├── DEPRECATED ├── .github │ └── workflows │ │ ├── check-md-supporting-files.yml │ │ └── update-md-files.yml ├── docs │ ├── biobank.md │ ├── care_pathway.md │ ├── consent.md │ ├── disability.md │ ├── disease_diagnosis.md │ ├── disease_history.md │ ├── disease_history_and_diagnosis.md │ ├── genetic_diagnosis.md │ ├── markupFilesConfig.yaml │ ├── patient_status.md │ ├── personal_information.md │ ├── phenotyping.md │ ├── pseudonym.md │ └── undiagnosed.md ├── example-data │ └── turtle │ │ ├── biobank.ttl │ │ ├── bodyMeasurement.ttl │ │ ├── carePathway.ttl │ │ ├── diagnosis.ttl │ │ ├── disability.ttl │ │ ├── diseaseHistory.ttl │ │ ├── drugTreatment.ttl │ │ ├── geneticDiagnosis.ttl │ │ ├── imaging.ttl │ │ ├── labData.ttl │ │ ├── patientConsent.ttl │ │ ├── patientStatus.ttl │ │ ├── personalInformation.ttl │ │ ├── phenotyping.ttl │ │ ├── pseudonym.ttl │ │ └── unDiagnosis.ttl ├── images │ ├── rdf │ │ ├── 10_Disability.png │ │ ├── 1_Pseudonym.png │ │ ├── 2_Personal_information.png │ │ ├── 3_Patient_status.png │ │ ├── 4_Care_pathway.png │ │ ├── 5_Diagnosis.png │ │ ├── 5_Disease_history.png │ │ ├── 6_Genetic_diagnosis.png │ │ ├── 7_Phenotyping.png │ │ ├── 7_Undiagnosis.png │ │ ├── 8_Consent.png │ │ ├── 9_Biobank.png │ │ ├── Annotated General model SIO.png │ │ ├── DCDE_body_measurement.drawio.png │ │ ├── DCDE_drug_treatment.png │ │ ├── DCDE_imaging.drawio.png │ │ ├── DCDE_lab_measurement.drawio.png │ │ └── complete_data_model_SIO.png │ └── shex │ │ ├── 10_Disability.svg │ │ ├── 1_Pseudonym.svg │ │ ├── 2_Personal_information.svg │ │ ├── 3_Patient_status.svg │ │ ├── 4_Care_pathway.svg │ │ ├── 5_Disease_diagnosis.svg │ │ ├── 5_Disease_history.svg │ │ ├── 6_Genetic_diagnosis.svg │ │ ├── 7_Phenotyping.svg │ │ ├── 7_Undiagnosed.svg │ │ ├── 8_Consent.svg │ │ └── 9_Biobank.svg └── shex │ ├── biobank.shex │ ├── carePathwayShape.shex │ ├── diagnosisShape.shex │ ├── disability.shex │ ├── diseaseHistoryShape.shex │ ├── drugTreatment.shex │ ├── geneticDiagnosisShape.shex │ ├── patientConsentShape.shex │ ├── patientStatusShape.shex │ ├── personalInformationShape.shex │ ├── phenotypingShape.shex │ ├── pseudonymShape.shex │ └── undiagnosedShape.shex ├── Images ├── Biobank.png ├── Birthdate.png ├── Birthyear.png ├── Body_measurement.png ├── Clinical_trials.png ├── Consent.png ├── Core_model.png ├── Deathdate.png ├── Diagnosis.png ├── Disability.png ├── First_visit.png ├── Genotype.png ├── Imaging.png ├── Intervention.png ├── Laboratory.png ├── Medication.png ├── Metadata_context.png ├── Sex.png ├── Status.png ├── Symptom.png └── Symptoms_onset.png ├── LICENSE ├── README.md ├── docs ├── Biobank.md ├── Birthdate.md ├── Birthyear.md ├── Body_measurement.md ├── Clinical_trials.md ├── Consent.md ├── Deathdate.md ├── Diagnosis.md ├── Disability.md ├── First_visit.md ├── Genotype.md ├── Imaging.md ├── Intervention.md ├── Laboratory.md ├── Medication.md ├── Sex.md ├── Status.md ├── Symptoms.md └── Symptoms_onset.md └── exemplar_rdf ├── Biobank.nt ├── Birthdate.nt ├── Body_measurement.nt ├── Consent.nt ├── Deathdate.nt ├── Diagnosis.nt ├── Disability.nt ├── First_visit.nt ├── Genotype.nt ├── Imaging.nt ├── Intervention.nt ├── Lab_measurement.nt ├── Medications.nt ├── Sex.nt ├── Status.nt ├── Symptoms.nt └── Symptoms_onset.nt /DEPRECATED/.github/workflows/check-md-supporting-files.yml: -------------------------------------------------------------------------------- 1 | name: Check markup supporting files 2 | on: 3 | push: 4 | branches: 5 | - master 6 | - develop 7 | pull_request: 8 | branches: 9 | - master 10 | - develop 11 | # allow workflow to run manually 12 | workflow_dispatch: 13 | 14 | jobs: 15 | build: 16 | runs-on: ubuntu-latest 17 | 18 | steps: 19 | # checkout cde model repository 20 | - uses: actions/checkout@v2 21 | # List files 22 | - name: List cde model repo content 23 | run: ls 24 | # checkout md file generator repository 25 | - uses: actions/checkout@v2 26 | with: 27 | repository: rajaram5/CDE-repo-markup-file-generator 28 | path: CDE-repo-markup-file-generator 29 | # List files 30 | - name: List md files creator repo content 31 | run: ls 32 | # install python 33 | - name: Install python 34 | uses: actions/setup-python@v2 35 | with: 36 | python-version: '3.x' 37 | # install python dependencies 38 | - name: Install dependency 39 | uses: py-actions/py-dependency-install@v2 40 | with: 41 | path: "CDE-repo-markup-file-generator/requirements.txt" 42 | # run script 43 | - name: Check supporting files exits 44 | working-directory: ./CDE-repo-markup-file-generator/script 45 | env: 46 | BASE_PATH: "../../" 47 | LINK_BASE_PATH: "../" 48 | OUTPUT_DIR: "../output/" 49 | MARKUP_CONFIG_FILE: "../../docs/markupFilesConfig.yaml" 50 | JOB_TO_RUN: "CHECK SUPPORTING FILES" 51 | run: 'python main.py' 52 | -------------------------------------------------------------------------------- /DEPRECATED/.github/workflows/update-md-files.yml: -------------------------------------------------------------------------------- 1 | name: Update markup supporting files 2 | on: 3 | # allow workflow to run manually 4 | workflow_dispatch: 5 | 6 | jobs: 7 | build: 8 | runs-on: ubuntu-latest 9 | 10 | steps: 11 | # checkout cde model repository 12 | - uses: actions/checkout@v2 13 | with: 14 | ref: ${{ github.head_ref }} 15 | # List files 16 | - name: List cde model repo content 17 | run: ls 18 | # checkout md file generator repository 19 | - uses: actions/checkout@v2 20 | with: 21 | repository: rajaram5/CDE-repo-markup-file-generator 22 | path: CDE-repo-markup-file-generator 23 | # List files 24 | - name: List md files creator repo content 25 | run: ls 26 | # install python 27 | - name: Install python 28 | uses: actions/setup-python@v2 29 | with: 30 | python-version: '3.x' 31 | # install python dependencies 32 | - name: Install dependency 33 | uses: py-actions/py-dependency-install@v2 34 | with: 35 | path: "CDE-repo-markup-file-generator/requirements.txt" 36 | # run script 37 | - name: Update markup files 38 | id: update-md-files 39 | working-directory: ./CDE-repo-markup-file-generator/script 40 | env: 41 | BASE_PATH: "../../" 42 | LINK_BASE_PATH: "../" 43 | OUTPUT_DIR: "../../docs/" 44 | MARKUP_CONFIG_FILE: "../../docs/markupFilesConfig.yaml" 45 | JOB_TO_RUN: "UPDATE MD FILES" 46 | run: 'python main.py' 47 | # Check if previous step succeed 48 | - name: Check if previous steps succeed 49 | if: steps.update-md-files.outcome != 'success' 50 | run: exit 1 51 | # List md files 52 | - name: List md files and update times 53 | run: ls -l docs/ 54 | # Update md file 55 | - name: Update markup files in the repository 56 | run: | 57 | git config --global user.name 'Rajaram Kaliyaperumal' 58 | git config --global user.email 'rr.kaliyaperumal@gmail.com' 59 | git remote set-url origin https://x-access-token:${{ secrets.GIT_TOKEN }}@github.com/${{ github.repository }} 60 | git add docs/*.md 61 | git commit -m '[automated commit] updated all markup files' 62 | git push 63 | -------------------------------------------------------------------------------- /DEPRECATED/docs/biobank.md: -------------------------------------------------------------------------------- 1 | ## Biobank 2 | 3 | ### Semantic model figure 4 | This module describes the data elements related to biological samples stored in a biobank. It specifically covers the CDE elements 7.3.'Biological Sample' and 7.4.'Link to a biobank'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | @prefix dc: . 22 | 23 | :identifier_ a sio:SIO_000115 ; 24 | sio:SIO_000020 :specimen_role_ ; 25 | sio:SIO_000300 "uid_000008"^^xsd:string . 26 | 27 | :person_ a sio:SIO_000498 ; 28 | sio:SIO_000228 :specimen_role_ . 29 | 30 | :specimen_role_ a obo:OBI_0000093, sio:SIO_000016 ; 31 | rdfs:label "Role: Patient for biobank sample collection"^^xsd:string ; 32 | sio:SIO_000356 :specimen_process_ . 33 | 34 | :specimen_process_ a sio:SIO_000006, obo:OBI_0000659 ; 35 | rdfs:label "Process: Sample collection"^^xsd:string ; 36 | sio:SIO_000229 :specimen_output_ . 37 | 38 | :specimen_output_ a sio:SIO_000015, obo:OBI_0100051 ; 39 | rdfs:label "Output Type: Specimen"^^xsd:string . 40 | 41 | :biobank_identifier_ a sio:SIO_000115 ; 42 | sio:SIO_000020 :biobank_role_ ; 43 | sio:SIO_000300 "biobankID_000008"^^xsd:string . 44 | 45 | :biobank_ a obo:OMIABIS_0000010 ; 46 | sio:SIO_000228 :biobank_role_ ; 47 | rdfs:label "UK Biobank"^^xsd:string . 48 | 49 | :biobank_role_ a obo:OBI_0000947, sio:SIO_000016; 50 | rdfs:label "Role: Biobank for sample storage"^^xsd:string ; 51 | sio:SIO_000356 :biobank_process_ . 52 | 53 | :biobank_process_ a sio:SIO_000006, obo:OBI_0302893 ; 54 | rdfs:label "Process: sample storage"^^xsd:string ; 55 | sio:SIO_000229 :specimen_output_ . 56 | ``` 57 | 58 | *** 59 | ### Validation artifacts 60 | ##### ShEx figure 61 | 62 |

