语义链接癌症模型

此图 gist 提供了一组 Cypher 查询，以使用属性图数据模型作为将癌症模型描述与元数据链接起来的方法。

癌症“模型”是指构成“模拟”基础的“数学”或“计算”模型。在这种情况下，我们指的是癌症生物学建模，因此指的是癌症功能和进展的模拟（即预测的癌症过程）。“模型描述”是对模型的抽象，包括元数据以及对模型实现（可能是代码或可执行文件）的引用。模型通常具有一些初始状态，其中模拟会产生该状态的一些变化或渐进变化。在癌症模型的情况下，我们可能有一些起始参数和肿瘤的 3D 模型，当运行模拟时，参数会更新，并且 3D 模型会发生变化以反映肿瘤生命周期随时间的预测。有关癌症生物学介绍，请查看此处提供的免费电子书 https://bookboon.com/en/introduction-to-cancer-biology-ebook

我们认为，在属性图中表示癌症模型集合将使我们能够创建可查询的系统，通过这些系统，我们可以通过与领域数据的语义链接来探索癌症模型的组合。使用属性图数据模型背后的理念是能够通过特定于领域的元数据（例如单位、计算类型以及生物学术语和分类学分类）将不同的癌症模型链接在一起。

使用此数据库，我们可以提出以下问题

哪些癌症模型属于同一类别？
哪些癌症模型具有共同的输入和输出参数？
哪些癌症模型是直接或间接链接在一起的？

数据模型

实体

MODEL - 表示抽象模型描述
PARAMETER - 表示模型接口参数
CATEGORY - 表示癌症模型分类的元数据
TERM - 表示受控词汇表术语的元数据
UNIT - 表示度量单位的元数据
PERSON - 表示一个人
ORGANISATION - 表示一个组织

关系

HAS_INPUT - 将模型与其输入参数连接起来
HAS_OUTPUT - 将模型与其输出参数连接起来
HAS_METADATA - 将模型和参数连接到元数据
HAS_CATEGORY - 将类别与其他类别连接起来（即子类别）
CONTAINS - 将模型与其他子模型连接起来（以显示模型组成）
SYNONYM_OF_TERM - 将术语与其同义词连接起来
CREATED_BY - 将模型与模型的创建者（或作者）连接起来
CONTRIBUTED_BY - 将模型与模型描述的发布者（即数据库记录）连接起来

查询控制台

填充图 ^顶部

// Create DB
// TUMOR taxonomy
CREATE (TumorMetadata:Category {name:'Tumor Model Metadata'})
CREATE (Math:Category {name:'Math'})
CREATE (SingleScale:Category {name:'Single-scale'})
CREATE (Multiscale:Category {name:'Multiscale'})
CREATE (Approach:Category {name:'Modeling approach'})
CREATE (Cancer:Category {name:'Cancer'})
CREATE (Homogeneity:Category {name:'Homogeneity'})
CREATE
  (TumorMetadata)-[:HAS_CATEGORY]->(Math),
  (TumorMetadata)-[:HAS_CATEGORY]->(SingleScale),
  (TumorMetadata)-[:HAS_CATEGORY]->(Multiscale),
  (TumorMetadata)-[:HAS_CATEGORY]->(Approach),
  (TumorMetadata)-[:HAS_CATEGORY]->(Cancer),
  (TumorMetadata)-[:HAS_CATEGORY]->(Homogeneity)
CREATE (Discrete:Category {name:'Discrete'})
CREATE (Continuous:Category {name:'Continuous'})
CREATE (Hybrid:Category {name:'Hybrid'})
CREATE
  (Math)-[:HAS_CATEGORY]->(Discrete),
  (Math)-[:HAS_CATEGORY]->(Continuous),
  (Math)-[:HAS_CATEGORY]->(Hybrid)
CREATE (Organ:Category {name:'Organ'})
CREATE (Tissue:Category {name:'Tissue'})
CREATE (Cell:Category {name:'Cell'})
CREATE (Subcellular:Category {name:'Subcellular'})
CREATE (Gene:Category {name:'Gene'})
CREATE
  (SingleScale)-[:HAS_CATEGORY]->(Organ),
  (SingleScale)-[:HAS_CATEGORY]->(Tissue),
  (SingleScale)-[:HAS_CATEGORY]->(Cell),
  (SingleScale)-[:HAS_CATEGORY]->(Subcellular),
  (SingleScale)-[:HAS_CATEGORY]->(Gene)

