diff --git a/docs/Data_Dictionary/gdcmvs.md b/docs/Data_Dictionary/gdcmvs.md new file mode 100644 index 000000000..0b51c2ef5 --- /dev/null +++ b/docs/Data_Dictionary/gdcmvs.md @@ -0,0 +1,70 @@ + + + +

GDC Metadata Validation Services

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+ Search in NCIt + Search in caDSR +
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GDC Dictionary Version
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+ + + + diff --git a/mkdocs.yml b/mkdocs.yml index 7d2f7ab26..9be2fc02c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -2,6 +2,8 @@ copyright: '© 2015-2016' extra: dictionary_app_root: /apps/dictionary dictionary_viewer_page_id: Viewer + gdcmvs_app_root: /apps/gdcmvs + gdcmvs_viewer_page_id: Search encyclopedia_entries_page_title: EncyclopediaEntries encyclopedia_page_title: Encyclopedia nav_exclude: @@ -79,6 +81,7 @@ pages: - Data Dictionary: - About: Data_Dictionary/index.md - Viewer: Data_Dictionary/viewer.md + - Search: Data_Dictionary/gdcmvs.md - Release Notes: Data_Dictionary/Release_Notes/Data_Dictionary_Release_Notes.md - Data: - Introduction: Data/Introduction.md diff --git a/theme/apps/gdcmvs/dist/bundle.js b/theme/apps/gdcmvs/dist/bundle.js new file mode 100644 index 000000000..69075ed95 --- /dev/null +++ b/theme/apps/gdcmvs/dist/bundle.js @@ -0,0 +1 @@ +!function(e){var t={};function a(n){if(t[n])return t[n].exports;var i=t[n]={i:n,l:!1,exports:{}};return 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GDC Property Values
caDSR CDE Reference
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{{:nm}}
{{:desc}}
{{if local}} {{if syn}} See All Values {{else}} {{/if}}
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Matched GDC Values
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{{:category}}
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{{for vs}} {{if #getIndex() == 5}}
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{{if n == "no match" || gdc_d == false}}
no match
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{{:psHtml}}
{{:trsHtml}}
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{{if targets !== null}} {{/if}}
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NCIt Code and Synonyms
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{{/if}}
{{if icdo !== false}}
GDC Term
ICD-O-3 Code
ICD-O-3 Term
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{{if icdo}}
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{{if i_c}}{{if i_c.n}} {{for i_c.n}} {{/for}}
Term Source Type
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{{else}}
{{:n}}
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Term Source Type
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{{if i_c}}{{if i_c.n}}{{for i_c.n}}{{:}}
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{{:n}}
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{{:n}}
{{/for}} {{/if}}
{{/if}}
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User Defined Values
Matched GDC Values
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GDC Values {{:items_length}}
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ICD-O-3 Code
ICD-O-3 Term
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NCIt Terms
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NCIt Code
NCIt Terms
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more details

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Sources
NCIt includes some data, notably terms, codes, and definitions, tagged as coming from the sources listed below. The extent and nature of this source data varies greatly:
  • Some sources, such as FDA and CDISC, are important partners in developing extensive tagged terminology subsets for regulatory and standards purposes;
  • Several, such as CTCAE, DCP, DTP, and NCI-GLOSS, represent separate NCI terminology that has been cross-linked to NCIt concepts in whole or partially;
  • Several outside sources, such as CRCH and JAX, have contributed terminology in particular fields; and
  • Other sources are included in a variety of more limited ways to provide useful cross-links and information.