63 | 64 | 65 | 66 |

67 | 68 | *** 69 | ##### ShEx 70 | 71 | ``` ShEx 72 | PREFIX : 73 | PREFIX obo: 74 | PREFIX sio: 75 | PREFIX xsd: 76 | PREFIX dc: 77 | PREFIX rdfs: 78 | 79 | :identifierShape IRI { 80 | a [sio:SIO_000115] ; 81 | sio:SIO_000020 @:specimenRoleShape ; 82 | rdfs:label xsd:string? ; 83 | sio:SIO_000300 xsd:string 84 | } 85 | 86 | :personShape IRI { 87 | a [sio:SIO_000498] ; 88 | rdfs:label xsd:string? ; 89 | sio:SIO_000228 @:specimenRoleShape 90 | } 91 | 92 | :specimenRoleShape IRI { 93 | a [obo:OBI_0000093] ; 94 | a [sio:SIO_000016] ; 95 | rdfs:label xsd:string? ; 96 | sio:SIO_000356 @:specimenProcessShape 97 | } 98 | 99 | :specimenProcessShape IRI { 100 | a [sio:SIO_000006] ; 101 | a [obo:OBI_0000659] ; 102 | rdfs:label xsd:string? ; 103 | sio:SIO_000229 @:specimenOutputShape 104 | } 105 | 106 | :specimenOutputShape IRI { 107 | a [sio:SIO_000015] ; 108 | a [obo:OBI_0100051] ; 109 | rdfs:label xsd:string? 110 | } 111 | 112 | :biobankIdentifierShape IRI { 113 | a [sio:SIO_000115] ; 114 | sio:SIO_000020 @:biobankRoleShape ; 115 | rdfs:label xsd:string? ; 116 | sio:SIO_000300 xsd:string 117 | } 118 | 119 | :biobankShape IRI { 120 | a [obo:OMIABIS_0000010] ; 121 | rdfs:label xsd:string? ; 122 | sio:SIO_000228 @:biobankRoleShape 123 | } 124 | 125 | :biobankRoleShape IRI { 126 | a [obo:OBI_0000947] ; 127 | a [sio:SIO_000016] ; 128 | rdfs:label xsd:string? ; 129 | sio:SIO_000356 @:biobankProcessShape 130 | } 131 | 132 | :biobankProcessShape IRI { 133 | a [sio:SIO_000006] ; 134 | a [obo:OBI_0302893] ; 135 | rdfs:label xsd:string? ; 136 | sio:SIO_000230 @:specimenOutputShape 137 | } 138 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/care_pathway.md: -------------------------------------------------------------------------------- 1 | ## Care pathway 2 | 3 | ### Semantic model figure 4 | This module describes the data elements related to the 'Care pathway'. It specifically covers the CDE element 4.1.'First contact with specialised centre'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :carepathway_role_ ; 24 | sio:SIO_000300 "uid_000007"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498; 27 | sio:SIO_000228 :carepathway_role_ . 28 | 29 | :carepathway_role_ a obo:OBI_0000093, sio:SIO_000016; 30 | rdfs:label "Role: First contact patient"^^xsd:string; 31 | sio:SIO_000356 :carepathway_process_ . 32 | 33 | :carepathway_process_ a sio:SIO_000006, obo:NCIT_C159705, obo:NCIT_C16205 ; 34 | rdfs:label "Process: First contact with specialized center"^^xsd:string; 35 | sio:SIO_000680 :carepathway_startdate_ ; 36 | sio:SIO_000681 :carepathway_enddate_ . 37 | 38 | :carepathway_startdate_ a sio:SIO_000031 ; 39 | rdfs:label "Startdate: 1991-02-12"^^xsd:string ; 40 | sio:SIO_000300 "1991-02-12"^^xsd:date . 41 | 42 | :carepathway_enddate_ a sio:SIO_000032 ; 43 | rdfs:label "Enddate: 1991-02-12"^^xsd:string ; 44 | sio:SIO_000300 "1991-02-12"^^xsd:date . 45 | ``` 46 | 47 | *** 48 | ### Validation artifacts 49 | ##### ShEx figure 50 | 51 |

52 | 53 | 54 | 55 |

56 | 57 | *** 58 | ##### ShEx 59 | 60 | ``` ShEx 61 | PREFIX : 62 | PREFIX obo: 63 | PREFIX sio: 64 | PREFIX xsd: 65 | PREFIX rdfs: 66 | 67 | :identifierShape IRI { 68 | a [sio:SIO_000115] ; 69 | sio:SIO_000020 @:carePathwayRoleShape ; 70 | rdfs:label xsd:string? ; 71 | sio:SIO_000300 xsd:string 72 | } 73 | 74 | :personShape IRI { 75 | a [sio:SIO_000498] ; 76 | rdfs:label xsd:string? ; 77 | sio:SIO_000228 @:carePathwayRoleShape 78 | } 79 | 80 | :carePathwayRoleShape IRI { 81 | a [obo:OBI_0000093] ; 82 | a [sio:SIO_000016] ; 83 | rdfs:label xsd:string? ; 84 | sio:SIO_000356 @:carePathwayProcessShape 85 | } 86 | 87 | :carePathwayProcessShape IRI { 88 | a [sio:SIO_000006] ; 89 | a [obo:NCIT_C159705] ; 90 | a [obo:NCIT_C16205] ; 91 | rdfs:label xsd:string? ; 92 | sio:SIO_000680 @:carePathwayDateShape ; 93 | sio:SIO_000681 @:carePathwayDateShape 94 | } 95 | 96 | :carePathwayDateShape IRI { 97 | a [sio:SIO_000031 sio:SIO_000032] ; 98 | rdfs:label xsd:string? ; 99 | sio:SIO_000300 xsd:date 100 | } 101 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/consent.md: -------------------------------------------------------------------------------- 1 | ## Consent 2 | 3 | ### Semantic model figure 4 | This module describes the data elements related to consent from the group 'Research'. It specifically covers the CDE elements 7.1.'Agreement to be contacted for research purposes' and 7.2.'Consent to the reuse of data'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :consent_role_ ; 24 | sio:SIO_000300 "uid_000010"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498 ; 27 | sio:SIO_000228 :consent_role_ ; 28 | sio:SIO_000008 :consent_attribute_ . 29 | 30 | :consent_role_ a obo:OBI_0000093, sio:SIO_000016; 31 | rdfs:label "Role: Patient for status recording"^^xsd:string; 32 | sio:SIO_000356 :consent_process_ . 33 | 34 | :consent_process_ a sio:SIO_000006, obo:OBI_0000810 ; 35 | rdfs:label "Process: Consenting"^^xsd:string; 36 | sio:SIO_000229 :consent_output_ ; 37 | sio:SIO_000230 :consent_input_ ; 38 | sio:SIO_000680 :consent_startdate_ ; 39 | sio:SIO_000681 :consent_enddate_ . 40 | 41 | :consent_output_ a sio:SIO_000015 ; 42 | rdfs:label "Output Type: Patient consent record"^^xsd:string ; 43 | sio:SIO_000300 "disease specific research"^^xsd:string ; 44 | sio:SIO_000628 :consent_attribute_ . 45 | 46 | :consent_input_ a sio:SIO_000015, obo:ICO_0000001 ; 47 | rdfs:label "Process Input: information content entity -Type: consent_document"^^xsd:string ; 48 | sio:SIO_000300 "http://example.org/my_consent_document_type2"^^xsd:string . 49 | 50 | :consent_attribute_ a sio:SIO_000614, obo:DUO_0000007 ; 51 | rdfs:label "Attribute Type: disease specific research"^^xsd:string . 52 | 53 | :consent_startdate_ a sio:SIO_000031 ; 54 | rdfs:label "Startdate: 1996-08-08"^^xsd:string ; 55 | sio:SIO_000300 "1996-08-08"^^xsd:date . 56 | 57 | :consent_enddate_ a sio:SIO_000032 ; 58 | rdfs:label "Enddate: 1996-08-08"^^xsd:string ; 59 | sio:SIO_000300 "1996-08-08"^^xsd:date . 60 | ``` 61 | 62 | *** 63 | ### Validation artifacts 64 | ##### ShEx figure 65 | 66 |