CREATE (TopDown:Category {name:'Top-down'})
CREATE (BottomUp:Category {name:'Bottom-up'})
CREATE (MiddleOut:Category {name:'Middle-out'})
CREATE
  (Approach)-[:HAS_CATEGORY]->(TopDown),
  (Approach)-[:HAS_CATEGORY]->(BottomUp),
  (Approach)-[:HAS_CATEGORY]->(MiddleOut)
CREATE (Glioma:Category {name:'Glioma'})
CREATE (Nephroblastoma:Category {name:'Nephroblastoma'})
CREATE (Lung:Category {name:'Lung'})
CREATE (Breast:Category {name:'Breast'})
CREATE (Generic:Category {name:'Generic'})
CREATE
  (Cancer)-[:HAS_CATEGORY]->(Glioma),
  (Cancer)-[:HAS_CATEGORY]->(Nephroblastoma),
  (Cancer)-[:HAS_CATEGORY]->(Lung),
  (Cancer)-[:HAS_CATEGORY]->(Breast),
  (Cancer)-[:HAS_CATEGORY]->(Generic)
CREATE (Homogeneous:Category {name:'Homogeneous'})
CREATE (NonHomogeneous:Category {name:'Non-homogeneous'})
CREATE
  (Homogeneity)-[:HAS_CATEGORY]->(Homogeneous),
  (Homogeneity)-[:HAS_CATEGORY]->(NonHomogeneous)
CREATE (TreatmentIncluded:Category {name:'Treatment included'})
CREATE (NoTreatmentIncluded:Category {name:'No treatment included'})
CREATE
  (TumorMetadata)-[:HAS_CATEGORY]->(TreatmentIncluded),
  (TumorMetadata)-[:HAS_CATEGORY]->(NoTreatmentIncluded)

// Units metadata
CREATE (SiBaseUnit:Unit {name:'SI base unit'})
CREATE (Meter:Unit {name:'Meter'})
CREATE (Kilogram:Unit {name:'Kilogram'})
CREATE (Second:Unit {name:'Second'})
CREATE (Ampere:Unit {name:'Ampere'})
CREATE (Kelvin:Unit {name:'Kelvin'})
CREATE (Mole:Unit {name:'Mole'})
CREATE (Candela:Unit {name:'Candela'})
CREATE
  (SiBaseUnit)-[:HAS_CATEGORY]->(Meter),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Kilogram),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Second),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Ampere),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Kelvin),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Mole),
  (SiBaseUnit)-[:HAS_CATEGORY]->(Candela)
CREATE (TumorExtraUnit:Unit {name:'TUMOR extra unit'})
CREATE (Item:Unit {name:'Item'})
CREATE (Gray:Unit {name:'Gray'})
CREATE (Unitless:Unit {name:'Unitless'})
CREATE
  (TumorExtraUnit)-[:HAS_CATEGORY]->(Item),
  (TumorExtraUnit)-[:HAS_CATEGORY]->(Gray),
  (TumorExtraUnit)-[:HAS_CATEGORY]->(Unitless)
CREATE (ConversionFactor:Unit {name:'Conversion factor'})
CREATE (Tera:Unit {name:'Tera'})
CREATE (Giga:Unit {name:'Giga'})
CREATE (Mega:Unit {name:'Mega'})
CREATE (Kilo:Unit {name:'Kilo'})
CREATE (Hecto:Unit {name:'Hecto'})
CREATE (Deca:Unit {name:'Deca'})
CREATE (Deci:Unit {name:'Deci'})
CREATE (Centi:Unit {name:'Centi'})
CREATE (Milli:Unit {name:'Milli'})
CREATE (Micro:Unit {name:'Micro'})
CREATE (Nano:Unit {name:'Nano'})
CREATE (Pico:Unit {name:'Pico'})
CREATE
  (ConversionFactor)-[:HAS_CATEGORY]->(Tera),
  (ConversionFactor)-[:HAS_CATEGORY]->(Giga),
  (ConversionFactor)-[:HAS_CATEGORY]->(Mega),
  (ConversionFactor)-[:HAS_CATEGORY]->(Kilo),
  (ConversionFactor)-[:HAS_CATEGORY]->(Hecto),
  (ConversionFactor)-[:HAS_CATEGORY]->(Deca),
  (ConversionFactor)-[:HAS_CATEGORY]->(Deci),
  (ConversionFactor)-[:HAS_CATEGORY]->(Centi),
  (ConversionFactor)-[:HAS_CATEGORY]->(Milli),
  (ConversionFactor)-[:HAS_CATEGORY]->(Micro),
  (ConversionFactor)-[:HAS_CATEGORY]->(Nano),
  (ConversionFactor)-[:HAS_CATEGORY]->(Pico)
//CLI data types
CREATE
	(CLImetadata:Type { name : 'CLI metadata' }),
	(CLImetadata)-[:HAS_CATEGORY]->(CLIdataType:Type { name :"CLI data type"}),
	(int:Type { name : 'Integer' }),
	(double:Type { name : 'Double precision floating point' }),
	(filename:Type { name :'Filename' }),
	(string:Type { name : 'String' }),
	(CLIdataType)-[:HAS_CATEGORY]->(int),
	(CLIdataType)-[:HAS_CATEGORY]->(double),
	(CLIdataType)-[:HAS_CATEGORY]->(filename),
	(CLIdataType)-[:HAS_CATEGORY]->(string)

