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Cancer Risk Based on Physical Activity Using an EntityStore
A 2016 study published in doi:10.1001/jamainternmed.2016.1548 studied cancer risk as a function of physical activity level during leisure time. This example combines Dataset, EntityStore, and other built-in functionality with this data to explore which cancer types have the greatest reduction in risk associated with high levels of leisure physical activity.
Create a Dataset using study data.
datagrid = !(*TagBox[GridBox[{{'<esophageal adenocarcinoma>', '899', '0.58', RowBox[{'{', TemplateBox[{'esophagus',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Esophagus'}], ']'}], 'Entity['AnatomicalStructure', 'Esophagus']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'esophageal cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine150'}], ']'}], 'Entity['Disease', 'ICDNine150']', 'disease'},'Entity']},{'<gallbladder>', '382', '0.72', RowBox[{'{', TemplateBox[{'gallbladder',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Gallbladder'}], ']'}], 'Entity['AnatomicalStructure', 'Gallbladder']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'gallbladder cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine156.0'}], ']'}], 'Entity['Disease', 'ICDNine156.0']', 'disease'},'Entity']},{'<liver>', '1384', '0.73', RowBox[{'{', TemplateBox[{'liver',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Liver'}], ']'}], 'Entity['AnatomicalStructure', 'Liver']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'primary liver cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine155.0'}], ']'}], 'Entity['Disease', 'ICDNine155.0']', 'disease'},'Entity']},{'<lung>', '19133', '0.74', RowBox[{'{', TemplateBox[{'lung',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Lung'}], ']'}], 'Entity['AnatomicalStructure', 'Lung']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{ 'cancer of the trachea, bronchus, and lung', RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine162'}], ']'}], 'Entity['Disease', 'ICDNine162']', 'disease'},'Entity']},{'<kidney>', '4548', '0.77', RowBox[{'{', TemplateBox[{'kidney',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Kidney'}], ']'}], 'Entity['AnatomicalStructure', 'Kidney']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{ 'cancer of the kidney and urinary organs', RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine189'}], ']'}], 'Entity['Disease', 'ICDNine189']', 'disease'},'Entity']},{'<small intestine>', '503', '0.78', RowBox[{'{', TemplateBox[{'small intestine',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'SmallIntestine'}], ']'}], 'Entity['AnatomicalStructure', 'SmallIntestine']','anatomical structure'},'Entity'], '}'}], TemplateBox[{ 'cancer of the small intestine',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine152'}], ']'}], 'Entity['Disease', 'ICDNine152']', 'disease'},'Entity']},{'<gastric cardia>', '790', '0.78', RowBox[{'{', TemplateBox[{'cardia of stomach',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'CardiaOfStomach'}], ']'}],'Entity['AnatomicalStructure', 'CardiaOfStomach']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'cancer of the cardia',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine151.0'}], ']'}], 'Entity['Disease', 'ICDNine151.0']', 'disease'},'Entity']},{'<endometrial>', '5346', '0.79', RowBox[{'{', TemplateBox[{'endometrium',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Endometrium'}], ']'}], 'Entity['AnatomicalStructure', 'Endometrium']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'cancer of the uterine body',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine182'}], ']'}], 'Entity['Disease', 'ICDNine182']', 'disease'},'Entity']},{'<esophageal squamous>', '442', '0.8', RowBox[{'{', TemplateBox[{'esophagus',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Esophagus'}], ']'}], 'Entity['AnatomicalStructure', 'Esophagus']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'esophageal cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine150'}], ']'}], 'Entity['Disease', 'ICDNine150']', 'disease'},'Entity']},{'<myeloid leukemia>', '1692', '0.8', RowBox[{'{', TemplateBox[{'bone marrow',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'BoneMarrow'}], ']'}], 'Entity['AnatomicalStructure', 'BoneMarrow']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'myeloid leukemia',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine205'}], ']'}], 'Entity['Disease', 