67 | 68 | 69 | 70 |

71 | 72 | *** 73 | ##### ShEx 74 | 75 | ``` ShEx 76 | PREFIX : 77 | PREFIX obo: 78 | PREFIX sio: 79 | PREFIX xsd: 80 | PREFIX rdfs: 81 | 82 | :identifierShape IRI { 83 | a [sio:SIO_000115] ; 84 | rdfs:label xsd:string? ; 85 | sio:SIO_000020 @:consentRoleShape ; 86 | sio:SIO_000300 xsd:string 87 | } 88 | 89 | :personShape IRI { 90 | a [sio:SIO_000498] ; 91 | rdfs:label xsd:string? ; 92 | sio:SIO_000228 @:consentRoleShape ; 93 | sio:SIO_000008 @:consentAttributeShape 94 | } 95 | 96 | :consentRoleShape IRI { 97 | a [obo:OBI_0000093] ; 98 | a [sio:SIO_000016] ; 99 | rdfs:label xsd:string? ; 100 | sio:SIO_000356 @:consentProcessShape 101 | } 102 | 103 | :consentProcessShape IRI { 104 | a [obo:OBI_0000810] ; 105 | a [sio:SIO_000006] ; 106 | rdfs:label xsd:string? ; 107 | sio:SIO_000680 @:consentDateShape ; 108 | sio:SIO_000681 @:consentDateShape ; 109 | sio:SIO_000229 @:patientconsentOutputShape ; 110 | sio:SIO_000230 @:consentInputShape 111 | } 112 | 113 | :patientconsentOutputShape IRI { 114 | a [sio:SIO_000015] ; 115 | rdfs:label xsd:string? ; 116 | sio:SIO_000300 xsd:string ; 117 | sio:SIO_000628 @:consentAttributeShape 118 | } 119 | 120 | :consentInputShape IRI { 121 | a [sio:SIO_000015] ; 122 | a [obo:ICO_0000001] ; 123 | rdfs:label xsd:string? ; 124 | sio:SIO_000300 xsd:string 125 | } 126 | 127 | :consentAttributeShape IRI { 128 | a [sio:SIO_000614] ; 129 | a IRI ; 130 | rdfs:label xsd:string? ; 131 | } 132 | 133 | :consentDateShape IRI { 134 | a [sio:SIO_000031 sio:SIO_000032] ; 135 | rdfs:label xsd:string? ; 136 | sio:SIO_000300 xsd:date 137 | } 138 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/disability.md: -------------------------------------------------------------------------------- 1 | ## Disability 2 | 3 | ### Semantic model figure 4 | This module describes the data element 8.1'Classification of functioning/disability' which is part of the group 'Disability'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix sio: . 18 | @prefix obo: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :disability_role_ ; 24 | sio:SIO_000300 "uid_000002"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498 ; 27 | sio:SIO_000228 :disability_role_ . 28 | 29 | :disability_role_ a obo:OBI_0000093, sio:SIO_000016 ; 30 | rdfs:label "Role: Patient"^^xsd:string ; 31 | sio:SIO_000356 :assessment_test_ . 32 | 33 | :assessment_test_ a sio:SIO_000006, obo:NCIT_C20993, obo:NCIT_C107391 ; 34 | rdfs:label "Process: Edmonton symptom assessment system"^^xsd:string ; 35 | sio:SIO_000680 :disability_startdate_ ; 36 | sio:SIO_000681 :disability_enddate_ ; 37 | sio:SIO_000230 :question_answering_input_ ; 38 | sio:SIO_000229 :test_output_ . 39 | 40 | :test_output_ a sio:SIO_000015 ; 41 | rdfs:label "Output Type: disability score"^^xsd:string ; 42 | sio:SIO_000300 "12"^^xsd:string . 43 | 44 | :question_answering_input_ a sio:SIO_000015, obo:NCIT_C17048 ; 45 | rdfs:label "Process Input: Information content entity - Type: Questionnaire"^^xsd:string . 46 | 47 | :disability_startdate_ a sio:SIO_000031 ; 48 | rdfs:label "Startdate: 2019-11-12"^^xsd:string ; 49 | sio:SIO_000300 "2019-11-12"^^xsd:date . 50 | 51 | :disability_enddate_ a sio:SIO_000032 ; 52 | rdfs:label "Enddate: 2019-11-12"^^xsd:string ; 53 | sio:SIO_000300 "2019-11-12"^^xsd:date . 54 | ``` 55 | 56 | *** 57 | ### Validation artifacts 58 | ##### ShEx figure 59 | 60 |

61 | 62 | 63 | 64 |

65 | 66 | *** 67 | ##### ShEx 68 | 69 | ``` ShEx 70 | PREFIX : 71 | PREFIX obo: 72 | PREFIX sio: 73 | PREFIX xsd: 74 | PREFIX rdfs: 75 | 76 | :identifierShape IRI { 77 | a [sio:SIO_000115] ; 78 | rdfs:label xsd:string? ; 79 | sio:SIO_000020 @:disabilityRoleShape ; 80 | sio:SIO_000300 xsd:string 81 | } 82 | 83 | :personShape IRI { 84 | a [sio:SIO_000498] ; 85 | rdfs:label xsd:string? ; 86 | sio:SIO_000228 @:disabilityRoleShape 87 | } 88 | 89 | :disabilityRoleShape IRI { 90 | a [obo:OBI_0000093] ; 91 | a [sio:SIO_000016] ; 92 | rdfs:label xsd:string? ; 93 | sio:SIO_000356 @:disabilityProcessShape 94 | } 95 | 96 | :disabilityProcessShape IRI { 97 | a [sio:SIO_000006] ; 98 | a [obo:NCIT_C20993] ; 99 | a IRI /^http:\/\/purl.obolibrary.org\/obo\// ; 100 | rdfs:label xsd:string? ; 101 | sio:SIO_000680 @:disabilityDateShape ; 102 | sio:SIO_000681 @:disabilityDateShape ; 103 | sio:SIO_000230 @:questionInputShape ; 104 | sio:SIO_000229 @:testOutputShape 105 | } 106 | 107 | :testOutputShape IRI { 108 | a [sio:SIO_000015] ; 109 | rdfs:label xsd:string? ; 110 | sio:SIO_000300 xsd:string 111 | } 112 | 113 | :questionInputShape IRI { 114 | a [sio:SIO_000015] ; 115 | a [obo:NCIT_C17048] ; 116 | rdfs:label xsd:string? 117 | } 118 | 119 | :disabilityDateShape IRI { 120 | a [sio:SIO_000031 sio:SIO_000032] ; 121 | rdfs:label xsd:string? ; 122 | sio:SIO_000300 xsd:date 123 | } 124 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/disease_diagnosis.md: -------------------------------------------------------------------------------- 1 | ## Disease diagnosis 2 | 3 | ### Semantic model figure 4 | This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history' and 'Diagnosis'. It specifically covers the CDE elements 5.1.'Age at onset', 5.2.'Age at diagnosis' and 6.1.'Diagnosis of the rare disease'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :diagnosis_role_ ; 24 | sio:SIO_000300 "uid_000007"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498; 27 | sio:SIO_000228 :diagnosis_role_ ; 28 | sio:SIO_000008 :diagnosis_attribute_ . 29 | 30 | :diagnosis_role_ a obo:OBI_0000093, sio:SIO_000016 ; 31 | rdfs:label "Role: Diagnosis patient"^^xsd:string; 32 | sio:SIO_000356 :diagnosis_process_ . 33 | 34 | :diagnosis_process_ a sio:SIO_000006, sio:SIO_001001 ; 35 | rdfs:label "Process: Medical diagnosis"^^xsd:string ; 36 | sio:SIO_000680 :diagnosis_startdate_ ; 37 | sio:SIO_000681 :diagnosis_enddate_ ; 38 | sio:SIO_000229 :diagnosis_output_ . 39 | 40 | :diagnosis_output_ a sio:SIO_000015, sio:SIO_001003 ; 41 | rdfs:label "Output Type: Diagnosis"^^xsd:string ; 42 | sio:SIO_000300 "Richards-Rundle syndrome is an extremely rare neurodegenerative disorder characterized by progressive spinocerebellar ataxia"^^xsd:string ; 43 | sio:SIO_000628 :diagnosis_attribute_ . 44 | 45 | :diagnosis_attribute_ a sio:SIO_000614, ; 46 | rdfs:label "Attribute Type: Richards-Rundle syndrome is an extremely rare neurodegenerative disorder characterized by progressive spinocerebellar ataxia"^^xsd:string . 47 | 48 | :diagnosis_startdate_ a sio:SIO_000031 ; 49 | rdfs:label "Startdate: 1996-02-12"^^xsd:string ; 50 | sio:SIO_000300 "1996-02-12"^^xsd:date . 51 | 52 | :diagnosis_enddate_ a sio:SIO_000032 ; 53 | rdfs:label "Enddate: 1996-02-12"^^xsd:string ; 54 | sio:SIO_000300 "1996-02-12"^^xsd:date . 55 | ``` 56 | 57 | *** 58 | ### Validation artifacts 59 | ##### ShEx figure 60 | 61 |