// Create Tom and Bill at CBML
CREATE (Tom:Person {URN:'urn:orcid:tumor:0000-0003-2850-3614', fullname:'Thomas S. Deisboeck'})
CREATE (Bill:Person {URN:'urn:tumorml.org:user:000001', fullname:'Zhihui Bill Wang'})
CREATE (CBML:Organisation {URN:'urn:tumorml.org:organisation:000001', fullname:'Complex Biosystems Modeling Laboratory (CBML), Massachusetts General Hospital'})
CREATE
  (Tom)-[:MEMBER_OF]->(CBML),
  (Bill)-[:MEMBER_OF]->(CBML)

// Create EGFR-ERK Pathway
CREATE (EgfrErkPathway:Model {URN:'urn:miriam:tumor:000001', title: 'EGFR-ERK Pathway'})
CREATE (EGF:Parameter {name:'EGF'})
CREATE (CellCycleTime1:Parameter {name:'Cell cycle time'})
CREATE (PLCg:Parameter {name:'PLCg'})
CREATE
  (EgfrErkPathway)-[:HAS_INPUT]->(EGF),
  (EgfrErkPathway)-[:HAS_OUTPUT]->(CellCycleTime1),
  (EgfrErkPathway)-[:HAS_OUTPUT]->(PLCg)
CREATE
  (EgfrErkPathway)-[:CONTRIBUTED_TO_BY]->(Tom),
  (EgfrErkPathway)-[:CREATED_BY]->(Bill),
  (EgfrErkPathway)-[:PUBLISHED_BY]->(CBML)
CREATE
  (EgfrErkPathway)-[:HAS_METADATA]->(Subcellular),
  (EgfrErkPathway)-[:HAS_METADATA]->(Continuous),
  (EgfrErkPathway)-[:HAS_METADATA]->(BottomUp),
  (EgfrErkPathway)-[:HAS_METADATA]->(Homogeneous),
  (EgfrErkPathway)-[:HAS_METADATA]->(NoTreatmentIncluded),
  (EgfrErkPathway)-[:HAS_METADATA]->(Lung)

// Create David and Anthony
CREATE (ImperialCollege:Organisation {URN:'urn:tumorml.org:organisation:000002', name:'Discovery Sciences Group, Imperial College London'})
CREATE (David:Person {URN:'urn:orcid:tumor:0000-0002-2323-6847', name:'David Johnson'})
CREATE 	(Anthony:Person {URN:'urn:tumorml.org:user:000002', name:'Anthony J. Connor'})
CREATE (OxfordUniversity:Organisation {URN:'urn:tumorml.org:organisation:000003', name:'Computational Biology Group, University of Oxford'})

CREATE
	(David)-[:MEMBER_OF]->(ImperialCollege),
	(Anthony)-[:MEMBER_OF]->(OxfordUniversity)