Source Description
ACC American College of Cardiology
BioCarta BioCarta online maps of molecular pathways, adapted for NCI use
BRIDG Biomedical Research Integrated Domain Model Group
CareLex CareLex electronic Trial Master File Terminology
CDC U.S. Centers for Disease Control and Prevention
CDISC Clinical Data Interchange Standards Consortium
CDISC-GLOSS CDISC Glossary Terminology
COH City of Hope
CRCH Cancer Research Center of Hawaii Nutrition Terminology
CTCAE Common Terminology Criteria for Adverse Events
CTEP Cancer Therapy Evaluation Program
CTRP Clinical Trials Reporting Program
DCP NCI Division of Cancer Prevention Program
DICOM Digital Imaging Communications in Medicine
DTP NCI Developmental Therapeutics Program
EDQM European Directorate for the Quality of Medicines & Healthcare
FDA U.S. Food and Drug Administration
GAIA Global Alignment of Immunization safety Assessment in pregnancy Terminology
GENC Geopolitical Entities, Names, and Codes Terminology
HGNC HUGO Gene Nomenclature Committee
ICH International Conference on Harmonization
IMDRF International Medical Device Regulators Forum
JAX Jackson Laboratories Mouse Terminology, adapted for NCI use
KEGG KEGG Pathway Database
MedDRA Medical Dictionary for Regulatory Activities
MMHCC Mouse Models of Human Cancer Consortium
NCCN National Comprehensive Cancer Network
NCI National Cancer Institute Thesaurus
NCI-GLOSS NCI Dictionary of Cancer Terms
NCI-HL7 NCI Health Level 7
NCPDP National Council for Prescription Drug Programs
NICHD National Institute of Child Health and Human Development
PID NCI Nature Pathway Interaction Database
PI-RADS Prostate Imaging-Reporting and Data System
RENI Registry Nomenclature Information System
UCUM Unified Code for Units of Measure
Zebrafish Zebrafish Model Organism Database
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Term Types

NCI Thesaurus Term Types use 2- or 3-character abbreviations to code the nature of each term associated with a concept. Here is a listing of the term type codes and their meanings:

Name Description
AB Abbreviation
AD Adjectival form (and other parts of grammer)
AQ* Antiquated preferred term
AQS Antiquated term, use when there are antiquated synonyms within a concept
BR US brand name, which may be trademarked
CA2 ISO 3166 alpha-2 country code
CA3 ISO 3166 alpha-3 country code
CNU ISO 3166 numeric country code
CI ISO Country code (deprecated)
CN Drug study code
CS US State Department country code
DN Display name
FB Foreign brand name, which may be trademarked
LLT Lower Level Term
HD* Header (groups concepts, but not used for coding data)
PT* Preferred term
SN Chemical structure name
SY Synonym

*Note on special rules governing NCI PT, HD, and AQ term types: Each concept should have one, and only one, term coded with one of these three values. The NCI Preferred Term is always taken from one of the NCI terms, normally that with a type of PT (Preferred Term). However, in special cases, a concept will not have a PT term, but instead, will have either an HD (Header) term or an AQ term. These tags are considered equivalent to PT by the software. This means that a concept may have only as single NCI PT, or HD, or AQ term. In those cases where multiple antiquated terms are needed for a concept which is itself coded as antiquated, one should be tagged AQ and the rest tagged AQS.

