/* Bioc Views Vocabular Definition in dot format */

/* How To Process this file:
   1. Use dot2gxl from graphviz to transform into GXL format.
	  dot2gxl biocViewsVocab.dot > biocViewsVocab.gxl
   2. use graph::fromGXL to obtain a graphNEL object

*/

digraph G {

/****************************************************************************
 *                               Software                                   *
 ****************************************************************************/
BiocViews -> Software;

/* Software -> AssayDomain */
Software -> AssayDomain;
AssayDomain -> aCGH;
AssayDomain -> CellBasedAssays;
AssayDomain -> ChIPchip;
AssayDomain -> CopyNumberVariation;
AssayDomain -> CpGIsland;
AssayDomain -> DNAMethylation;
AssayDomain -> ExonArray;
AssayDomain -> GeneExpression;
AssayDomain -> GeneticVariability;
AssayDomain -> SNP;
AssayDomain -> Transcription;

/* Software -> Technology */
Software -> Technology;
Technology -> Sequencing;
Sequencing -> ATACSeq;
Sequencing -> DNASeq;
Sequencing -> DNaseSeq;
Sequencing -> RiboSeq;
Sequencing -> RNASeq;
Sequencing -> ChIPSeq;
Sequencing -> RIPSeq;
Sequencing -> MethylSeq;
Sequencing -> ExomeSeq;
Sequencing -> miRNA;
Sequencing -> SangerSeq;
Sequencing -> SmallRNA;
Sequencing -> Microbiome;
Sequencing -> WholeGenome;
Sequencing -> DenovoGenome;
Sequencing -> TargetedResequencing;
Sequencing -> DenovoTranscriptome;
Sequencing -> MicrobialStrain;
Sequencing -> HiC;
Sequencing -> PooledScreens;
Sequencing -> MNaseSeq;
Sequencing -> LongRead;
Technology -> Microarray;
Microarray -> MultiChannel;
Microarray -> OneChannel;
Microarray -> TwoChannel;
Microarray -> MethylationArray;
Microarray -> GenotypingArray;
Microarray -> MicroRNAArray;
Microarray -> mRNAMicroarray;
Microarray -> ChipOnChip;
Microarray -> ReversePhaseProteinArray;
Microarray -> TissueMicroarray;
Microarray -> ProprietaryPlatforms;
Technology -> FlowCytometry;
Technology -> MassSpectrometry;
MassSpectrometry -> ImagingMassSpectrometry;
Technology -> qPCR;
Technology -> MicrotitrePlateAssay;
Technology -> SAGE;
Technology -> CRISPR;
Technology -> SingleCell;
Technology -> Spatial;
Technology -> ddPCR;
Technology -> AnnotationHubSoftware;
Technology -> ExperimentHubSoftware;

/* Software -> ResearchFields */
Software -> ResearchField;
ResearchField -> CellBiology;
ResearchField -> Genetics;
ResearchField -> Metabolomics;
ResearchField -> Metagenomics;
ResearchField -> Proteomics;
ResearchField -> Lipidomics;
ResearchField -> Epigenetics;
ResearchField -> Phylogenetics;
ResearchField -> Pharmacogenomics;
ResearchField -> Pharmacogenetics;
ResearchField -> Cheminformatics;
ResearchField -> StructuralGenomics;
ResearchField -> StructuralPrediction;
ResearchField -> Biophysics;
ResearchField -> MathematicalBiology;
ResearchField -> BiomedicalInformatics;
ResearchField -> ComparativeGenomics;
ResearchField -> FunctionalGenomics;
ResearchField -> SystemsBiology;
ResearchField -> ComputationalChemistry;
ResearchField -> Agroinformatics;
ResearchField -> Transcriptomics;
ResearchField -> Epitranscriptomics;
ResearchField -> Immunology;
Immunology -> Immunogenetics;
Immunology -> ImmunoOncology;
Immunology -> ImmunoPrevention;