//Create model for VTG Framework
CREATE
	(model3:Model { URN : 'urn:miriam:tumor:000003', title : 'Vascular Tumour Growth Framework'}),
	(model3)-[:HAS_CREATOR]->(Anthony),
	(model3)-[:HAS_PUBLISHER]->(David),
	(model3)-[:HAS_METADATA]->(Continuous),
	(model3)-[:HAS_METADATA]->(BottomUp),
	(model3)-[:HAS_METADATA]->(NonHomogeneous)

//Import term for VEGF from NCIt
CREATE (C1272:Term { term : 'C1272', source : 'NCI Thesaurus' })
CREATE (C1272_term1:Term { term : 'Recombinant Vascular Endothelial Growth Factor' })
CREATE (C1272_term2:Term { term : 'rhuVEGF' })
CREATE (C1272_term3:Term { term : 'vascular endothelial growth factor' })
CREATE (C1272_term4:Term { term : 'Vascular Endothelial Growth Factor' })
CREATE (C1272_term5:Term { term : 'Vascular Permeability Factor' })
CREATE (C1272_term6:Term { term : 'VEGF' })
CREATE (C1272_term7:Term { term : 'VPF' })
CREATE
	(C1272)-[:PREFERRED_TERM]->(C1272_term1),
	(C1272)-[:PREFERRED_TERM]->(C1272_term3),
	(C1272)-[:ABBREVIATION]->(C1272_term2),
	(C1272)-[:ABBREVIATION]->(C1272_term6),
	(C1272)-[:ABBREVIATION]->(C1272_term7),
	(C1272)-[:SYNONYM]->(C1272_term4),
	(C1272)-[:SYNONYM]->(C1272_term5)

//Import term for intracellular from NCIt
CREATE (C28217:Term { term : 'C28217', source : 'NCI Thesaurus' })
CREATE (C28217_term1:Term { term : 'Intracellular' })
CREATE (C28217_term2:Term { term : 'intracellular' })
CREATE
	(C28217)-[:PREFERRED_TERM]->(C28217_term1),
	(C28217)-[:PREFERRED_TERM]->(C28217_term2)

//Import term for extracellular from NCIt
CREATE (C26055:Term { term : 'C26055', source : 'NCI Thesaurus' })
CREATE (C26055_term1:Term { term : 'Extracellular Space' })
CREATE (C26055)-[:PREFERRED_TERM]->(C26055_term1)

//Combine terms into single nodes
CREATE (IntraCellVEGF:Term { term : 'Intracellular VEGF', source : 'User-defined' })
CREATE
   (IntraCellVEGF)-[:HAS_METADATA]->(C1272),
   (IntraCellVEGF)-[:HAS_METADATA]->(C28217)
CREATE (ExtraCellVEGF:Term { term : 'Extracellular VEGF', source : 'User-defined' })
CREATE
   (ExtraCellVEGF)-[:HAS_METADATA]->(C1272),
   (ExtraCellVEGF)-[:HAS_METADATA]->(C26055)

//Create model for Alarcon 2005 Subcellular
CREATE (model4:Model {URN:'urn:miriam:tumor:000004', title:'Alarcon 2005 Subcellular model'})
CREATE
	(model4)-[:HAS_CREATOR]->(Anthony),
	(model4)-[:HAS_PUBLISHER]->(David)
CREATE (Oxygen:Parameter {name:'oxygen'})
CREATE (CellDistribution:Parameter {name:'cell_distribution'})
CREATE (VEGF:Parameter {name:'vegf'})
CREATE (P53:Parameter {name:'p53'})
CREATE (CellCycleTime2:Parameter {name:'cell_cycle_time'})
CREATE (CellState:Parameter {name:'cell_state'})
CREATE
	(model4)-[:HAS_INPUT]->(Oxygen),
	(model4)-[:HAS_INPUT]->(CellDistribution),
	(model4)-[:HAS_OUTPUT]->(VEGF),
	(model4)-[:HAS_OUTPUT]->(P53),
	(model4)-[:HAS_OUTPUT]->(CellCycleTime2),
	(model4)-[:HAS_OUTPUT]->(CellState),
	(model4)-[:HAS_METADATA]->(Continuous),
	(model4)-[:HAS_METADATA]->(BottomUp),
	(model4)-[:HAS_METADATA]->(NonHomogeneous),
	(model4)-[:HAS_METADATA]->(NoTreatmentIncluded),
	(VEGF)-[:HAS_METADATA]->(IntraCellVEGF)