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this[0].labels&&this[0].labels.length?this.pushStack(this[0].labels):(n=this.eq(0).parents("label"),s=this.attr("id"),s&&(e=this.eq(0).parents().last(),o=e.add(e.length?e.siblings():this.siblings()),i="label[for='"+t.ui.escapeSelector(s)+"']",n=n.add(o.find(i).addBack(i))),this.pushStack(n))},t.fn.scrollParent=function(e){var i=this.css("position"),s="absolute"===i,n=e?/(auto|scroll|hidden)/:/(auto|scroll)/,o=this.parents().filter(function(){var e=t(this);return s&&"static"===e.css("position")?!1:n.test(e.css("overflow")+e.css("overflow-y")+e.css("overflow-x"))}).eq(0);return"fixed"!==i&&o.length?o:t(this[0].ownerDocument||document)},t.extend(t.expr[":"],{tabbable:function(e){var i=t.attr(e,"tabindex"),s=null!=i;return(!s||i>=0)&&t.ui.focusable(e,s)}}),t.fn.extend({uniqueId:function(){var t=0;return function(){return this.each(function(){this.id||(this.id="ui-id-"+ ++t)})}}(),removeUniqueId:function(){return 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i=this,s=1===e.which,o="string"==typeof this.options.cancel&&e.target.nodeName?t(e.target).closest(this.options.cancel).length:!1;return s&&!o&&this._mouseCapture(e)?(this.mouseDelayMet=!this.options.delay,this.mouseDelayMet||(this._mouseDelayTimer=setTimeout(function(){i.mouseDelayMet=!0},this.options.delay)),this._mouseDistanceMet(e)&&this._mouseDelayMet(e)&&(this._mouseStarted=this._mouseStart(e)!==!1,!this._mouseStarted)?(e.preventDefault(),!0):(!0===t.data(e.target,this.widgetName+".preventClickEvent")&&t.removeData(e.target,this.widgetName+".preventClickEvent"),this._mouseMoveDelegate=function(t){return i._mouseMove(t)},this._mouseUpDelegate=function(t){return i._mouseUp(t)},this.document.on("mousemove."+this.widgetName,this._mouseMoveDelegate).on("mouseup."+this.widgetName,this._mouseUpDelegate),e.preventDefault(),n=!0,!0)):!0}},_mouseMove:function(e){if(this._mouseMoved){if(t.ui.ie&&(!document.documentMode||9>document.documentMode)&&!e.button)return this._mouseUp(e);if(!e.which)if(e.originalEvent.altKey||e.originalEvent.ctrlKey||e.originalEvent.metaKey||e.originalEvent.shiftKey)this.ignoreMissingWhich=!0;else if(!this.ignoreMissingWhich)return this._mouseUp(e)}return(e.which||e.button)&&(this._mouseMoved=!0),this._mouseStarted?(this._mouseDrag(e),e.preventDefault()):(this._mouseDistanceMet(e)&&this._mouseDelayMet(e)&&(this._mouseStarted=this._mouseStart(this._mouseDownEvent,e)!==!1,this._mouseStarted?this._mouseDrag(e):this._mouseUp(e)),!this._mouseStarted)},_mouseUp:function(e){this.document.off("mousemove."+this.widgetName,this._mouseMoveDelegate).off("mouseup."+this.widgetName,this._mouseUpDelegate),this._mouseStarted&&(this._mouseStarted=!1,e.target===this._mouseDownEvent.target&&t.data(e.target,this.widgetName+".preventClickEvent",!0),this._mouseStop(e)),this._mouseDelayTimer&&(clearTimeout(this._mouseDelayTimer),delete 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e||(e=t.body),e.nodeName||(e=t.body),e},t.ui.safeBlur=function(e){e&&"body"!==e.nodeName.toLowerCase()&&t(e).trigger("blur")},t.widget("ui.draggable",t.ui.mouse,{version:"1.12.1",widgetEventPrefix:"drag",options:{addClasses:!0,appendTo:"parent",axis:!1,connectToSortable:!1,containment:!1,cursor:"auto",cursorAt:!1,grid:!1,handle:!1,helper:"original",iframeFix:!1,opacity:!1,refreshPositions:!1,revert:!1,revertDuration:500,scope:"default",scroll:!0,scrollSensitivity:20,scrollSpeed:20,snap:!1,snapMode:"both",snapTolerance:20,stack:!1,zIndex:!1,drag:null,start:null,stop:null},_create:function(){"original"===this.options.helper&&this._setPositionRelative(),this.options.addClasses&&this._addClass("ui-draggable"),this._setHandleClassName(),this._mouseInit()},_setOption:function(t,e){this._super(t,e),"handle"===t&&(this._removeHandleClassName(),this._setHandleClassName())},_destroy:function(){return(this.helper||this.element).is(".ui-draggable-dragging")?(this.destroyOnClear=!0,void 0):(this._removeHandleClassName(),this._mouseDestroy(),void 0)},_mouseCapture:function(e){var i=this.options;return this.helper||i.disabled||t(e.target).closest(".ui-resizable-handle").length>0?!1:(this.handle=this._getHandle(e),this.handle?(this._blurActiveElement(e),this._blockFrames(i.iframeFix===!0?"iframe":i.iframeFix),!0):!1)},_blockFrames:function(e){this.iframeBlocks=this.document.find(e).map(function(){var e=t(this);return t("