/* Software -> BiologicalQuestion */
Software -> BiologicalQuestion;
BiologicalQuestion -> AlternativeSplicing;
BiologicalQuestion -> Coverage;
BiologicalQuestion -> DemethylateRegionDetection;
BiologicalQuestion -> DenovoAssembler;
BiologicalQuestion -> DifferentialDNA3DStructure;
BiologicalQuestion -> DifferentialExpression;
BiologicalQuestion -> DifferentialMethylation;
BiologicalQuestion -> DifferentialPeakCalling;
BiologicalQuestion -> DifferentialSplicing;
BiologicalQuestion -> DNA3DStructure;
BiologicalQuestion -> DriverMutation;
BiologicalQuestion -> FunctionalPrediction;
BiologicalQuestion -> GeneFusionDetection;
BiologicalQuestion -> GenePrediction;
BiologicalQuestion -> GeneRegulation;
BiologicalQuestion -> GeneSetEnrichment;
BiologicalQuestion -> GeneSignaling;
BiologicalQuestion -> GeneTarget;
BiologicalQuestion -> GenomeAssembly;
BiologicalQuestion -> GenomeWideAssociation;
BiologicalQuestion -> GenomicVariation;
BiologicalQuestion -> GenomeAnnotation;
BiologicalQuestion -> GermlineMutation;
BiologicalQuestion -> HistoneModification;
BiologicalQuestion -> IndelDetection;
BiologicalQuestion -> LinkageDisequilibrium;
BiologicalQuestion -> MetagenomeAssembly;
BiologicalQuestion -> MicrosatelliteDetection;
BiologicalQuestion -> MotifAnnotation;
BiologicalQuestion -> MotifDiscovery;
BiologicalQuestion -> NetworkEnrichment;
BiologicalQuestion -> NetworkInference;
BiologicalQuestion -> NucleosomePositioning;
BiologicalQuestion -> PeakDetection;
BiologicalQuestion -> QuantitativeTrailLocus;
BiologicalQuestion -> Scaffolding;
BiologicalQuestion -> SequenceMatching;
BiologicalQuestion -> SomaticMutation;
BiologicalQuestion -> SplicedAlignment;
BiologicalQuestion -> StructuralVariation;
BiologicalQuestion -> TranscriptomeVariant;
BiologicalQuestion -> VariantAnnotation;
BiologicalQuestion -> VariantDetection;

/* Software -> WorkflowStep */
Software -> WorkflowStep;
WorkflowStep -> ExperimentalDesign;
WorkflowStep -> Alignment;
Alignment -> MultipleSequenceAlignment;
WorkflowStep -> Annotation;
WorkflowStep -> BatchEffect;
WorkflowStep -> MultipleComparison;
WorkflowStep -> Normalization;
WorkflowStep -> Pathways;
Pathways -> GO;
Pathways -> KEGG;
Pathways -> Reactome;
Pathways -> BioCarta;
Pathways -> NCINatureCurated;
WorkflowStep -> Preprocessing;
WorkflowStep -> QualityControl;
WorkflowStep -> ReportWriting;
WorkflowStep -> Visualization;
Visualization -> Network;
WorkflowStep -> GenomeBrowsers;

/* Software -> WorkflowManagement */
Software -> WorkflowManagement;

/* Software -> StatisticalMethod */
Software -> StatisticalMethod;
StatisticalMethod -> Bayesian;
StatisticalMethod -> Classification;
StatisticalMethod -> Clustering;
StatisticalMethod -> DecisionTree;
StatisticalMethod -> DimensionReduction;
StatisticalMethod -> FeatureExtraction;
StatisticalMethod -> GraphAndNetwork;
StatisticalMethod -> HiddenMarkovModel;
StatisticalMethod -> MultidimensionalScaling;
StatisticalMethod -> NeuralNetwork;
StatisticalMethod -> PatternLogic;
StatisticalMethod -> PrincipalComponent;
StatisticalMethod -> Regression;
StatisticalMethod -> StructuralEquationModels;
StatisticalMethod -> SupportVectorMachine;
StatisticalMethod -> Survival;
StatisticalMethod -> TimeCourse;

/* Software -> Infrastructure */
Software -> Infrastructure;
Infrastructure -> ThirdPartyClient
Infrastructure -> DataImport;
Infrastructure -> DataRepresentation;
Infrastructure -> GUI;
Infrastructure -> GPU;

/* Software -> ShinyApps */
Software -> ShinyApps;

/****************************************************************************
 *                            AnnotationData                                *
 ****************************************************************************/
BiocViews -> AnnotationData;