'ICDNine205']', 'disease'},'Entity']},{'<myeloma>', '2161', '0.83', RowBox[{'{', TemplateBox[{'bone marrow',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'BoneMarrow'}], ']'}], 'Entity['AnatomicalStructure', 'BoneMarrow']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'multiple myeloma',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine203.0'}], ']'}], 'Entity['Disease', 'ICDNine203.0']', 'disease'},'Entity']},{'<colon>', '14160', '0.84', RowBox[{'{', TemplateBox[{'colon',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Colon'}], ']'}], 'Entity['AnatomicalStructure', 'Colon']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'colon cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine153'}], ']'}], 'Entity['Disease', 'ICDNine153']', 'disease'},'Entity']},{'<head and neck>', '3985', '0.85', RowBox[{'{', RowBox[{TemplateBox[{'head',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Head'}], ']'}], 'Entity['AnatomicalStructure', 'Head']', 'anatomical structure'},'Entity'], ',', TemplateBox[{'neck',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Neck'}], ']'}], 'Entity['AnatomicalStructure', 'Neck']', 'anatomical structure'},'Entity']}], '}'}], TemplateBox[{ ':f3b5cancer of the connective and soft tissue of the head, face, and neck:f3b5',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine171.0'}], ']'}], 'Entity['Disease', 'ICDNine171.0']', 'disease'},'Entity']},{'<rectum>', '5531', '0.87', RowBox[{'{', TemplateBox[{'rectum',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Rectum'}], ']'}], 'Entity['AnatomicalStructure', 'Rectum']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'rectal cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine154.1'}], ']'}], 'Entity['Disease', 'ICDNine154.1']', 'disease'},'Entity']},{'<bladder>', '9073', '0.87', RowBox[{'{', TemplateBox[{'urinary bladder',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'UrinaryBladder'}], ']'}], 'Entity['AnatomicalStructure', 'UrinaryBladder']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'bladder cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine188'}], ']'}], 'Entity['Disease', 'ICDNine188']', 'disease'},'Entity']},{'<breast>', '35178', '0.9', RowBox[{'{', TemplateBox[{'breast',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Breast'}], ']'}], 'Entity['AnatomicalStructure', 'Breast']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'female breast cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine174'}], ']'}], 'Entity['Disease', 'ICDNine174']', 'disease'},'Entity']},{'<non-hodgkin lymphoma>', '6953', '0.91', RowBox[{'{', TemplateBox[{'lymphocyte',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Lymphocyte'}], ']'}], 'Entity['AnatomicalStructure', 'Lymphocyte']','anatomical structure'},'Entity'], '}'}], TemplateBox[{ 'lymphosarcoma, reticulosarcoma, and other malignant tumors of lymphatic tissue',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine200'}], ']'}], 'Entity['Disease', 'ICDNine200']', 'disease'},'Entity']},{'<thyroid>', '1829', '0.92', RowBox[{'{', TemplateBox[{'thyroid gland',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'ThyroidGland'}], ']'}], 'Entity['AnatomicalStructure', 'ThyroidGland']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'thyroid cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine193'}], ']'}], 'Entity['Disease', 'ICDNine193']', 'disease'},'Entity']},{'<gastric noncardia>', '1428', '0.93', RowBox[{'{', TemplateBox[{'stomach',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Stomach'}], ']'}], 'Entity['AnatomicalStructure', 'Stomach']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'stomach cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine151'}], ']'}], 'Entity['Disease', 'ICDNine151']', 'disease'},'Entity']},{'<soft tissue>', '851', '0.94', RowBox[{'{', RowBox[{TemplateBox[{'tendon',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Tendon'}], ']'}], 'Entity['AnatomicalStructure', 'Tendon']', 'anatomical structure'},'Entity'], ',', TemplateBox[{'ligament',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'SetOfLigaments'}], ']'}], 'Entity['AnatomicalStructure', 'SetOfLigaments']','anatomical structure'},'Entity'], ',', TemplateBox[{'fascia (organ subdivision)',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'FasciaOrganSubdivision'}], ']'}], 'Entity['AnatomicalStructure', 'FasciaOrganSubdivision']','anatomical structure'},'Entity'], ',', TemplateBox[{'skin',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Skin'}], ']'}], 