"Why?","v":"Integrate radiomic features into CaPTk predictive models"}, {"po":14,"n":"Status","v":"Exists"}, {"po":14,"n":"Suggested By","v":"Jayashree Kalpathy-Cramer"}, {"po":14,"n":"name","v":"C-BIBOP (Connected with) TCIA"}, {"po":14,"n":"Why?","v":"Algorithm comparison on data hosted in TCIA"}, {"po":13,"n":"Status","v":"Exists"}, {"po":13,"n":"Suggested By","v":"Jayashree Kalpathy-Cramer"}, {"po":13,"n":"name","v":"C-BIBOP (Connected with) LesionTracker"}, {"po":13,"n":"Evidence","v":"www.crowds-cure.org"}, {"po":13,"n":"Why?","v":"Integrate Cornerstone viewer within C-BIBOP"}, {"po":12,"n":"Status","v":"Ongoing"}, {"po":12,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":12,"n":"name","v":"C-BIBOP (Connected with) dcmqi"}, {"po":12,"n":"Why?","v":"dcmqi provides converters used by C-BIBOP for normalizing data stored in research formats"}, {"po":11,"n":"Status","v":"Proposed"}, {"po":11,"n":"Suggested By","v":"Jayashree Kalpathy-Cramer"}, {"po":11,"n":"name","v":"C-BIBOP (Connected with) CaPTK"}, {"po":11,"n":"Why?","v":"Integrate CapTk algorithms into C-BIBOP"}, {"po":10,"n":"Status","v":"Ongoing"}, {"po":10,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":10,"n":"name","v":"C-BIBOP (Connected with) 3D Slicer"}, {"po":10,"n":"Why?","v":"Quantitative image analysis tools are used in C-BIBOP to implement processing pipelines"}, {"po":132,"n":"Status","v":"Exists"}, {"po":132,"n":"Suggested By","v":"Hailey Dingerdissen"}, {"po":132,"n":"name","v":"SingleCellTK (Connected with) OncoMX"}, {"po":132,"n":"Why?","v":"The proposed connection will enable OncoMX access to new scRNA-seq expression data and analysis as it becomes available through SingleCellTK, and SCTK will reciprocally benefit by retrieving value-added functional annotation of scRNA-seq expression after processing by OncoMX, ultimately enhancing both projects' missions."}, {"po":110,"n":"Status","v":"Exists"}, {"po":110,"n":"Suggested By","v":"Evan Johnson"}, {"po":110,"n":"name","v":"SingleCellTK (Connected with) Bioconductor"}, {"po":110,"n":"Why?","v":"Use Bioconductor data structures, such as the summarizedExperiment and SingleCellExperiment to manage data and analyses"}, {"po":109,"n":"Status","v":"Proposed"}, {"po":109,"n":"Suggested By","v":"Evan Johnson"}, {"po":109,"n":"name","v":"SingleCellTK (Connected with) GenePattern"}, {"po":109,"n":"Why?","v":"Implement the singleCellTK workflkow and pipeline into GenePatternNotebooks"}, {"po":108,"n":"Status","v":"Proposed"}, {"po":108,"n":"Suggested By","v":"Evan Johnson"}, {"po":108,"n":"name","v":"SingleCellTK (Connected with) cBioPortal"}, {"po":108,"n":"Why?","v":"Link single cell analysis results to public bulk RNA-sequencing data"}, {"po":107,"n":"Status","v":"Proposed"}, {"po":107,"n":"Suggested By","v":"Evan Johnson"}, {"po":107,"n":"name","v":"SingleCellTK (Connected with) Single Cell Genome Viewer"}, {"po":107,"n":"Why?","v":"Additional visualization. Link DNA sequencing and RNA-sequencing from same cell"}, {"po":152,"n":"Status","v":"Ongoing"}, {"po":152,"n":"Suggested By","v":"Jeremy Warner"}, {"po":152,"n":"name","v":"CIViC (Connected with) HemOnc"}, {"po":84,"n":"Status","v":"Proposed"}, {"po":84,"n":"Suggested By","v":"Malachi Griffith"}, {"po":84,"n":"name","v":"CIViC (Connected with) CLAMP-Cancer"}, {"po":84,"n":"Why?","v":"Use CLAMP-Cancer to identify pathology reports that might benefit from variant knowledge in CIViC and also identify patient classes with genomic events that are not well represented in CIViC"}, {"po":83,"n":"Status","v":"Proposed"}, {"po":83,"n":"Suggested By","v":"Malachi Griffith"}, {"po":83,"n":"name","v":"CIViC (Connected with) OmniSearch"}, {"po":83,"n":"Why?","v":"Use OmniSearch to identify miRNA genes whose clinical relevance should be documented in