jhipster-jdl.jdl

/**
 * Enumeration
 */

enum AlterationType {
    GENOMIC_CHANGE,
    CDNA_CHANGE,
    PROTEIN_CHANGE,
    MUTATION,
    COPY_NUMBER_ALTERATION,
    STRUCTURAL_VARIANT,
    ANY,
    UNKNOWN,
    NA
}

enum ArticleType {
    PUBMED, ABSTRACT, REFERENCE, FDADRUG_LETTER, FDADRUG_LABEL, FDADRUG_SUMMARY, FDADRUG_SUMMARY_REVIEW
}

enum CategoricalAlterationType{
    ONCOGENIC_MUTATIONS,
    GAIN_OF_FUNCTION_MUTATIONS,
    LOSS_OF_FUNCTION_MUTATIONS,
    SWITCH_OF_FUNCTION_MUTATIONS,
    KINASE_DOMAIN_DUPLICATIONS,
    INTERNAL_TANDEM_DUPLICATIONS,
    PARTIAL_TANDEM_DUPLICATIONS,
    OVEREXPRESSION,
    HYPERMETHYLATION,
    MSIH,
    TMBH,
    EPIGENETIC_SILENCING,
    VI,
    VII,
    VIII,
    VIV,
    VV
    VUS,
    TRUNCATING_MUTATIONS,
    FUSIONS,
    AMPLIFICATION,
    DELETION,
    GAIN,
    LOSS,
    PROMOTER,
    WILDTYPE
}

enum EligibilityCriteriaType {
    INCLUSION, EXCLUSION
}

enum EvidenceType {
    GENE_SUMMARY,
    MUTATION_SUMMARY,
    TUMOR_TYPE_SUMMARY,
    GENE_TUMOR_TYPE_SUMMARY,
    PROGNOSTIC_SUMMARY,
    DIAGNOSTIC_SUMMARY,
    GENE_BACKGROUND,
    ONCOGENIC,
    MUTATION_EFFECT,
    VUS,
    PROGNOSTIC_IMPLICATION,
    DIAGNOSTIC_IMPLICATION
}

enum FdaSubmissionTypeKey {
    DEVICE_PMA, DEVICE_DENOVO, DEVICE_HDE, DEVICE_PMN, DRUG_NDA, DRUG_BLA
}

enum FlagType {
    GENE_TYPE
    GENE_PANEL
    TRANSCRIPT
    DRUG
}

enum GeographicRegion {
    US, EU
}

enum GenePanelFlagEnum {
     ONCOKB,
     MSK_IMPACT_505,
     MSK_ACCESS,
     MSK_HEME,
     VOGELSTEIN,
     CGC_T1,
     FOUNDATION_ONE,
     FOUNDATION_HEME,
     TEMPUS_XT,
     TEMPUS_XR,
     TEMPUS_XF,
     TEMPUS_XG,
     TEMPUS_XG_PLUS,
     TEMPUS_XE,
     GUARDANT_360,
     ONCOMINE_DX
     ONCOMINE_CA_V3
     ONCOMINE_CA_PLUS
     CARIS_MI
     TRUSIGHT_ONCOLOGY_500
}

enum GenomeFragmentType {
    GENE,
    EXON,
    FIVE_PRIME_UTR,
    THREE_PRIME_UTR
}

enum GenomicIndicatorType {
    GERMLINE
}

enum InfoType {
    NCIT_VERSION,
    GENE_VERSION,
    ONCOKB_TRANSCRIPT_VERSION,
    MANE_TRANSCRIPT_VERSION,
    ENSEMBL_VERSION
}

enum LevelOfEvidenceType {
    TX, DX, PX, FDA, TX_LIQUID_PROPAGATION, TX_SOLID_PROPAGATION
}

enum ReferenceGenome {
    GRCh37, GRCh38
}

enum SequenceType {
    PROTEIN, CDNA, GENOMIC
}

enum StructuralVariantType {
    FUSION
}

enum SynonymType {
    GENE, NCIT, CANCER_TYPE, ARTICLE
}

enum TranscriptFlagEnum {
     MANE_SELECT,
     MANE_PLUS_CLINICAL,
     GN_CANONICAL,
     ONCOKB,
     ENSEMBL_CANONICAL
}

enum TumorForm {
    SOLID, LIQUID, MIXED
}

/**
 * Entity
 */

entity AlleleState {
    name String required unique
}

entity Alteration {
    type AlterationType required
    name String required
    alteration String required
    proteinChange String required
    start Integer
    end Integer
    refResidues String
    variantResidues String
}

entity Article {
    type ArticleType required
    uid String
    title TextBlob
    content TextBlob
    link String
    authors String
    date Instant
}

entity Association {
    name String
}

entity Rule {
    entity String required
    rule String
    name String
}

entity CancerType {
    code String
    color String
    level Integer required
    mainType String required
    subtype String
    tissue String
    tumorForm TumorForm required
}

entity CategoricalAlteration {
    alterationType AlterationType required
    type String required unique
    name String required
}