/* AnnotationData -> Organism */
AnnotationData -> Organism;
Organism -> Anopheles_gambiae;
Organism -> Apis_mellifera;
Organism -> Arabidopsis_lyrata;
Organism -> Arabidopsis_thaliana;
Organism -> Asparagus_officinalis;
Organism -> Bacillus_subtilis;
Organism -> Bos_taurus;
Organism -> Caenorhabditis_elegans;
Organism -> Callithrix_jacchus;
Organism -> Canis_familiaris;
Organism -> Cicer_arietinum;
Organism -> Ciona_intestinalis;
Organism -> Chlamydomonas_reinhardtii;
Organism -> Danio_rerio;
Organism -> Drosophila_melanogaster;
Organism -> Drosophila_virilis;
Organism -> Eremothecium_gossypii;
Organism -> Escherichia_coli;
Organism -> Gallus_gallus;
Organism -> Gasterosteus_aculeatus;
Organism -> Glycine_max;
Organism -> Homo_sapiens;
Organism -> Hordeum_vulgare;
Organism -> Kluyveromyces_lactis;
Organism -> Macaca_fascicularis;
Organism -> Macaca_mulatta;
Organism -> Magnaporthe_grisea;
Organism -> Medicago_truncatula;
Organism -> Monodelphis_domestica;
Organism -> Mus_musculus;
Organism -> Neurospora_crassa;
Organism -> Oncorhynchus_mykiss;
Organism -> Oryza_sativa;
Organism -> Pan_paniscus;
Organism -> Pan_troglodytes;
Organism -> Plasmodium_falciparum;
Organism -> Pseudomonas_aeruginosa;
Organism -> Rattus_norvegicus;
Organism -> Saccharomyces_cerevisiae;
Organism -> Saccharum_officinarum;
Organism -> Salmo_salar;
Organism -> Schizosaccharomyces_pombe;
Organism -> Staphylococcus_aureus;
Organism -> Sus_scrofa;
Organism -> Taeniopygia_guttata;
Organism -> Toxoplasma_gondii;
Organism -> Triticum_aestivum;
Organism -> Vitis_vinifera;
Organism -> Xenopus_laevis;
Organism -> Xenopus_tropicalis;
Organism -> Zea_mays;

/* AnnotationData -> ChipManufacturer */
AnnotationData -> ChipManufacturer;
ChipManufacturer -> AffymetrixChip;
ChipManufacturer -> AgilentChip;
ChipManufacturer -> ClonetechChip;
ChipManufacturer -> GEChip;
ChipManufacturer -> INDACChip;
ChipManufacturer -> IlluminaChip;
ChipManufacturer -> QiagenChip;
ChipManufacturer -> RNG_MRCChip;
ChipManufacturer -> RocheChip;
ChipManufacturer -> UniversityHealthNetwork;
ChipManufacturer -> CodelinkChip;

/* AnnotationData -> CustomCDF */
AnnotationData -> CustomCDF;
CustomCDF -> GACustomCDF;
CustomCDF -> MBNICustomCDF;

/* AnnotationData -> CustomArray */
AnnotationData -> CustomArray;

/* AnnotationData -> CustomDBSchema */
AnnotationData -> CustomDBSchema;
CustomDBSchema -> GeneCardsCustomSchema;

/* AnnotationData -> FunctionalAnnotation */
AnnotationData -> FunctionalAnnotation;

/* AnnotationData -> SequenceAnnotation */
AnnotationData -> SequenceAnnotation;
SequenceAnnotation -> GenomicSequence;