CIViC"}, {"po":82,"n":"Status","v":"Proposed"}, {"po":82,"n":"Suggested By","v":"Malachi Griffith"}, {"po":82,"n":"name","v":"CIViC (Connected with) TIES"}, {"po":82,"n":"Why?","v":"Use TIES to identify patient records that might benefit from variant knowledge in CIViC and also identify patient classes with genomic events that are not well represented in CIViC"}, {"po":81,"n":"Status","v":"Exists"}, {"po":81,"n":"Suggested By","v":"Malachi Griffith"}, {"po":81,"n":"name","v":"CIViC (Connected with) cBioPortal"}, {"po":81,"n":"Why?","v":"Provides clinical interpretation of variants along side pan cancer genomic information from cBioPortal"}, {"po":25,"n":"Status","v":"Exists"}, {"po":25,"n":"Suggested By","v":"Mike Ryan"}, {"po":25,"n":"name","v":"CIViC (Connected with) CRAVAT"}, {"po":25,"n":"Why?","v":"Shows 3D structure location Variant annotation- 3D structures with variants"}, {"po":24,"n":"Status","v":"Exists"}, {"po":24,"n":"Suggested By","v":"Obi Griffith"}, {"po":24,"n":"name","v":"CIViC (Connected with) IGV"}, {"po":24,"n":"Evidence","v":"https://github.com/igvteam/igv.js/blob/2c21e74613cace56852e7561dcc6a0cdb5126e55/js/civic/civicReader.js"}, {"po":24,"n":"Why?","v":"Provide CIViC variants as optional annotation track"}, {"po":139,"n":"Status","v":"Proposed"}, {"po":139,"n":"Suggested By","v":"Nathalie Pochet, Brian Haas, Aviv Regev"}, {"po":139,"n":"name","v":"AMARETTO (Connected with) Trinity"}, {"po":139,"n":"Why?","v":"To infer regulatory networks driven by genetic, epigenetic and transcriptomic heterogeneity identified from de novo assembled cancer transcriptomes, and to use these networks for diagnostic, prognostic and therapeutic decision-making in cancer"}, {"po":138,"n":"Status","v":"Proposed"}, {"po":138,"n":"Suggested By","v":"Nathalie Pochet, Vincent Carey"}, {"po":138,"n":"name","v":"AMARETTO (Connected with) NDEx"}, {"po":138,"n":"Why?","v":"To disseminate the regulatory networks inferred from multiomics with AMARETTO into the NDEx database"}, {"po":137,"n":"Status","v":"Proposed"}, {"po":137,"n":"Suggested By","v":"Nathalie Pochet, Vincent Carey"}, {"po":137,"n":"name","v":"AMARETTO (Connected with) NG-CHM"}, {"po":137,"n":"Why?","v":"To use NG-CHM for interactive heatmap visualization of the regulatory networks inferred from multiomics with AMARETTO"}, {"po":80,"n":"Status","v":"Ongoing"}, {"po":80,"n":"Suggested By","v":"Dan Marcus"}, {"po":80,"n":"name","v":"XNAT (Connected with) LesionTracker"}, {"po":80,"n":"Why?","v":"Emded LesionTracker as visualization/measurement app in XNAT"}, {"po":79,"n":"Status","v":"Proposed"}, {"po":79,"n":"Suggested By","v":"John Flavin"}, {"po":79,"n":"name","v":"XNAT (Connected with) DICOM ToolKit (DCMTK)"}, {"po":79,"n":"Why?","v":"Integration of DICOM object headers and images into XNAT data model"}, {"po":78,"n":"Status","v":"Proposed"}, {"po":78,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":78,"n":"name","v":"XNAT (Connected with) dcmqi"}, {"po":78,"n":"Why?","v":"Conversion of the analysis results into structured and standardized format"}, {"po":76,"n":"Status","v":"Exists"}, {"po":76,"n":"Suggested By","v":"Andrey Fedorov"}, {"po":76,"n":"name","v":"XNAT (Connected with) 3D Slicer"}, {"po":76,"n":"Why?","v":"Use 3D Slicer as an interface to interact with the XNAT-hosted data"}]},