62 | 63 | 64 | 65 |

66 | 67 | *** 68 | ##### ShEx 69 | 70 | ``` ShEx 71 | PREFIX : 72 | PREFIX obo: 73 | PREFIX sio: 74 | PREFIX xsd: 75 | PREFIX rdfs: 76 | 77 | :identifierShape IRI { 78 | a [sio:SIO_000115] ; 79 | sio:SIO_000020 @:medicalDiagnosisRoleShape ; 80 | rdfs:label xsd:string? ; 81 | sio:SIO_000300 xsd:string 82 | } 83 | 84 | :personShape IRI { 85 | a [sio:SIO_000498] ; 86 | rdfs:label xsd:string? ; 87 | sio:SIO_000228 @:medicalDiagnosisRoleShape ; 88 | sio:SIO_000008 @:medicalDiagnosisAttributeShape 89 | } 90 | 91 | :medicalDiagnosisRoleShape IRI { 92 | a [obo:OBI_0000093] ; 93 | a [sio:SIO_000016] ; 94 | rdfs:label xsd:string? ; 95 | sio:SIO_000356 @:medicalDiagnosisProcessShape 96 | } 97 | 98 | :medicalDiagnosisProcessShape IRI { 99 | a [sio:SIO_000006] ; 100 | a [sio:SIO_001001] ; 101 | rdfs:label xsd:string? ; 102 | sio:SIO_000680 @:medicalDiagnosisDateShape ; 103 | sio:SIO_000681 @:medicalDiagnosisDateShape ; 104 | sio:SIO_000229 @:medicalDiagnosisOutputShape 105 | } 106 | 107 | :medicalDiagnosisOutputShape IRI { 108 | a [sio:SIO_000015] ; 109 | a [sio:SIO_001003] ; 110 | rdfs:label xsd:string? ; 111 | sio:SIO_000300 xsd:string ; 112 | sio:SIO_000628 @:medicalDiagnosisAttributeShape 113 | } 114 | 115 | :medicalDiagnosisAttributeShape IRI { 116 | a [sio:SIO_000614] ; 117 | a IRI /^http:\/\/www.orpha.net\/ORDO\/Orphanet_/ ; 118 | rdfs:label xsd:string? 119 | } 120 | 121 | :medicalDiagnosisDateShape IRI { 122 | a [sio:SIO_000031 sio:SIO_000032] ; 123 | rdfs:label xsd:string? ; 124 | sio:SIO_000300 xsd:date 125 | } 126 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/disease_history.md: -------------------------------------------------------------------------------- 1 | ## Disease history 2 | 3 | ### Semantic model figure 4 | This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history' and 'Diagnosis'. It specifically covers the CDE elements 5.1.'Age at onset', 5.2.'Age at diagnosis' and 6.1.'Diagnosis of the rare disease'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :symptom_onset_role_ ; 24 | sio:SIO_000020 :diagnosis_date_role_ ; 25 | sio:SIO_000300 "uid_000008"^^xsd:string . 26 | 27 | :person_ a sio:SIO_000498; 28 | sio:SIO_000228 :symptom_onset_role_ ; 29 | sio:SIO_000008 :symptom_onset_attribute_ ; 30 | sio:SIO_000228 :diagnosis_date_role_ ; 31 | sio:SIO_000008 :diagnosis_date_attribute_ . 32 | 33 | :symptom_onset_role_ a obo:OBI_0000093, sio:SIO_000016; 34 | rdfs:label "Role: Symptom onset patient"^^xsd:string; 35 | sio:SIO_000356 :symptom_onset_process_ . 36 | 37 | :symptom_onset_process_ a sio:SIO_000006, sio:SIO_001052 ; 38 | rdfs:label "Process: Data collection - symptom onset date recording process"^^xsd:string; 39 | sio:SIO_000229 :symptom_onset_output_ . 40 | 41 | :symptom_onset_output_ a sio:SIO_000015, obo:NCIT_C25164 ; 42 | rdfs:label "Output Type: Date of onset"^^xsd:string ; 43 | sio:SIO_000300 "1982-04-06"^^xsd:date ; 44 | sio:SIO_000628 :symptom_onset_attribute_ . 45 | 46 | :symptom_onset_attribute_ a sio:SIO_000614, obo:NCIT_C25279 ; 47 | rdfs:label "Attribute: Stage or date of onset"^^xsd:string . 48 | 49 | :diagnosis_date_role_ a obo:OBI_0000093, sio:SIO_000016 ; 50 | rdfs:label "Role: Diagnosis date patient"^^xsd:string ; 51 | sio:SIO_000356 :diagnosis_date_process_ . 52 | 53 | :diagnosis_date_process_ a sio:SIO_000006, sio:SIO_001052 ; 54 | rdfs:label "Process: Data collection - diagnosis date recording process"^^xsd:string ; 55 | sio:SIO_000229 :diagnosis_date_output_ . 56 | 57 | :diagnosis_date_output_ a sio:SIO_000015, obo:NCIT_C25164 ; 58 | rdfs:label "Output Type: Age at diagnosis"^^xsd:string ; 59 | sio:SIO_000300 "1992-04-06"^^xsd:date ; 60 | sio:SIO_000628 :diagnosis_date_attribute_ . 61 | 62 | :diagnosis_date_attribute_ a sio:SIO_000614, obo:NCIT_C156420 ; 63 | rdfs:label "Attribute Type: Stage or date of diagnosis"^^xsd:string . 64 | ``` 65 | 66 | *** 67 | ### Validation artifacts 68 | ##### ShEx figure 69 | 70 |

71 | 72 | 73 | 74 |

75 | 76 | *** 77 | ##### ShEx 78 | 79 | ``` ShEx 80 | PREFIX : 81 | PREFIX obo: 82 | PREFIX sio: 83 | PREFIX xsd: 84 | PREFIX rdfs: 85 | 86 | :identifierShape IRI { 87 | a [sio:SIO_000115] ; 88 | rdfs:label xsd:string? ; 89 | sio:SIO_000020 @:symptomOnsetRoleShape ; 90 | sio:SIO_000020 @:diagnosisDateRoleShape; 91 | sio:SIO_000300 xsd:string 92 | } 93 | 94 | :personShape IRI { 95 | a [sio:SIO_000498] ; 96 | rdfs:label xsd:string? ; 97 | sio:SIO_000228 @:symptomOnsetRoleShape ; 98 | sio:SIO_000008 @:symptomOnsetAttributeShape ; 99 | sio:SIO_000228 @:diagnosisDateRoleShape ; 100 | sio:SIO_000008 @:diagnosisDateAttributeShape 101 | } 102 | 103 | :symptomOnsetRoleShape IRI { 104 | a [obo:OBI_0000093] ; 105 | a [sio:SIO_000016] ; 106 | rdfs:label xsd:string? ; 107 | sio:SIO_000356 @:symptomOnsetProcessShape 108 | } 109 | 110 | :symptomOnsetProcessShape IRI { 111 | a [sio:SIO_000006] ; 112 | a [sio:SIO_001052] ; 113 | rdfs:label xsd:string? ; 114 | sio:SIO_000229 @:symptomOnsetOutputShape 115 | } 116 | 117 | :symptomOnsetOutputShape IRI { 118 | a [sio:SIO_000015] ; 119 | a [obo:HP_0410280 obo:HP_0003577 obo:HP_0030674 obo:HP_0003623 obo:HP_0003577 obo:NCIT_C124294 obo:NCIT_C25164] ; 120 | rdfs:label xsd:string? ; 121 | sio:SIO_000300 xsd:date? ; 122 | sio:SIO_000628 @:symptomOnsetAttributeShape 123 | } 124 | 125 | :symptomOnsetAttributeShape IRI { 126 | a [sio:SIO_000614] ; 127 | a [obo:NCIT_C25279] ; 128 | rdfs:label xsd:string? 129 | } 130 | 131 | :diagnosisDateRoleShape IRI { 132 | a [obo:OBI_0000093] ; 133 | a [sio:SIO_000016] ; 134 | rdfs:label xsd:string? ; 135 | sio:SIO_000356 @:diagnosisDateProcessShape 136 | } 137 | 138 | :diagnosisDateProcessShape IRI { 139 | a [sio:SIO_000006] ; 140 | a [sio:SIO_001052] ; 141 | rdfs:label xsd:string? ; 142 | sio:SIO_000229 @:diagnosisDateOutputShape 143 | } 144 | 145 | :diagnosisDateOutputShape IRI { 146 | a [sio:SIO_000015] ; 147 | a [obo:NCIT_C81318 obo:NCIT_C81317 obo:NCIT_C124294 obo:NCIT_C25164] ; 148 | rdfs:label xsd:string? ; 149 | sio:SIO_000300 xsd:date? ; 150 | sio:SIO_000628 @:diagnosisDateAttributeShape 151 | } 152 | 153 | :diagnosisDateAttributeShape IRI { 154 | a [sio:SIO_000614] ; 155 | a [obo:NCIT_C156420] ; 156 | rdfs:label xsd:string? 157 | } 158 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/disease_history_and_diagnosis.md: -------------------------------------------------------------------------------- 1 | ## Diagnosis 2 | 3 | This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history' and 'Diagnosis'. It specifically covers the CDE elements 5.1.'Age at onset', 5.2.'Age at diagnosis' and 6.1.'Diagnosis of the rare disease'. 4 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 | 6 | ### Semantic model figure 7 | 8 |