/* AnnotationData -> ChipName */
AnnotationData -> ChipName;
ChipName -> adme16cod;
ChipName -> ag;
ChipName -> ath1121501;
ChipName -> celegans;
ChipName -> drosgenome1;
ChipName -> drosophila2;
ChipName -> h10kcod;
ChipName -> h20kcod;
ChipName -> hcg110;
ChipName -> hgfocus;
ChipName -> hgu133a2;
ChipName -> hgu133a;
ChipName -> hgu133b;
ChipName -> hgu133plus2;
ChipName -> hgu95a;
ChipName -> hgu95av2;
ChipName -> hgu95b;
ChipName -> hgu95c;
ChipName -> hgu95d;
ChipName -> hgu95e;
ChipName -> hguatlas13k;
ChipName -> hgug4100a;
ChipName -> hgug4101a;
ChipName -> hgug4110b;
ChipName -> hgug4111a;
ChipName -> hgug4112a;
ChipName -> hguqiagenv3;
ChipName -> hi16cod;
ChipName -> hs25kresogen;
ChipName -> hu35ksuba;
ChipName -> hu35ksubb;
ChipName -> hu35ksubc;
ChipName -> hu35ksubd;
ChipName -> hu6800;
ChipName -> HuO22;
ChipName -> hwgcod;
ChipName -> indac;
ChipName -> illuminaHumanv1;
ChipName -> illuminaHumanv2;
ChipName -> illuminaMousev1;
ChipName -> illuminaMousev1p1;
ChipName -> illuminaRatv1;
ChipName -> JazaerimetaData;
ChipName -> lumiHumanV1;
ChipName -> lumiMouseV1;
ChipName -> lumiHumanV2;
ChipName -> lumiRatV1;
ChipName -> m10kcod;
ChipName -> m20kcod;
ChipName -> mi16cod;
ChipName -> mm24kresogen;
ChipName -> mgu74a;
ChipName -> mgu74av2;
ChipName -> mgu74b;
ChipName -> mgu74bv2;
ChipName -> mgu74c;
ChipName -> mgu74cv2;
ChipName -> mguatlas5k;
ChipName -> mgug4121a;
ChipName -> mgug4122a;
ChipName -> moe430a;
ChipName -> moe430b;
ChipName -> mouse4302;
ChipName -> mouse430a2;
ChipName -> mpedbarray;
ChipName -> mu11ksuba;
ChipName -> mu11ksubb;
ChipName -> mu19ksuba;
ChipName -> mu19ksubb;
ChipName -> mu19ksubc;
ChipName -> Mu15v1;
ChipName -> Mu22v3;
ChipName -> mwgcod;
ChipName -> Norway981;
ChipName -> OperonHumanV3;
ChipName -> pedbarrayv9;
ChipName -> pedbarrayv10;
ChipName -> PartheenMetaData;
ChipName -> r10kcod;
ChipName -> rae230a;
ChipName -> rae230b;
ChipName -> rat2302;
ChipName -> rgu34a;
ChipName -> rgu34b;
ChipName -> rgu34c;
ChipName -> rgug4130a;
ChipName -> ri16cod;
ChipName -> rnu34;
ChipName -> Roberts2005Annotation;
ChipName -> rtu34;
ChipName -> rwgcod;
ChipName -> SHDZ;
ChipName -> u133x3p;
ChipName -> xenopuslaevis;
ChipName -> yeast2;
ChipName -> ygs98;
ChipName -> zebrafish;
ChipName -> hcgi12k;
ChipName -> hcgi8k;

/* AnnotationData -> PackageType */
AnnotationData -> PackageType;
PackageType -> BSgenome;
PackageType -> cdf;
PackageType -> ChipDb;
PackageType -> db0;
PackageType -> InparanoidDb;
PackageType -> OrganismDb;
PackageType -> OrgDb;
PackageType -> PolyPhen;
PackageType -> probe;
PackageType -> SIFT;
PackageType -> SNPlocs;
PackageType -> XtraSNPlocs;
PackageType -> TxDb;
PackageType -> MeSHDb;
PackageType -> FRMA;
PackageType -> AnnotationHub;
PackageType -> EuPathDB;

/****************************************************************************
 *                            ExperimentData                                *
 ****************************************************************************/
BiocViews -> ExperimentData;

ExperimentData -> ReproducibleResearch;

ExperimentData -> SpecimenSource;
SpecimenSource -> Tissue;
SpecimenSource -> Proteome;
SpecimenSource -> Genome;
SpecimenSource -> StemCell;
SpecimenSource -> CellCulture;
SpecimenSource -> Germline;
SpecimenSource -> Somatic;

ExperimentData -> OrganismData;
OrganismData -> Anopheles_gambiae_Data;
OrganismData -> Apis_mellifera_Data;
OrganismData -> Arabidopsis_lyrata_Data;
OrganismData -> Arabidopsis_thaliana_Data;
OrganismData -> Bacillus_subtilis_Data;
OrganismData -> Bos_taurus_Data;
OrganismData -> Caenorhabditis_elegans_Data;
OrganismData -> Callithrix_jacchus_Data;
OrganismData -> Canis_familiaris_Data;
OrganismData -> Ciona_intestinalis_Data;
OrganismData -> Danio_rerio_Data;
OrganismData -> Drosophila_melanogaster_Data;
OrganismData -> Drosophila_virilis_Data;
OrganismData -> Eremothecium_gossypii_Data;
OrganismData -> Escherichia_coli_Data;
OrganismData -> Gallus_gallus_Data;
OrganismData -> Gasterosteus_aculeatus_Data;
OrganismData -> Glycine_max_Data;
OrganismData -> Homo_sapiens_Data;
OrganismData -> Hordeum_vulgare_Data;
OrganismData -> Kluyveromyces_lactis_Data;
OrganismData -> Macaca_mulatta_Data;
OrganismData -> Magnaporthe_grisea_Data;
OrganismData -> Medicago_truncatul_Data;
OrganismData -> Monodelphis_domestica_Data;
OrganismData -> Mus_musculus_Data;
OrganismData -> Neurospora_crassa_Data;
OrganismData -> Oncorhynchus_mykiss_Data;
OrganismData -> Oryza_sativa_Data;
OrganismData -> Pan_paniscus_Data;
OrganismData -> Pan_troglodytes_Data;
OrganismData -> Plasmodium_falciparum_Data;
OrganismData -> Pseudomonas_aeruginosa_Data;
OrganismData -> Rattus_norvegicus_Data;
OrganismData -> Saccharomyces_cerevisiae_Data;
OrganismData -> Saccharum_officinarum_Data;
OrganismData -> Schizosaccharomyces_pombe_Data;
OrganismData -> Staphylococcus_aureus_Data;
OrganismData -> Sus_scrofa_Data;
OrganismData -> Taeniopygia_guttata_Data;
OrganismData -> Triticum_aestivum_Data;
OrganismData -> Vitis_vinifera_Data;
OrganismData -> Xenopus_laevis_Data;
OrganismData -> Xenopus_tropicalis_Data;
OrganismData -> Zea_mays_Data;