entity ClinicalTrial {
    nctId String
    briefTitle String required
    phase String
    status String
}

entity ClinicalTrialArm {
    name String required
}

entity CompanionDiagnosticDevice {
    name String required
    manufacturer String required
    indicationDetails String
    platformType String
    lastUpdated Instant
}

entity Consequence {
    term String required unique
    name String required
    isGenerallyTruncating Boolean required
    description String
}

entity Drug {
    uuid String required unique
    name TextBlob required
}

entity EligibilityCriteria {
    type EligibilityCriteriaType required
    priority Integer
    criteria TextBlob
}

entity EnsemblGene {
    referenceGenome ReferenceGenome
    ensemblGeneId String required
    canonical Boolean required
    start Integer required
    end Integer required
    strand Integer required
}

entity Evidence {
    uuid String
    evidenceType String required
    knownEffect String
    description TextBlob
    note TextBlob
}

entity FdaDrug {
    applicationNumber String unique required
    sponsorName String
    overallMarketingStatus String
}

entity FdaSubmission {
    number String required
    supplementNumber String required

    deviceName String required
    genericName String

    dateReceived Instant
    decisionDate Instant

    description TextBlob

    curated Boolean required
    genetic Boolean required

    note TextBlob
}

entity FdaSubmissionType {
    type FdaSubmissionTypeKey required unique
    name String required
    shortName String
    submissionPrefix String
    submissionLink String
    description TextBlob
}

entity Flag {
    type String required
    flag String required
    name String required
    description TextBlob required
}

entity Gene {
    entrezGeneId Integer required unique
    hugoSymbol String required
    hgncId String
}

entity GenomeFragment {
    start Integer required
    end Integer required
    strand Integer required
    type GenomeFragmentType required
}

entity GenomicIndicator {
    uuid String required unique
    type String required
    name String required
    description TextBlob
}

entity Info {
    type String unique required
    value String
    created Instant required
    lastUpdated Instant
}

entity LevelOfEvidence {
    type String  required
    level String  required unique
    description String required
    htmlDescription String required
    color String required
}

entity NciThesaurus {
    version String required
    code String unique required
    preferredName String
    displayName String
}


entity SeqRegion {
    name String required unique
    chromosome String
    description TextBlob
}

entity Sequence {
    sequenceType SequenceType required
    sequence TextBlob required
}

entity SpecimenType{
    type String required
    name String required
}

entity Synonym {
    type String required
    source String required
    code String
    name String required
    note TextBlob
}

entity Transcript {
    referenceGenome ReferenceGenome
    ensemblTranscriptId String
    canonical Boolean required
    ensemblProteinId String
    referenceSequenceId String
    description String
}

/**
 * Relationship
 */

relationship OneToOne {
    Drug{nciThesaurus(code)} to NciThesaurus
    Evidence to Association
}

relationship OneToMany {
    Association to Rule
    CancerType{children} to CancerType {parent}
    ClinicalTrial to ClinicalTrialArm
    ClinicalTrial to EligibilityCriteria
    CompanionDiagnosticDevice to FdaSubmission
    Consequence to Alteration {consequence(term)}
    Consequence to CategoricalAlteration {consequence(term)}
    Drug to FdaDrug
    EnsemblGene to Transcript
    FdaDrug to FdaSubmission
    FdaSubmissionType to FdaSubmission{type(type)}
    Gene to EnsemblGene
    Gene to Evidence
    Gene to Transcript
    SeqRegion to EnsemblGene {seqRegion(name)}
    SeqRegion to GenomeFragment {seqRegion(name)}
    Transcript to Sequence
    Transcript{fragments} to GenomeFragment{transcript}
}

relationship ManyToMany {
    Alteration to Flag
    Alteration to Gene
    Alteration to Transcript
    Article to Flag
    Article to Synonym
    Association to Alteration
    Association to Article
    Association to CancerType
    Association to Drug
    CancerType to Synonym
    ClinicalTrial to Association
    ClinicalTrialArm to Association
    CompanionDiagnosticDevice to SpecimenType
    Drug to Flag
    EligibilityCriteria to Association
    Evidence to LevelOfEvidence
    FdaSubmission to Article
    FdaSubmission to Association
    Gene to Flag
    Gene to Synonym
    GenomicIndicator to AlleleState
    GenomicIndicator to Association
    NciThesaurus to Synonym
    Transcript to Flag
}

paginate Alteration, Article, CancerType, ClinicalTrial, ClinicalTrialArm,
EligibilityCriteria, EnsemblGene, Evidence, FdaDrug, FdaSubmission, Flag , Gene, GenomeFragment,
NciThesaurus, Sequence, Synonym, Transcript with pagination

service * with serviceClass

filter Alteration, Article, CancerType, ClinicalTrial, ClinicalTrialArm,
CompanionDiagnosticDevice, Consequence, Drug, EligibilityCriteria,
EnsemblGene, Evidence, FdaDrug, FdaSubmission, Flag, Gene, GenomeFragment,
GenomicIndicator, NciThesaurus, Sequence, Synonym, Transcript

dto Transcript with mapstruct