'Entity['AnatomicalStructure', 'Skin']', 'anatomical structure'},'Entity'], ',', TemplateBox[{'fibrous tissue',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'FibrousTissue'}], ']'}], 'Entity['AnatomicalStructure', 'FibrousTissue']','anatomical structure'},'Entity'], ',', TemplateBox[{'adipose tissue',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'AdiposeTissue'}], ']'}], 'Entity['AnatomicalStructure', 'AdiposeTissue']','anatomical structure'},'Entity'], ',', TemplateBox[{'synovial membrane',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'SynovialMembrane'}], ']'}],'Entity['AnatomicalStructure', 'SynovialMembrane']','anatomical structure'},'Entity'], ',', TemplateBox[{'muscle',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Muscle'}], ']'}], 'Entity['AnatomicalStructure', 'Muscle']', 'anatomical structure'},'Entity'], ',', TemplateBox[{'nerve',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Nerve'}], ']'}], 'Entity['AnatomicalStructure', 'Nerve']', 'anatomical structure'},'Entity'], ',', TemplateBox[{ 'blood vessel viewed macroscopically', RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'BloodVesselViewedMacroscopically'}], ']'}], 'Entity['AnatomicalStructure', 'BloodVesselViewedMacroscopically']', 'anatomical structure'},'Entity']}], '}'}], TemplateBox[{ 'cancer of connective and soft tissue', RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine171'}], ']'}], 'Entity['Disease', 'ICDNine171']', 'disease'},'Entity']},{'<pancreas>', '4186', '0.95', RowBox[{'{', TemplateBox[{'pancreas',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Pancreas'}], ']'}], 'Entity['AnatomicalStructure', 'Pancreas']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'pancreatic cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine157'}], ']'}], 'Entity['Disease', 'ICDNine157']', 'disease'},'Entity']},{'<lymphocytic leukemia>', '2160', '0.98', RowBox[{'{', TemplateBox[{'lymphocyte',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Lymphocyte'}], ']'}], 'Entity['AnatomicalStructure', 'Lymphocyte']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'lymphoid leukemia',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine204'}], ']'}], 'Entity['Disease', 'ICDNine204']', 'disease'},'Entity']},{'<ovary>', '2880', '1.01', RowBox[{'{', TemplateBox[{'ovary',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Ovary'}], ']'}], 'Entity['AnatomicalStructure', 'Ovary']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'ovarian cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine183.0'}], ']'}], 'Entity['Disease', 'ICDNine183.0']', 'disease'},'Entity']},{'<prostate>', '46890', '1.05', RowBox[{'{', TemplateBox[{'prostate',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Prostate'}], ']'}], 'Entity['AnatomicalStructure', 'Prostate']','anatomical structure'},'Entity'], '}'}], TemplateBox[{'prostate cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine185'}], ']'}], 'Entity['Disease', 'ICDNine185']', 'disease'},'Entity']},{'<brain>', '2110', '1.06', RowBox[{'{', TemplateBox[{'brain',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Brain'}], ']'}], 'Entity['AnatomicalStructure', 'Brain']', 'anatomical structure'},'Entity'], '}'}], TemplateBox[{'brain cancer',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine191'}], ']'}], 'Entity['Disease', 'ICDNine191']', 'disease'},'Entity']},{'<malignant melanoma>', '12438', '1.27', RowBox[{'{', TemplateBox[{'melanocyte',RowBox[{'Entity', '[', RowBox[{'AnatomicalStructure', ',', 'Melanocyte'}], ']'}], 'Entity['AnatomicalStructure', 'Melanocyte']','anatomical structure'},'Entity'], '}'}], TemplateBox[{ 'malignant melanoma of the skin',RowBox[{'Entity', '[', RowBox[{'Disease', ',', 'ICDNine172'}], ']'}], 'Entity['Disease', 'ICDNine172']', 'disease'},'Entity']}},AutoDelete->False,BaseStyle->8,GridBoxAlignment->{ 'Columns' -> {{Left}}, 'ColumnsIndexed' -> {}, 'Rows' -> {}, 'RowsIndexed' -> {}, 'Items' -> {}, 'ItemsIndexed' -> {}},GridBoxDividers->{ 'Columns' -> {{True}}, 'ColumnsIndexed' -> {}, 'Rows' -> {{True}}, 'RowsIndexed' -> {}, 'Items' -> {}, 'ItemsIndexed' -> {}},GridBoxItemSize->{ 'Columns' -> {{Automatic}}, 'ColumnsIndexed' -> {}, 'Rows' -> {{Automatic}}, 'RowsIndexed' -> {}, 'Items' -> {}, 'ItemsIndexed' -> {}}],'Grid']);
dataset = Dataset[Association[ Rule @@@ Transpose[{{'Cancer', 'Case count', 'Hazard ratio', 'Anatomical site', 'Disease'}, #}]] & /@ datagrid[[1]]]
Extract the total number of cases and mean hazard ratio.