9 | 10 | 11 | 12 |

13 | 14 | *** 15 | 16 | ### Example RDF (turtle) 17 | 18 | ```ttl 19 | @prefix : . 20 | @prefix obo: . 21 | @prefix sio: . 22 | @prefix xsd: . 23 | @prefix rdfs: . 24 | 25 | :identifier_ a sio:SIO_000115 ; 26 | sio:SIO_000020 :diagnosis_role_ ; 27 | sio:SIO_000300 "uid_000007"^^xsd:string . 28 | 29 | :person_ a sio:SIO_000498; 30 | sio:SIO_000228 :diagnosis_role_ ; 31 | sio:SIO_000008 :diagnosis_attribute_ . 32 | 33 | :diagnosis_role_ a obo:OBI_0000093, sio:SIO_000016 ; 34 | rdfs:label "Diagnosis Patient"^^xsd:string; 35 | sio:SIO_000356 :diagnosis_process_ . 36 | 37 | :diagnosis_process_ a sio:SIO_000006, sio:SIO_001001 ; 38 | rdfs:label "medical diagnosis"^^xsd:string ; 39 | sio:SIO_000680 :diagnosis_startdate_ ; 40 | sio:SIO_000229 :diagnosis_output_ . 41 | 42 | :diagnosis_output_ a sio:SIO_000015, sio:SIO_001003 ; 43 | rdfs:label "rare non-syndromic central nervous system malformation characterized by complete or near-complete absence of the cerebellum with a normal sized posterior fossa, possibly accompanied by hypoplasia of the brainstem."^^xsd:string ; 44 | sio:SIO_000300 "rare non-syndromic central nervous system malformation characterized by complete or near-complete absence of the cerebellum with a normal sized posterior fossa, possibly accompanied by hypoplasia of the brainstem."^^xsd:string ; 45 | sio:SIO_000628 :diagnosis_attribute_ . 46 | 47 | :diagnosis_attribute_ a sio:SIO_000614, ; 48 | rdfs:label "rare non-syndromic central nervous system malformation characterized by complete or near-complete absence of the cerebellum with a normal sized posterior fossa, possibly accompanied by hypoplasia of the brainstem."^^xsd:string . 49 | 50 | :diagnosis_startdate_ a sio:SIO_000031 ; 51 | sio:SIO_000300 "1996-02-12"^^xsd:date . 52 | ``` 53 | 54 | 55 | 56 | *** 57 | 58 | ### Validation artifacts 59 | ##### ShEx figure 60 | 61 |

62 | 63 | 64 | 65 |

66 | 67 | *** 68 | 69 | ##### ShEx 70 | 71 | ``` ShEx 72 | PREFIX : 73 | PREFIX obo: 74 | PREFIX sio: 75 | PREFIX xsd: 76 | PREFIX rdfs: 77 | 78 | :identifierShape IRI { 79 | a [sio:SIO_000115] ; 80 | sio:SIO_000020 @:medicalDiagnosisRoleShape ; 81 | rdfs:label xsd:string? ; 82 | sio:SIO_000300 xsd:string 83 | } 84 | 85 | :personShape IRI { 86 | a [sio:SIO_000498] ; 87 | rdfs:label xsd:string? ; 88 | sio:SIO_000228 @:medicalDiagnosisRoleShape ; 89 | sio:SIO_000008 @:medicalDiagnosisAttributeShape 90 | } 91 | 92 | :medicalDiagnosisRoleShape IRI { 93 | a [obo:OBI_0000093] ; 94 | a [sio:SIO_000016] ; 95 | rdfs:label xsd:string? ; 96 | sio:SIO_000356 @:medicalDiagnosisProcessShape 97 | } 98 | 99 | :medicalDiagnosisProcessShape IRI { 100 | a [sio:SIO_000006] ; 101 | a [sio:SIO_001001] ; 102 | rdfs:label xsd:string? ; 103 | sio:SIO_000680 @:medicalDiagnosisStartDateShape ; 104 | sio:SIO_000229 @:medicalDiagnosisOutputShape 105 | } 106 | 107 | :medicalDiagnosisOutputShape IRI { 108 | a [sio:SIO_000015] ; 109 | a [sio:SIO_001003] ; 110 | rdfs:label xsd:string? ; 111 | sio:SIO_000300 xsd:string ; 112 | sio:SIO_000628 @:medicalDiagnosisAttributeShape 113 | } 114 | 115 | :medicalDiagnosisAttributeShape IRI { 116 | a [sio:SIO_000614] ; 117 | a IRI /^http:\/\/www.orpha.net\/ORDO\/Orphanet_/ ; 118 | rdfs:label xsd:string? 119 | } 120 | 121 | :medicalDiagnosisStartDateShape IRI { 122 | a [sio:SIO_000031] ; 123 | rdfs:label xsd:string? ; 124 | sio:SIO_000300 xsd:date 125 | } 126 | ``` 127 | 128 | 129 | ## Disease_history 130 | 131 | ### Semantic model figure 132 | 133 |

134 | 135 | 136 | 137 |

138 | 139 | *** 140 | 141 | ### Example RDF (turtle) 142 | 143 | ```ttl 144 | @prefix : . 145 | @prefix obo: . 146 | @prefix sio: . 147 | @prefix xsd: . 148 | @prefix rdfs: . 149 | 150 | :identifier_ a sio:SIO_000115 ; 151 | sio:SIO_000020 :symptom_onset_role_ ; 152 | sio:SIO_000020 :diagnosis_date_role_ ; 153 | sio:SIO_000300 "uid_000008"^^xsd:string . 154 | 155 | :person_ a sio:SIO_000498; 156 | sio:SIO_000228 :symptom_onset_role_ ; 157 | sio:SIO_000008 :symptom_onset_attribute_ ; 158 | sio:SIO_000228 :diagnosis_date_role_ ; 159 | sio:SIO_000008 :diagnosis_date_attribute_ . 160 | 161 | :symptom_onset_role_ a obo:OBI_0000093, sio:SIO_000016; 162 | rdfs:label "Symptom Onset Patient"^^xsd:string; 163 | sio:SIO_000356 :symptom_onset_process_ . 164 | 165 | :symptom_onset_process_ a sio:SIO_000006, sio:SIO_001052 ; 166 | rdfs:label "data collection - symptom onset date recording process"^^xsd:string; 167 | sio:SIO_000229 :symptom_onset_output_ . 168 | 169 | :symptom_onset_output_ a sio:SIO_000015, obo:HP_0030674 ; 170 | rdfs:label "date of onset (in official CDE this is age of onset)"^^xsd:string ; 171 | sio:SIO_000300 "1998-06-08"^^xsd:date ; 172 | sio:SIO_000628 :symptom_onset_attribute_ . 173 | 174 | :symptom_onset_attribute_ a sio:SIO_000614, obo:NCIT_C124353 ; 175 | rdfs:label "Age at onset"^^xsd:string . 176 | 177 | :diagnosis_date_role_ a obo:OBI_0000093, sio:SIO_000016 ; 178 | rdfs:label "Diagnosis Date Patient"^^xsd:string ; 179 | sio:SIO_000356 :diagnosis_date_process_ . 180 | 181 | :diagnosis_date_process_ a sio:SIO_000006, sio:SIO_001052 ; 182 | rdfs:label "data collection - diagnosis date recording process"^^xsd:string ; 183 | sio:SIO_000229 :diagnosis_date_output_ . 184 | 185 | :diagnosis_date_output_ a sio:SIO_000015, obo:HP_0030674 ; 186 | rdfs:label "age at diagnosis"^^xsd:string ; 187 | sio:SIO_000300 "1999-06-08"^^xsd:date ; 188 | sio:SIO_000628 :diagnosis_date_attribute_ . 189 | 190 | :diagnosis_date_attribute_ a sio:SIO_000614, obo:NCIT_C156420 ; 191 | rdfs:label "Age at diagnosis"^^xsd:string . 192 | ``` 193 | 194 | 195 | *** 196 | 197 | ### Validation artifacts 198 | ##### ShEx figure 199 | 200 |