ExperimentData -> DiseaseModel;
DiseaseModel -> CancerData;
CancerData -> BreastCancerData;
CancerData -> ColonCancerData;
CancerData -> KidneyCancerData;
CancerData -> LeukemiaCancerData;
CancerData -> LungCancerData;
CancerData -> OvarianCancerData;
CancerData -> ProstateCancerData;
CancerData -> LeukemiaCancerData;
DiseaseModel -> HIVData;
DiseaseModel -> COPDData;

ExperimentData -> TechnologyData;
TechnologyData -> FlowCytometryData;
TechnologyData -> HighThroughputImagingData;
TechnologyData -> MassSpectrometryData;
MassSpectrometryData -> ImagingMassSpectrometryData;
TechnologyData -> qPCRData;
TechnologyData -> MicrotitrePlateAssayData;
TechnologyData -> SAGEData;
TechnologyData -> CGHData;
TechnologyData -> SequencingData;
SequencingData -> DNASeqData;
SequencingData -> RNASeqData;
SequencingData -> ChIPSeqData;
SequencingData -> RIPSeqData;
SequencingData -> MethylSeqData;
SequencingData -> ExomeSeqData;
SequencingData -> miRNAData;
SequencingData -> SangerSeqData;
SequencingData -> SmallRNAData;
SequencingData -> MicrobiomeData;
SequencingData -> SingleCellData;
SequencingData -> SpatialData;
TechnologyData -> MicroarrayData;
MicroarrayData -> MultiChannelData;
MicroarrayData -> OneChannelData;
MicroarrayData -> TwoChannelData;
MicroarrayData -> MethylationArrayData;
MicroarrayData -> GenotypingArrayData;
MicroarrayData -> MicroRNAArrayData;
MicroarrayData -> mRNAArrayData;
MicroarrayData -> ChipOnChipData;
MicroarrayData -> ReversePhaseProteinArrayData;
MicroarrayData -> TissueMicroarrayData;
MicroarrayData -> ProprietaryPlatformsData;

ExperimentData -> AssayDomainData;
AssayDomainData -> CopyNumberVariationData;
AssayDomainData -> CpGIslandData;
AssayDomainData -> SNPData;
AssayDomainData -> ExpressionData;

ExperimentData -> RepositoryData;
RepositoryData -> HapMap;
RepositoryData -> GEO;
RepositoryData -> ArrayExpress;
RepositoryData -> NCI;
RepositoryData -> PathwayInteractionDatabase;
RepositoryData -> Project1000genomes;
RepositoryData -> ENCODE;

ExperimentData -> PackageTypeData;
PackageTypeData -> ExperimentHub;
PackageTypeData -> ImmunoOncologyData;

/****************************************************************************
 *                            ExperimentData                                *
 ****************************************************************************/
BiocViews -> Workflow;

Workflow -> BasicWorkflow;
Workflow -> AnnotationWorkflow;
Workflow -> GeneExpressionWorkflow;
Workflow -> SingleCellWorkflow;
Workflow -> SpatialWorkflow;
Workflow -> GenomicVariantsWorkflow;
Workflow -> EpigeneticsWorkflow;
Workflow -> ProteomicsWorkflow;
Workflow -> ResourceQueryingWorkflow;
Workflow -> DifferentialSplicingWorkflow;
Workflow -> ImmunoOncologyWorkflow;

}