dataset[Total, 'Case count']
dataset[Mean, 'Hazard ratio']
Store customized cancer entities and their data in an entity store.
entities = <| Map[#['Cancer'] -> <| 'Label' -> #['Cancer'], 'CaseCount' -> #['Case count'], 'HazardRatio' -> #['Hazard ratio'], 'AnatomicalSite' -> #['Anatomical site'], 'Disease' -> #['Disease'] |> &, Normal@dataset] |>;
properties = <| 'Label' -> <|'Label' -> 'label'|>, 'CaseCount' -> <|'Label' -> 'case count'|>, 'HazardRatio' -> <|'Label' -> 'hazard ratio'|>, 'AnatomicalSite' -> <|'Label' -> 'anatomical site'|>, 'Disease' -> <|'Label' -> 'disease'|> |>;
store = EntityStore['Cancer' -> <| 'Label' -> 'cancer', 'Entities' -> entities, 'Properties' -> properties |>]
Register the store for this session.
PrependTo[$EntityStores, store];
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Ezip 1 7 3 x 4. Retrieve entities and available properties in the entity store. The sims 4 24 hour clock.
EntityList['Cancer']
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EntityValue['Cancer', 'Properties']
Show diseases associated with cancers. Fileloupe 1 7 14.
EntityValue['Cancer', 'Disease', 'EntityAssociation'] // Take[#, 5] & // Normal // Column
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Retrieve body mass index (BMI) information from the entity store.
bmi = EntityValue[EntityValue['Cancer', 'Disease'], EntityProperty['Disease', 'BodyMassIndexMean'], 'EntityAssociation']
Make a histogram of BMI for groups of normal patients and patients with common types of cancer.
Histogram[{MedicalTestData['BodyMassIndex', 'DistributionData'][[2, 1]], bmi}, Automatic, 'Probability', ChartElementFunction -> 'FadingRectangle', PlotLabel -> 'body mass index', ChartLegends -> {'normal', 'patients with common types of cancer'}]
Retrieve information about hazard ratio associated with high vs. low leisure physical activity.
hr = Normal[EntityValue['Cancer', 'HazardRatio', 'EntityAssociation']]
Plot cancer type vs. hazard ratio associated with high vs. low leisure physical activity.
ListPlot[Tooltip[#2, #1] & @@@ hr, Axes -> True, PlotRange -> {.5, 1.3}, PlotStyle -> Directive[Orange, PointSize[Large]], Ticks -> {Transpose[{Range[Length[hr]], Rotate[#, -Pi/2, {Left, 0}] & /@ hr[[All, 1]]}], Automatic}, PlotLabel -> 'Hazard ratio associated with leisure[Hyphen]time physical activity', PlotRange -> {{1, 30}, All}, AxesLabel -> {'type of cancer', 'Hazard ratio'}]
Use an implicitly defined entity class to find the types of cancer in which higher leisure physical activity is associated with reduction in risk by more than 20%.
TextGrid[EntityValue[ EntityClass[ 'Cancer', {'HazardRatio' -> LessThan[1 - 0.2]}], {'Entity', 'HazardRatio'}], Dividers -> All, Background -> {Automatic, {{LightBlue, None}}}] // TraditionalForm