201 | 202 | 203 | 204 |

205 | 206 | *** 207 | 208 | ##### ShEx 209 | 210 | 211 | ``` ShEx 212 | PREFIX : 213 | PREFIX obo: 214 | PREFIX sio: 215 | PREFIX xsd: 216 | PREFIX rdfs: 217 | 218 | :identifierShape IRI { 219 | a [sio:SIO_000115] ; 220 | rdfs:label xsd:string? ; 221 | sio:SIO_000020 @:symptomOnsetRoleShape ; 222 | sio:SIO_000020 @:diagnosisDateRoleShape; 223 | sio:SIO_000300 xsd:string 224 | } 225 | 226 | :personShape IRI { 227 | a [sio:SIO_000498] ; 228 | rdfs:label xsd:string? ; 229 | sio:SIO_000228 @:symptomOnsetRoleShape ; 230 | sio:SIO_000008 @:symptomOnsetAttributeShape ; 231 | sio:SIO_000228 @:diagnosisDateRoleShape ; 232 | sio:SIO_000008 @:diagnosisDateAttributeShape 233 | } 234 | 235 | :symptomOnsetRoleShape IRI { 236 | a [obo:OBI_0000093] ; 237 | a [sio:SIO_000016] ; 238 | rdfs:label xsd:string? ; 239 | sio:SIO_000356 @:symptomOnsetProcessShape 240 | } 241 | 242 | :symptomOnsetProcessShape IRI { 243 | a [sio:SIO_000006] ; 244 | a [sio:SIO_001052] ; 245 | rdfs:label xsd:string? ; 246 | sio:SIO_000229 @:symptomOnsetOutputShape 247 | } 248 | 249 | :symptomOnsetOutputShape IRI { 250 | a [sio:SIO_000015] ; 251 | a [obo:HP_0030674 obo:HP_0003577 obo:NCIT_C124294 obo:HP_0003674] ; 252 | rdfs:label xsd:string? ; 253 | sio:SIO_000300 xsd:date ; 254 | sio:SIO_000628 @:symptomOnsetAttributeShape 255 | } 256 | 257 | :symptomOnsetAttributeShape IRI { 258 | a [sio:SIO_000614] ; 259 | a [obo:NCIT_C124353] ; 260 | rdfs:label xsd:string? 261 | } 262 | 263 | :diagnosisDateRoleShape IRI { 264 | a [obo:OBI_0000093] ; 265 | a [sio:SIO_000016] ; 266 | rdfs:label xsd:string? ; 267 | sio:SIO_000356 @:diagnosisDateProcessShape 268 | } 269 | 270 | :diagnosisDateProcessShape IRI { 271 | a [sio:SIO_000006] ; 272 | a [sio:SIO_001052] ; 273 | rdfs:label xsd:string? ; 274 | sio:SIO_000229 @:diagnosisDateOutputShape 275 | } 276 | 277 | :diagnosisDateOutputShape IRI { 278 | a [sio:SIO_000015] ; 279 | a [obo:HP_0030674 obo:HP_0003577 obo:NCIT_C124294 obo:HP_0003674] ; 280 | rdfs:label xsd:string? ; 281 | sio:SIO_000300 xsd:date ; 282 | sio:SIO_000628 @:diagnosisDateAttributeShape 283 | } 284 | 285 | :diagnosisDateAttributeShape IRI { 286 | a [sio:SIO_000614] ; 287 | a [obo:NCIT_C156420] ; 288 | rdfs:label xsd:string? 289 | } 290 | ``` 291 | -------------------------------------------------------------------------------- /DEPRECATED/docs/genetic_diagnosis.md: -------------------------------------------------------------------------------- 1 | ## Genetic diagnosis 2 | 3 | ### Semantic model figure 4 | This module describes the data element 6.2'Genetic Diagnosis' which is part of the group 'Diagnosis'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | @prefix edam: . 22 | 23 | :identifier_ a sio:SIO_000115 ; 24 | sio:SIO_000020 :genetic_role_ ; 25 | sio:SIO_000300 "uid_000008"^^xsd:string . 26 | 27 | :person_ a sio:SIO_000498 ; 28 | sio:SIO_000228 :genetic_role_ ; 29 | sio:SIO_000008 :hgvs_attribute_ ; 30 | sio:SIO_000008 ; 31 | sio:SIO_000008 . 32 | 33 | :genetic_role_ a obo:OBI_0000093, sio:SIO_000016 ; 34 | rdfs:label "Role: Genetic Diagnosis patient"^^xsd:string ; 35 | sio:SIO_000356 :hgvs_process_ ; 36 | sio:SIO_000356 :omim_process_ ; 37 | sio:SIO_000356 :hgnc_process_ . 38 | 39 | :hgvs_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 40 | rdfs:label "Process: HGVS genetic testing"^^xsd:string ; 41 | sio:SIO_000229 :hgvs_output_ . 42 | 43 | :hgvs_output_ a sio:SIO_000015, sio:SIO_001388 ; 44 | rdfs:label "Output Type: measurement-value"^^xsd:string ; 45 | sio:SIO_000300 "NM_004006.3:c.4375C>T"^^xsd:string ; 46 | sio:SIO_000628 :hgvs_attribute_ . 47 | 48 | :hgvs_attribute_ a sio:SIO_000614, sio:SIO_000015, obo:NCIT_C171178 ; 49 | xsd:label "NM_004006.3:c.4375C>T"^^xsd:string . 50 | 51 | :omim_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 52 | rdfs:label "Process: OMIM genetic testing"^^xsd:string ; 53 | sio:SIO_000229 :omim_output_ . 54 | 55 | :omim_output_ a sio:SIO_000015, sio:SIO_001381 ; 56 | rdfs:label "Output Type: OMIM genome sequence variant"^^xsd:string ; 57 | sio:SIO_000300 "https://www.omim.org/entry/192977"^^xsd:string ; 58 | sio:SIO_000628 . 59 | 60 | a sio:SIO_000614, sio:SIO_000015, edam:data_1153 ; 61 | rdfs:label "Attribute Type: https://www.omim.org/entry/192977"^^xsd:string . 62 | 63 | :hgnc_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 64 | rdfs:label "Process: HGNC genetic testing"^^xsd:string ; 65 | sio:SIO_000229 :hgnc_output_ . 66 | 67 | :hgnc_output_ a sio:SIO_000015, sio:SIO_001381 ; 68 | rdfs:label "Output Type: HGNC genome sequence variant"^^xsd:string ; 69 | sio:SIO_000300 "https://identifiers.org/HGNC:12698"^^xsd:string ; 70 | sio:SIO_000628 . 71 | 72 | a sio:SIO_000614, sio:SIO_000015, edam:data_2298 ; 73 | rdfs:label "Attribute Type: https://identifiers.org/HGNC:12698"^^xsd:string . 74 | ``` 75 | 76 | *** 77 | ### Validation artifacts 78 | ##### ShEx figure 79 | 80 |