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this.helper=this._createHelper(e),this._addClass(this.helper,"ui-draggable-dragging"),this._cacheHelperProportions(),t.ui.ddmanager&&(t.ui.ddmanager.current=this),this._cacheMargins(),this.cssPosition=this.helper.css("position"),this.scrollParent=this.helper.scrollParent(!0),this.offsetParent=this.helper.offsetParent(),this.hasFixedAncestor=this.helper.parents().filter(function(){return"fixed"===t(this).css("position")}).length>0,this.positionAbs=this.element.offset(),this._refreshOffsets(e),this.originalPosition=this.position=this._generatePosition(e,!1),this.originalPageX=e.pageX,this.originalPageY=e.pageY,i.cursorAt&&this._adjustOffsetFromHelper(i.cursorAt),this._setContainment(),this._trigger("start",e)===!1?(this._clear(),!1):(this._cacheHelperProportions(),t.ui.ddmanager&&!i.dropBehaviour&&t.ui.ddmanager.prepareOffsets(this,e),this._mouseDrag(e,!0),t.ui.ddmanager&&t.ui.ddmanager.dragStart(this,e),!0)},_refreshOffsets:function(t){this.offset={top:this.positionAbs.top-this.margins.top,left:this.positionAbs.left-this.margins.left,scroll:!1,parent:this._getParentOffset(),relative:this._getRelativeOffset()},this.offset.click={left:t.pageX-this.offset.left,top:t.pageY-this.offset.top}},_mouseDrag:function(e,i){if(this.hasFixedAncestor&&(this.offset.parent=this._getParentOffset()),this.position=this._generatePosition(e,!0),this.positionAbs=this._convertPositionTo("absolute"),!i){var 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e=this.offsetParent.offset(),i=this.document[0];return"absolute"===this.cssPosition&&this.scrollParent[0]!==i&&t.contains(this.scrollParent[0],this.offsetParent[0])&&(e.left+=this.scrollParent.scrollLeft(),e.top+=this.scrollParent.scrollTop()),this._isRootNode(this.offsetParent[0])&&(e={top:0,left:0}),{top:e.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:e.left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if("relative"!==this.cssPosition)return{top:0,left:0};var t=this.element.position(),e=this._isRootNode(this.scrollParent[0]);return{top:t.top-(parseInt(this.helper.css("top"),10)||0)+(e?0:this.scrollParent.scrollTop()),left:t.left-(parseInt(this.helper.css("left"),10)||0)+(e?0:this.scrollParent.scrollLeft())}},_cacheMargins:function(){this.margins={left:parseInt(this.element.css("marginLeft"),10)||0,top:parseInt(this.element.css("marginTop"),10)||0,right:parseInt(this.element.css("marginRight"),10)||0,bottom:parseInt(this.element.css("marginBottom"),10)||0}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var e,i,s,n=this.options,o=this.document[0];return this.relativeContainer=null,n.containment?"window"===n.containment?(this.containment=[t(window).scrollLeft()-this.offset.relative.left-this.offset.parent.left,t(window).scrollTop()-this.offset.relative.top-this.offset.parent.top,t(window).scrollLeft()+t(window).width()-this.helperProportions.width-this.margins.left,t(window).scrollTop()+(t(window).height()||o.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top],void 0):"document"===n.containment?(this.containment=[0,0,t(o).width()-this.helperProportions.width-this.margins.left,(t(o).height()||o.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top],void 0):n.containment.constructor===Array?(this.containment=n.containment,void 0):("parent"===n.containment&&(n.containment=this.helper[0].parentNode),i=t(n.containment),s=i[0],s&&(e=/(scroll|auto)/.test(i.css("overflow")),this.containment=[(parseInt(i.css("borderLeftWidth"),10)||0)+(parseInt(i.css("paddingLeft"),10)||0),(parseInt(i.css("borderTopWidth"),10)||0)+(parseInt(i.css("paddingTop"),10)||0),(e?Math.max(s.scrollWidth,s.offsetWidth):s.offsetWidth)-(parseInt(i.css("borderRightWidth"),10)||0)-(parseInt(i.css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left-this.margins.right,(e?Math.max(s.scrollHeight,s.offsetHeight):s.offsetHeight)-(parseInt(i.css("borderBottomWidth"),10)||0)-(parseInt(i.css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top-this.margins.bottom],this.relativeContainer=i),void 0):(this.containment=null,void 0)},_convertPositionTo:function(t,e){e||(e=this.position);var i="absolute"===t?1:-1,s=this._isRootNode(this.scrollParent[0]);return{top:e.top+this.offset.relative.top*i+this.offset.parent.top*i-("fixed"===this.cssPosition?