{"cartesianLayout":[{"node":3,"x":254.02991183353845,"y":105.37439727783203}, {"node":36,"x":675.8823728677455,"y":399.6935132910714}, {"node":4,"x":-1104.1160971587324,"y":578.5801919037676}, {"node":37,"x":557.5804581510573,"y":-611.8310846930958}, {"node":5,"x":-838.1552734375,"y":494.1905517578125}, {"node":38,"x":-871.8496608225106,"y":-720.3948002016047}, {"node":6,"x":990.9758065056792,"y":-363.59105306772716}, {"node":39,"x":38.751060485839844,"y":-87.14175540935472}, {"node":7,"x":559.5441802444983,"y":-1196.6359010727308}, {"node":40,"x":-1259.525390625,"y":-164.37355041503906}, {"node":8,"x":825.0137939453125,"y":-661.115966796875}, {"node":41,"x":-438.40972900390625,"y":575.3349609375}, {"node":9,"x":41.45631853233719,"y":-580.3615560455761}, {"node":42,"x":556.2157592773438,"y":-269.1994934082031}, {"node":10,"x":-225.71633911132812,"y":167.86452633522714}, {"node":43,"x":1204.1893407844866,"y":0.7661018371582031}, {"node":11,"x":276.26583119293264,"y":447.8336486816406}, {"node":44,"x":-788.6109905863458,"y":-1182.3121769586646}, {"node":12,"x":-197.02993774414062,"y":490.625}, {"node":45,"x":895.9989547851308,"y":376.87676796623947}, {"node":13,"x":151.6102752685547,"y":335.35229036021843}, {"node":46,"x":436.9041183765072,"y":272.0404357910156}, {"node":14,"x":488.62725830078125,"y":-39.0060318286556}, {"node":47,"x":1113.8022804512984,"y":228.1656050706151}, {"node":15,"x":-1386.8142685266328,"y":-375.74197962774906}, {"node":48,"x":-1193.8321423874656,"y":-312.84629687211964}, {"node":16,"x":966.9632568359375,"y":-31.215255737304688}, {"node":49,"x":-1155.4706649550053,"y":-612.3077062282647}, {"node":17,"x":711.847900390625,"y":120.00963592529297}, {"node":50,"x":303.1738792603208,"y":-346.03748412108814}, {"node":18,"x":1251.70068359375,"y":-149.49771118164062}, {"node":51,"x":-1286.756791949171,"y":-512.5096421411625}, {"node":19,"x":-711.871769157791,"y":-360.22822952052735}, {"node":52,"x":-477.99151466103837,"y":-558.9326482435763}, {"node":20,"x":-1015.653566606171,"y":-293.8257794525764}, {"node":21,"x":316.64031617149425,"y":-148.0754212637463}, {"node":22,"x":-1099.8965514239653,"y":-835.3601320487908}, {"node":23,"x":-289.65454963222635,"y":-1067.5588520445767}, {"node":24,"x":-30.242141723632812,"y":271.4009712561056}, {"node":25,"x":-1273.068501429473,"y":202.78480281293446}, {"node":26,"x":-655.1026000976562,"y":-12.244277754821251}, {"node":27,"x":11.876296686859039,"y":-927.6091470353638}, {"node":28,"x":-585.9625682783268,"y":-842.3153593306034}, {"node":29,"x":-344.3613586425781,"y":-50.76545715332031}, {"node":30,"x":-304.1192167304819,"y":-295.03486257172517}, {"node":32,"x":-245.85650634765625,"y":329.42233732532844}, {"node":0,"x":-1068.3514852523244,"y":-98.3294585809718}, {"node":33,"x":-10.797882080078125,"y":431.7838365640264}, {"node":1,"x":-3.6291122436523438,"y":87.81184387207031}, {"node":34,"x":-1034.2472994349241,"y":-444.05853103954104}, {"node":2,"x":1074.586669921875,"y":-914.3712158203125}, {"node":35,"x":-780.8419286274658,"y":-180.17932299171036}]},
{"cyTableColumn":[{"applies_to":"node_table","n":"shared name"}, {"applies_to":"node_table","n":"name"}, {"applies_to":"node_table","n":"Connectivity Score","d":"integer"}, {"applies_to":"node_table","n":"Resource Website"}, {"applies_to":"edge_table","n":"shared name"}, {"applies_to":"edge_table","n":"shared interaction"}, {"applies_to":"edge_table","n":"name"}, {"applies_to":"edge_table","n":"interaction"}, {"applies_to":"edge_table","n":"Status"}, {"applies_to":"edge_table","n":"Suggested By"}, {"applies_to":"edge_table","n":"Why?"}, {"applies_to":"edge_table","n":"Evidence"}, {"applies_to":"network_table","n":"shared name"}, {"applies_to":"network_table","n":"name"}, {"applies_to":"network_table","n":"author"}, {"applies_to":"network_table","n":"rights"}, {"applies_to":"network_table","n":"description"}, {"applies_to":"network_table","n":"networkType"}, {"applies_to":"network_table","n":"version"}, {"applies_to":"network_table","n":"labels"}, {"applies_to":"network_table","n":"__Annotations","d":"list_of_string"}, {"applies_to":"network_table","n":"rightsHolder"}]},
{"cyHiddenAttributes":[{"n":"NDEx UUID","v":"04c0a7e8-af92-11e7-94d3-0ac135e8bacf"}, {"n":"NDEx Modification Timestamp","v":"2020-04-16 11:21:21.364"}]},
{"status":[{"error":"","success":true}]}]