//Create model for Owen 2011 Subcellular model
CREATE (model5:Model {URN:'urn:miriam:tumor:000005', title:'Owen 2011 Subcellular model'})
CREATE
	(model5)-[:HAS_CREATOR]->(Anthony),
	(model5)-[:HAS_PUBLISHER]->(David),
	(model5)-[:HAS_METADATA]->(Continuous),
	(model5)-[:HAS_METADATA]->(BottomUp),
	(model5)-[:HAS_METADATA]->(NonHomogeneous),
	(model5)-[:HAS_METADATA]->(NoTreatmentIncluded)

//Create model for Fixed Duration Subcellular model (Alarcon 2003)
CREATE (model6:Model {URN:'urn:miriam:tumor:000006', title:'Fixed Duration Subcellular model'})
CREATE
	(model6)-[:HAS_CREATOR]->(Anthony),
	(model6)-[:HAS_PUBLISHER]->(David),
	(model6)-[:HAS_METADATA]->(Continuous),
	(model6)-[:HAS_METADATA]->(BottomUp),
	(model6)-[:HAS_METADATA]->(NonHomogeneous),
	(model6)-[:HAS_METADATA]->(NoTreatmentIncluded)

//Create model for VEGF calculator (Alarcon 2005)
CREATE (model7:Model {URN:'urn:miriam:tumor:000007', title:'Alarcon 2005 VEGF Calculator'})
CREATE
	(model7)-[:HAS_CREATOR]->(Anthony),
	(model7)-[:HAS_PUBLISHER]->(David)
CREATE
	(model7)-[:HAS_METADATA]->(Continuous),
	(model7)-[:HAS_METADATA]->(BottomUp),
	(model7)-[:HAS_METADATA]->(NonHomogeneous),
	(model7)-[:HAS_METADATA]->(NoTreatmentIncluded)
CREATE (VEGFin1:Parameter {name:'cellular_vegf'} )
CREATE (VEGFout1:Parameter {name:'extracellular_vegf'} )
CREATE
	(model7)-[:HAS_INPUT]->(VEGFin1),
	(model7)-[:HAS_OUTPUT]->(VEGFout1)
CREATE
	(VEGFin1)-[:HAS_CLIDATATYPE]->(double),
	(VEGFin1)-[:HAS_UNIT]->(Mole),
	(VEGFin1)-[:HAS_FACTOR]->(Nano),
	(VEGFin1)-[:HAS_METADATA]->(IntraCellVEGF)
CREATE
	(VEGFout1)-[:HAS_CLIDATATYPE]->(double),
	(VEGFout1)-[:HAS_UNIT]->(Mole),
	(VEGFout1)-[:HAS_FACTOR]->(Nano),
	(VEGFout1)-[:HAS_METADATA]->(ExtraCellVEGF)

//Create model for VEGF calculator (Alarcon 2006)
CREATE (model8:Model {URN:'urn:miriam:tumor:000008', title:'Alarcon 2006 VEGF Calculator'})
CREATE
	(model8)-[:HAS_CREATOR]->(Anthony),
	(model8)-[:HAS_PUBLISHER]->(David)
CREATE
	(model8)-[:HAS_METADATA]->(Continuous),
	(model8)-[:HAS_METADATA]->(BottomUp),
	(model8)-[:HAS_METADATA]->(NonHomogeneous),
	(model8)-[:HAS_METADATA]->(NoTreatmentIncluded)
CREATE (VEGFin2:Parameter {name:'cellular_vegf'} )
CREATE (VEGFout2:Parameter {name:'extracellular_vegf'} )
CREATE
	(model8)-[:HAS_INPUT]->(VEGFin2),
	(model8)-[:HAS_OUTPUT]->(VEGFout2)
CREATE
	(VEGFin2)-[:HAS_CLIDATATYPE]->(double),
	(VEGFin2)-[:HAS_UNIT]->(Mole),
	(VEGFin2)-[:HAS_FACTOR]->(Nano),
	(VEGFin2)-[:HAS_METADATA]->(IntraCellVEGF)
CREATE
	(VEGFout2)-[:HAS_CLIDATATYPE]->(double),
	(VEGFout2)-[:HAS_UNIT]->(Mole),
	(VEGFout2)-[:HAS_FACTOR]->(Nano),
	(VEGFout2)-[:HAS_METADATA]->(ExtraCellVEGF)