-this.offset.scroll.top:s?0:this.offset.scroll.top)*i,left:e.left+this.offset.relative.left*i+this.offset.parent.left*i-("fixed"===this.cssPosition?-this.offset.scroll.left:s?0:this.offset.scroll.left)*i}},_generatePosition:function(t,e){var i,s,n,o,a=this.options,r=this._isRootNode(this.scrollParent[0]),l=t.pageX,h=t.pageY;return r&&this.offset.scroll||(this.offset.scroll={top:this.scrollParent.scrollTop(),left:this.scrollParent.scrollLeft()}),e&&(this.containment&&(this.relativeContainer?(s=this.relativeContainer.offset(),i=[this.containment[0]+s.left,this.containment[1]+s.top,this.containment[2]+s.left,this.containment[3]+s.top]):i=this.containment,t.pageX-this.offset.click.lefti[2]&&(l=i[2]+this.offset.click.left),t.pageY-this.offset.click.top>i[3]&&(h=i[3]+this.offset.click.top)),a.grid&&(n=a.grid[1]?this.originalPageY+Math.round((h-this.originalPageY)/a.grid[1])*a.grid[1]:this.originalPageY,h=i?n-this.offset.click.top>=i[1]||n-this.offset.click.top>i[3]?n:n-this.offset.click.top>=i[1]?n-a.grid[1]:n+a.grid[1]:n,o=a.grid[0]?this.originalPageX+Math.round((l-this.originalPageX)/a.grid[0])*a.grid[0]:this.originalPageX,l=i?o-this.offset.click.left>=i[0]||o-this.offset.click.left>i[2]?o:o-this.offset.click.left>=i[0]?o-a.grid[0]:o+a.grid[0]:o),"y"===a.axis&&(l=this.originalPageX),"x"===a.axis&&(h=this.originalPageY)),{top:h-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+("fixed"===this.cssPosition?-this.offset.scroll.top:r?0:this.offset.scroll.top),left:l-this.offset.click.left-this.offset.relative.left-this.offset.parent.left+("fixed"===this.cssPosition?-this.offset.scroll.left:r?0:this.offset.scroll.left)} +},_clear:function(){this._removeClass(this.helper,"ui-draggable-dragging"),this.helper[0]===this.element[0]||this.cancelHelperRemoval||this.helper.remove(),this.helper=null,this.cancelHelperRemoval=!1,this.destroyOnClear&&this.destroy()},_trigger:function(e,i,s){return s=s||this._uiHash(),t.ui.plugin.call(this,e,[i,s,this],!0),/^(drag|start|stop)/.test(e)&&(this.positionAbs=this._convertPositionTo("absolute"),s.offset=this.positionAbs),t.Widget.prototype._trigger.call(this,e,i,s)},plugins:{},_uiHash:function(){return{helper:this.helper,position:this.position,originalPosition:this.originalPosition,offset:this.positionAbs}}}),t.ui.plugin.add("draggable","connectToSortable",{start:function(e,i,s){var n=t.extend({},i,{item:s.element});s.sortables=[],t(s.options.connectToSortable).each(function(){var i=t(this).sortable("instance");i&&!i.options.disabled&&(s.sortables.push(i),i.refreshPositions(),i._trigger("activate",e,n))})},stop:function(e,i,s){var n=t.extend({},i,{item:s.element});s.cancelHelperRemoval=!1,t.each(s.sortables,function(){var t=this;t.isOver?(t.isOver=0,s.cancelHelperRemoval=!0,t.cancelHelperRemoval=!1,t._storedCSS={position:t.placeholder.css("position"),top:t.placeholder.css("top"),left:t.placeholder.css("left")},t._mouseStop(e),t.options.helper=t.options._helper):(t.cancelHelperRemoval=!0,t._trigger("deactivate",e,n))})},drag:function(e,i,s){t.each(s.sortables,function(){var n=!1,o=this;o.positionAbs=s.positionAbs,o.helperProportions=s.helperProportions,o.offset.click=s.offset.click,o._intersectsWith(o.containerCache)&&(n=!0,t.each(s.sortables,function(){return this.positionAbs=s.positionAbs,this.helperProportions=s.helperProportions,this.offset.click=s.offset.click,this!==o&&this._intersectsWith(this.containerCache)&&t.contains(o.element[0],this.element[0])&&(n=!1),n})),n?(o.isOver||(o.isOver=1,s._parent=i.helper.parent(),o.currentItem=i.helper.appendTo(o.element).data("ui-sortable-item",!0),o.options._helper=o.options.helper,o.options.helper=function(){return 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