81 | 82 | 83 | 84 |

85 | 86 | *** 87 | ##### ShEx 88 | 89 | ``` ShEx 90 | PREFIX : 91 | PREFIX obo: 92 | PREFIX sio: 93 | PREFIX xsd: 94 | PREFIX rdfs: 95 | PREFIX edam: 96 | 97 | :identifierShape IRI { 98 | a [sio:SIO_000115] ; 99 | rdfs:label xsd:string? ; 100 | sio:SIO_000020 @:geneticRoleShape ; 101 | sio:SIO_000300 xsd:string 102 | } 103 | 104 | :personShape IRI { 105 | a [sio:SIO_000498] ; 106 | rdfs:label xsd:string? ; 107 | sio:SIO_000228 @:geneticRoleShape ; 108 | sio:SIO_000008 @:hgvsAttributeShape ; 109 | sio:SIO_000008 @:omimAttributeShape ; 110 | sio:SIO_000008 @:hgncAttributeShape 111 | } 112 | 113 | :geneticRoleShape IRI { 114 | a [obo:OBI_0000093] ; 115 | a [sio:SIO_000016] ; 116 | rdfs:label xsd:string? ; 117 | sio:SIO_000356 @:hgvsProcessShape ; 118 | sio:SIO_000356 @:omimProcessShape ; 119 | sio:SIO_000356 @:hgncProcessShape 120 | } 121 | 122 | :hgvsProcessShape IRI { 123 | a [sio:SIO_000006] ; 124 | a [obo:NCIT_C15709] ; 125 | rdfs:label xsd:string? ; 126 | sio:SIO_000229 @:hgvsOutputShape 127 | } 128 | 129 | :hgvsOutputShape IRI { 130 | a [sio:SIO_000015] ; 131 | a [sio:SIO_001388] ; 132 | rdfs:label xsd:string? ; 133 | sio:SIO_000300 xsd:string ; 134 | sio:SIO_000628 @:hgvsAttributeShape 135 | } 136 | 137 | :hgvsAttributeShape IRI { 138 | a [sio:SIO_000614] ; 139 | a [obo:NCIT_C171178] ; 140 | a [sio:SIO_000015] ; 141 | rdfs:label xsd:string? 142 | } 143 | 144 | :omimProcessShape IRI { 145 | a [sio:SIO_000006] ; 146 | a [obo:NCIT_C15709] ; 147 | rdfs:label xsd:string? ; 148 | sio:SIO_000229 @:omimOutputShape 149 | } 150 | 151 | :omimOutputShape IRI { 152 | a [sio:SIO_000015] ; 153 | a [sio:SIO_001381] ; 154 | rdfs:label xsd:string? ; 155 | sio:SIO_000300 xsd:string ; 156 | sio:SIO_000628 @:omimAttributeShape 157 | } 158 | 159 | :omimAttributeShape IRI /^https:\/\/www.omim.org\/entry\// { 160 | a [sio:SIO_000614] ; 161 | a [edam:data_1153] ; 162 | a [sio:SIO_000015] ; 163 | rdfs:label xsd:string? 164 | } 165 | 166 | :hgncProcessShape IRI { 167 | a [sio:SIO_000006] ; 168 | a [obo:NCIT_C15709] ; 169 | rdfs:label xsd:string? ; 170 | sio:SIO_000229 @:hgncOutputShape 171 | } 172 | 173 | :hgncOutputShape IRI { 174 | a [sio:SIO_000015] ; 175 | a [sio:SIO_001381] ; 176 | rdfs:label xsd:string? ; 177 | sio:SIO_000300 xsd:string ; 178 | sio:SIO_000628 @:hgncAttributeShape 179 | } 180 | 181 | :hgncAttributeShape IRI /^https:\/\/identifiers.org\// { 182 | a [sio:SIO_000614] ; 183 | a [edam:data_2298] ; 184 | a [sio:SIO_000015] ; 185 | rdfs:label xsd:string? 186 | } 187 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/markupFilesConfig.yaml: -------------------------------------------------------------------------------- 1 | base-path: "/home/rajaram/work/ejp-rd/ERN-common-data-elements/" 2 | links-base-path: "../" 3 | output-dir: "../output/" 4 | 5 | modules: 6 | pseudonym: 7 | name: "Pseudonym" 8 | md-file-name: "pseudonym.md" 9 | template-file: "../templates/module.mustache" 10 | example-rdf: 11 | text: "This module describes the data element pseudonym which is CDE 1.1'Pseudonym'. 12 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 13 | figure-file-path: "images/rdf/1_Pseudonym.png" 14 | file-path: "example-data/turtle/pseudonym.ttl" 15 | shex: 16 | figure-file-path: "images/shex/1_Pseudonym.svg" 17 | file-path: "shex/pseudonymShape.shex" 18 | 19 | personal_information: 20 | name: "Personal information" 21 | md-file-name: "personal_information.md" 22 | template-file: "../templates/module.mustache" 23 | example-rdf: 24 | text: "This module describes the data elements in the CDE 'Personal information' group. It specifically covers the CDE elements 2.1.'Date of Birth' and 2.2.'Sex'. 25 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 26 | figure-file-path: "images/rdf/2_Personal_information.png" 27 | file-path: "example-data/turtle/personalInformation.ttl" 28 | shex: 29 | figure-file-path: "images/shex/2_Personal_information.svg" 30 | file-path: "shex/personalInformationShape.shex" 31 | 32 | patient_status: 33 | name: "Patient status" 34 | md-file-name: "patient_status.md" 35 | template-file: "../templates/module.mustache" 36 | example-rdf: 37 | text: "This module describes the data elements in the module 'Patient's status'. It specifically covers the CDE elements 3.1.'Patient's status' and 3.2.'Date of death'. 38 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 39 | figure-file-path: "images/rdf/3_Patient_status.png" 40 | file-path: "example-data/turtle/patientStatus.ttl" 41 | shex: 42 | figure-file-path: "images/shex/3_Patient_status.svg" 43 | file-path: "shex/patientStatusShape.shex" 44 | 45 | care_pathway: 46 | name: "Care pathway" 47 | md-file-name: "care_pathway.md" 48 | template-file: "../templates/module.mustache" 49 | example-rdf: 50 | text: "This module describes the data elements related to the 'Care pathway'. It specifically covers the CDE element 4.1.'First contact with specialised centre'. 51 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 52 | figure-file-path: "images/rdf/4_Care_pathway.png" 53 | file-path: "example-data/turtle/carePathway.ttl" 54 | shex: 55 | figure-file-path: "images/shex/4_Care_pathway.svg" 56 | file-path: "shex/carePathwayShape.shex" 57 | 58 | disease_diagnosis: 59 | name: "Disease diagnosis" 60 | md-file-name: "disease_diagnosis.md" 61 | template-file: "../templates/module.mustache" 62 | example-rdf: 63 | text: "This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history' and 'Diagnosis'. It specifically covers the CDE elements 5.1.'Age at onset', 5.2.'Age at diagnosis' and 6.1.'Diagnosis of the rare disease'. 64 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 65 | figure-file-path: "images/rdf/5_Diagnosis.png" 66 | file-path: "example-data/turtle/diagnosis.ttl" 67 | shex: 68 | figure-file-path: "images/shex/5_Disease_diagnosis.svg" 69 | file-path: "shex/diagnosisShape.shex" 70 | 71 | disease_history: 72 | name: "Disease history" 73 | md-file-name: "disease_history.md" 74 | template-file: "../templates/module.mustache" 75 | example-rdf: 76 | text: "This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history' and 'Diagnosis'. It specifically covers the CDE elements 5.1.'Age at onset', 5.2.'Age at diagnosis' and 6.1.'Diagnosis of the rare disease'. 77 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 78 | figure-file-path: "images/rdf/5_Disease_history.png" 79 | file-path: "example-data/turtle/diseaseHistory.ttl" 80 | shex: 81 | figure-file-path: "images/shex/5_Disease_history.svg" 82 | file-path: "shex/diseaseHistoryShape.shex" 83 | 84 | genetic_diagnosis: 85 | name: "Genetic diagnosis" 86 | md-file-name: "genetic_diagnosis.md" 87 | template-file: "../templates/module.mustache" 88 | example-rdf: 89 | text: "This module describes the data element 6.2'Genetic Diagnosis' which is part of the group 'Diagnosis'. 90 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 91 | figure-file-path: "images/rdf/6_Genetic_diagnosis.png" 92 | file-path: "example-data/turtle/geneticDiagnosis.ttl" 93 | shex: 94 | figure-file-path: "images/shex/6_Genetic_diagnosis.svg" 95 | file-path: "shex/geneticDiagnosisShape.shex" 96 | 97 | undiagnosed: 98 | name: "Undiagnosed" 99 | md-file-name: "undiagnosed.md" 100 | template-file: "../templates/module.mustache" 101 | example-rdf: 102 | text: "This module describes the data element 6.2'Undiagnosed case' which is part of the group 'Diagnosis'. 103 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 104 | figure-file-path: "images/rdf/7_Undiagnosis.png" 105 | file-path: "example-data/turtle/unDiagnosis.ttl" 106 | shex: 107 | figure-file-path: "images/shex/7_Undiagnosed.svg" 108 | file-path: "shex/undiagnosedShape.shex" 109 | 110 | 111 | phenotyping: 112 | name: "Phenotyping" 113 | md-file-name: "phenotyping.md" 114 | template-file: "../templates/module.mustache" 115 | example-rdf: 116 | text: "This module describes the data element 6.2'Undiagnosed case' which is part of the group 'Diagnosis'. 117 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 118 | figure-file-path: "images/rdf/7_Phenotyping.png" 119 | file-path: "example-data/turtle/phenotyping.ttl" 120 | shex: 121 | figure-file-path: "images/shex/7_Phenotyping.svg" 122 | file-path: "shex/phenotypingShape.shex" 123 | 124 | consent: 125 | name: "Consent" 126 | md-file-name: "consent.md" 127 | template-file: "../templates/module.mustache" 128 | example-rdf: 129 | text: "This module describes the data elements related to consent from the group 'Research'. It specifically covers the CDE elements 7.1.'Agreement to be contacted for research purposes' and 7.2.'Consent to the reuse of data'. 130 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 131 | figure-file-path: "images/rdf/8_Consent.png" 132 | file-path: "example-data/turtle/patientConsent.ttl" 133 | shex: 134 | figure-file-path: "images/shex/8_Consent.svg" 135 | file-path: "shex/patientConsentShape.shex" 136 | 137 | biobank: 138 | name: "Biobank" 139 | md-file-name: "biobank.md" 140 | template-file: "../templates/module.mustache" 141 | example-rdf: 142 | text: "This module describes the data elements related to biological samples stored in a biobank. It specifically covers the CDE elements 7.3.'Biological Sample' and 7.4.'Link to a biobank'. 143 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 144 | figure-file-path: "images/rdf/9_Biobank.png" 145 | file-path: "example-data/turtle/biobank.ttl" 146 | shex: 147 | figure-file-path: "images/shex/9_Biobank.svg" 148 | file-path: "shex/biobank.shex" 149 | 150 | disability: 151 | name: "Disability" 152 | md-file-name: "disability.md" 153 | template-file: "../templates/module.mustache" 154 | example-rdf: 155 | text: "This module describes the data element 8.1'Classification of functioning/disability' which is part of the group 'Disability'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 156 | figure-file-path: "images/rdf/10_Disability.png" 157 | file-path: "example-data/turtle/disability.ttl" 158 | shex: 159 | figure-file-path: "images/shex/10_Disability.svg" 160 | file-path: "shex/disability.shex" 161 | -------------------------------------------------------------------------------- /DEPRECATED/docs/patient_status.md: -------------------------------------------------------------------------------- 1 | ## Patient status 2 | 3 | ### Semantic model figure 4 | This module describes the data elements in the module 'Patient's status'. It specifically covers the CDE elements 3.1.'Patient's status' and 3.2.'Date of death'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :status_role_ ; 24 | sio:SIO_000300 "uid_000008"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498; 27 | sio:SIO_000228 :status_role_ ; 28 | sio:SIO_000008 :status_attribute_ ; 29 | sio:SIO_000008 :death_information_attribute_ . 30 | 31 | :status_role_ a obo:OBI_0000093, sio:SIO_000016; 32 | rdfs:label "Role: Patient for status recording"^^xsd:string ; 33 | sio:SIO_000356 :status_process_ ; 34 | sio:SIO_000356 :death_information_process_ . 35 | 36 | :status_process_ a sio:SIO_000006, sio:SIO_001052 ; 37 | rdfs:label "Process: Status recording process"^^xsd:string ; 38 | sio:SIO_000229 :status_output_ . 39 | 40 | :status_output_ a sio:SIO_000015 ; 41 | rdfs:label "Output Type: Dead"^^xsd:string ; 42 | sio:SIO_000300 "dead"^^xsd:string ; 43 | sio:SIO_000628 :status_attribute_ . 44 | 45 | :status_attribute_ a sio:SIO_000614, sio:SIO_010059 ; 46 | rdfs:label "Attribute Type: Patient status attribute"^^xsd:string . 47 | 48 | :death_information_process_ a sio:SIO_000006 ; 49 | rdfs:label "Process: Death information recording process"^^xsd:string ; 50 | sio:SIO_000229 :death_information_output_ . 51 | 52 | :death_information_output_ a sio:SIO_000015 ; 53 | rdfs:label "Output Type: Patient death information"^^xsd:string ; 54 | sio:SIO_000300 "2010-06-08"^^xsd:date ; 55 | sio:SIO_000628 :death_information_attribute_ . 56 | 57 | :death_information_attribute_ a sio:SIO_000614, obo:NCIT_C70810 ; 58 | rdfs:label "Attribute Type: Date of death"^^xsd:string . 59 | ``` 60 | 61 | *** 62 | ### Validation artifacts 63 | ##### ShEx figure 64 | 65 |