//Create model for VEGF calculator (Owen 2011)
CREATE (model9:Model {URN:'urn:miriam:tumor:000009', title:'Owen 2011 VEGF Calculator'})
CREATE
	(model9)-[:HAS_CREATOR]->(Anthony),
	(model9)-[:HAS_PUBLISHER]->(David)
CREATE
	(model9)-[:HAS_METADATA]->(Continuous),
	(model9)-[:HAS_METADATA]->(BottomUp),
	(model9)-[:HAS_METADATA]->(NonHomogeneous),
	(model8)-[:HAS_METADATA]->(NoTreatmentIncluded)
CREATE (VEGFin3:Parameter {name:'cellular_vegf'} )
CREATE (VEGFout3:Parameter {name:'extracellular_vegf'} )
CREATE
	(model8)-[:HAS_INPUT]->(VEGFin3),
	(model8)-[:HAS_OUTPUT]->(VEGFout3)
CREATE
	(VEGFin3)-[:HAS_CLIDATATYPE]->(double),
	(VEGFin3)-[:HAS_UNIT]->(Mole),
	(VEGFin3)-[:HAS_FACTOR]->(Nano),
	(VEGFin3)-[:HAS_METADATA]->(IntraCellVEGF)
CREATE
	(VEGFout3)-[:HAS_CLIDATATYPE]->(double),
	(VEGFout3)-[:HAS_UNIT]->(Mole),
	(VEGFout3)-[:HAS_FACTOR]->(Nano),
	(VEGFout3)-[:HAS_METADATA]->(ExtraCellVEGF)

//Create model for Metabolic Stimulus Calculation (Alarcon 2005)
CREATE (model10:Model {URN:'urn:miriam:tumor:000010', title:'Alarcon 2005 Metabolic Stimulus Calculation'})
CREATE
	(model10)-[:HAS_CREATOR]->(Anthony),
	(model10)-[:HAS_PUBLISHER]->(David)
CREATE
	(model10)-[:HAS_METADATA]->(Continuous),
	(model10)-[:HAS_METADATA]->(BottomUp),
	(model10)-[:HAS_METADATA]->(NonHomogeneous),
	(model10)-[:HAS_METADATA]->(NoTreatmentIncluded)

//Create model for Angiogenesis Model (Owen 2009)
CREATE (model11:Model {URN:'urn:miriam:tumor:000011', title:'Owen 2009 Angiogenesis Model'})
CREATE
	(model11)-[:HAS_CREATOR]->(Anthony),
	(model11)-[:HAS_PUBLISHER]->(David)
CREATE
	(model11)-[:HAS_METADATA]->(Continuous),
	(model11)-[:HAS_METADATA]->(BottomUp),
	(model11)-[:HAS_METADATA]->(NonHomogeneous),
	(model11)-[:HAS_METADATA]->(NoTreatmentIncluded)


//Create model for Angiogenesis Model (Owen 2011)
CREATE (model12:Model {URN:'urn:miriam:tumor:000012', title:'Owen 2011 Angiogenesis Model'})
CREATE
	(model12)-[:HAS_CREATOR]->(Anthony),
	(model12)-[:HAS_PUBLISHER]->(David)
CREATE
	(model12)-[:HAS_METADATA]->(Continuous),
	(model12)-[:HAS_METADATA]->(BottomUp),
	(model12)-[:HAS_METADATA]->(NonHomogeneous),
	(model12)-[:HAS_METADATA]->(NoTreatmentIncluded)

//Create model for Alarcon 03 Subcellular Model
CREATE (model14:Model {URN:'urn:miriam:tumor:000014', title:'Alarcon 03 Subcellular Model'})
CREATE
	(model14)-[:HAS_CREATOR]->(Anthony),
	(model14)-[:HAS_PUBLISHER]->(David)
CREATE
	(model14)-[:HAS_METADATA]->(Subcellular)

//Create model for Alarcon 03 Cell Proliferation Model
CREATE (model15:Model {URN:'urn:miriam:tumor:000015', title:'Alarcon 03 Cell Proliferation Model'})
CREATE
	(model15)-[:HAS_CREATOR]->(Anthony),
	(model15)-[:HAS_PUBLISHER]->(David)
CREATE
	(model15)-[:HAS_METADATA]->(Cell)

//Create model for Alarcon 03 Oxygen Calculator
CREATE (model16:Model {URN:'urn:miriam:tumor:000016', title:'Alarcon 03  Oxygen Calculator'})
CREATE
	(model16)-[:HAS_CREATOR]->(Anthony),
	(model16)-[:HAS_PUBLISHER]->(David)
CREATE
	(model16)-[:HAS_METADATA]->(Tissue)

//Create model for Alarcon 03 Vascular Structural Adaptation Model
CREATE (model17:Model {URN:'urn:miriam:tumor:000017', title:'Alarcon 03  Vascular Structural Adaptation Model'})
CREATE
	(model17)-[:HAS_CREATOR]->(Anthony),
	(model17)-[:HAS_PUBLISHER]->(David)
CREATE
	(model17)-[:HAS_METADATA]->(Tissue)

//Create model for Alarcon 03 Model
CREATE (model13:Model {URN:'urn:miriam:tumor:000013', title:'Alarcon 03 Model'})
CREATE
	(model13)-[:HAS_CREATOR]->(Anthony),
	(model13)-[:HAS_PUBLISHER]->(David)
CREATE
	(model13)-[:HAS_METADATA]->(Multiscale),
	(model13)-[:CONTAINS]->(model14),
	(model13)-[:CONTAINS]->(model15),
	(model13)-[:CONTAINS]->(model16),
	(model13)-[:CONTAINS]->(model17)

可视化图 ^顶部

以下是使用癌症模型描述的测试数据集对整个属性图进行可视化的示例。有关所用癌症模型的更多信息，请查看我们的论文“语义链接计算机模拟癌症模型” https://www.la-press.com/semantically-linking-in-silico-cancer-models-article-a4552

完整的图本身并没有特别有用。但是，它为更有趣的查询（例如以下查询）提供了基础。

癌症模型描述

这就是模型如何被可视化为属性图。在这种情况下，这是 Z. Wang 等人在“使用多尺度基于代理的模型模拟非小细胞肺癌，Theor Biol Med Model，4(1):50+，2007 年 12 月”中提出的 EGFR-ERK 分子通路模型。 https://dx.doi.org/10.1186/1742-4682-4-50

模型具有元数据，例如创建者、贡献者、发布者、模型分类（例如肺癌、均匀肿瘤块、亚细胞尺度）以及输入和输出参数（例如 EGF 浓度、细胞周期时间）。参数可以链接到领域图中表示的其他领域元数据。

领域元数据

类别

癌症模型的分类学分类。

MATCH (n:Category)
RETURN collect(n.name) AS Categories

单位

数值单位，包括 SI 单位和一些派生单位。

MATCH (n:Unit)
RETURN collect(n.name) AS Units

CLI 数据类型

命令行界面数据类型，例如字符串、文件名和格式不同的数字。

MATCH (n:Type)
RETURN collect(n.name) AS CLIdatatypes

人员和组织

对模型开发或描述拥有某种所有权或贡献权的外部实体。

MATCH (n:Person)-[:MEMBER_OF]-(m:Organisation)
RETURN n.name AS Name, m.name AS Organisation

哪些癌症模型使用连续数学建模？ ^顶部

MATCH (n:Model)
WHERE (n)-[:HAS_METADATA]-({ name:'Continuous'})
RETURN n.title AS Model

哪些癌症模型具有共同且兼容的输入和输出参数？ ^顶部

MATCH (n:Model)-[:HAS_INPUT]-(p:Parameter)-[:HAS_METADATA]-(meta:Term)-[:HAS_METADATA]-(q:Parameter)-[:HAS_OUTPUT]-(m:Model)
WHERE n<>m
RETURN DISTINCT m.title AS ModelA, n.title AS ModelB, q.name AS OutputA, p.name AS InputB, meta.term

在多尺度 Alarcon 2003 模型中，组件模型和对应尺度是什么？ ^顶部

MATCH (n:Model {URN: 'urn:miriam:tumor:000013'})-[:HAS_METADATA]-(:Category {name: 'Multiscale'}), (m:Model)
MATCH (n)-[:CONTAINS]-(m)
MATCH (m)-[:HAS_METADATA]-(scale:Category)-[:HAS_CATEGORY]-(:Category {name: 'Single-scale'})
RETURN m.title AS ComponentModel, scale.name As Scale

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