66 | 67 | 68 | 69 |

70 | 71 | *** 72 | ##### ShEx 73 | 74 | ``` ShEx 75 | PREFIX : 76 | PREFIX obo: 77 | PREFIX sio: 78 | PREFIX xsd: 79 | PREFIX rdfs: 80 | 81 | :identifierShape IRI { 82 | a [sio:SIO_000115] ; 83 | rdfs:label xsd:string? ; 84 | sio:SIO_000020 @:statusRoleShape ; 85 | sio:SIO_000300 xsd:string 86 | } 87 | 88 | :personShape IRI { 89 | a [sio:SIO_000498] ; 90 | rdfs:label xsd:string? ; 91 | sio:SIO_000228 @:statusRoleShape ; 92 | sio:SIO_000008 @:statusAttributeShape ; 93 | sio:SIO_000008 @:deadDateAttributeShape 94 | } 95 | 96 | :statusRoleShape IRI { 97 | a [obo:OBI_0000093] ; 98 | a [sio:SIO_000016] ; 99 | rdfs:label xsd:string? ; 100 | sio:SIO_000356 @:statusProcessShape ; 101 | sio:SIO_000356 @:deadDateProcessShape 102 | } 103 | 104 | :statusProcessShape IRI { 105 | a [sio:SIO_000006] ; 106 | a [sio:SIO_001052] ; 107 | rdfs:label xsd:string? ; 108 | sio:SIO_000229 @:statusOutputShape 109 | } 110 | 111 | :statusOutputShape IRI { 112 | a [sio:SIO_000015] ; 113 | rdfs:label xsd:string? ; 114 | sio:SIO_000300 xsd:string ; 115 | sio:SIO_000628 @:statusAttributeShape 116 | } 117 | 118 | :statusAttributeShape IRI { 119 | a [sio:SIO_000614] ; 120 | a [sio:SIO_010059 sio:SIO_010058 obo:NCIT_C70740 obo:NCIT_C124784] ; 121 | rdfs:label xsd:string? 122 | } 123 | 124 | :deadDateProcessShape IRI { 125 | a [sio:SIO_000006] ; 126 | rdfs:label xsd:string? ; 127 | sio:SIO_000229 @:deadDateOutputShape 128 | } 129 | 130 | :deadDateOutputShape IRI { 131 | a [sio:SIO_000015] ; 132 | rdfs:label xsd:string? ; 133 | sio:SIO_000300 xsd:date ; 134 | sio:SIO_000628 @:deadDateAttributeShape 135 | } 136 | 137 | :deadDateAttributeShape IRI { 138 | a [sio:SIO_000614] ; 139 | a [obo:NCIT_C70810] ; 140 | rdfs:label xsd:string? 141 | } 142 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/personal_information.md: -------------------------------------------------------------------------------- 1 | ## Personal information 2 | 3 | ### Semantic model figure 4 | This module describes the data elements in the CDE 'Personal information' group. It specifically covers the CDE elements 2.1.'Date of Birth' and 2.2.'Sex'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :birthdate_role_ ; 24 | sio:SIO_000020 :sex_role_ ; 25 | sio:SIO_000300 "uid_000008"^^xsd:string . 26 | 27 | :person_ a sio:SIO_000498; 28 | sio:SIO_000228 :birthdate_role_ ; 29 | sio:SIO_000008 :birthdate_attribute_ ; 30 | sio:SIO_000228 :sex_role_ ; 31 | sio:SIO_000008 :sex_attribute_ . 32 | 33 | :birthdate_role_ a obo:OBI_0000093, sio:SIO_000016 ; 34 | rdfs:label "Role: Patient for age assessment"^^xsd:string ; 35 | sio:SIO_000356 :birthdate_process_ . 36 | 37 | :birthdate_process_ a sio:SIO_000006 ; 38 | rdfs:label "Process: Age measuring process"^^xsd:string ; 39 | sio:SIO_000229 :birthdate_output_ . 40 | 41 | :birthdate_output_ a sio:SIO_000015 ; 42 | rdfs:label "Output Type: Birth date"^^xsd:string ; 43 | sio:SIO_000300 "1991-02-12"^^xsd:date ; 44 | sio:SIO_000628 :birthdate_attribute_ . 45 | 46 | :birthdate_attribute_ a sio:SIO_000614, obo:NCIT_C68615 ; 47 | rdfs:label "Attribute Type: Birth date"^^xsd:string . 48 | 49 | :sex_role_ a obo:OBI_0000093, sio:SIO_000016 ; 50 | rdfs:label "Role: Patient for gender assessment"^^xsd:string ; 51 | sio:SIO_000356 :sex_process_ . 52 | 53 | :sex_process_ a sio:SIO_000006 ; 54 | rdfs:label "Process: sex measuring process"^^xsd:string ; 55 | sio:SIO_000229 :sex_output_ . 56 | 57 | :sex_output_ a sio:SIO_000015; 58 | rdfs:label "Output Type: Female"^^xsd:string ; 59 | sio:SIO_000300 "Female"^^xsd:string ; 60 | sio:SIO_000628 :sex_attribute_ . 61 | 62 | :sex_attribute_ a sio:SIO_000614, obo:NCIT_C28421, obo:NCIT_C16576 ; 63 | rdfs:label "Attribute Type: Female"^^xsd:string . 64 | ``` 65 | 66 | *** 67 | ### Validation artifacts 68 | ##### ShEx figure 69 | 70 |

71 | 72 | 73 | 74 |

75 | 76 | *** 77 | ##### ShEx 78 | 79 | ``` ShEx 80 | PREFIX : 81 | PREFIX obo: 82 | PREFIX sio: 83 | PREFIX xsd: 84 | PREFIX rdfs: 85 | 86 | :identifierShape IRI { 87 | a [sio:SIO_000115]; 88 | rdfs:label xsd:string? ; 89 | sio:SIO_000020 @:birthdateRoleShape ; 90 | sio:SIO_000020 @:sexRoleShape ; 91 | sio:SIO_000300 xsd:string 92 | } 93 | 94 | :personShape IRI { 95 | a [sio:SIO_000498] ; 96 | rdfs:label xsd:string? ; 97 | sio:SIO_000228 @:birthdateRoleShape ; 98 | sio:SIO_000008 @:birthdateAttributeShape ; 99 | sio:SIO_000228 @:sexRoleShape ; 100 | sio:SIO_000008 @:sexAttributeShape 101 | } 102 | 103 | :birthdateRoleShape IRI { 104 | a [obo:OBI_0000093] ; 105 | a [sio:SIO_000016] ; 106 | rdfs:label xsd:string? ; 107 | sio:SIO_000356 @:birthdateProcessShape 108 | } 109 | 110 | :birthdateProcessShape IRI { 111 | a [sio:SIO_000006] ; 112 | rdfs:label xsd:string? ; 113 | sio:SIO_000229 @:birthdateOutputShape 114 | } 115 | 116 | :birthdateOutputShape IRI { 117 | a [sio:SIO_000015] ; 118 | rdfs:label xsd:string? ; 119 | sio:SIO_000300 xsd:date ; 120 | sio:SIO_000628 @:birthdateAttributeShape 121 | } 122 | 123 | :birthdateAttributeShape IRI { 124 | a [sio:SIO_000614] ; 125 | a [obo:NCIT_C68615] ; 126 | rdfs:label xsd:string? 127 | } 128 | 129 | :sexRoleShape IRI { 130 | a [obo:OBI_0000093] ; 131 | a [sio:SIO_000016] ; 132 | rdfs:label xsd:string? ; 133 | sio:SIO_000356 @:sexProcessShape 134 | } 135 | 136 | :sexProcessShape IRI { 137 | a [sio:SIO_000006] ; 138 | rdfs:label xsd:string? ; 139 | sio:SIO_000229 @:sexOutputShape 140 | } 141 | 142 | :sexOutputShape IRI { 143 | a [sio:SIO_000015] ; 144 | rdfs:label xsd:string? ; 145 | sio:SIO_000300 xsd:string ; 146 | sio:SIO_000628 @:sexAttributeShape 147 | } 148 | 149 | :sexAttributeShape IRI { 150 | a [sio:SIO_000614] ; 151 | a [obo:NCIT_C28421] ; 152 | a [obo:NCIT_C16576 obo:NCIT_C20197 obo:NCIT_C124294 obo:NCIT_C17998] ; 153 | rdfs:label xsd:string? 154 | } 155 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/phenotyping.md: -------------------------------------------------------------------------------- 1 | ## Phenotyping 2 | 3 | ### Semantic model figure 4 | This module describes the data element 6.2'Undiagnosed case' which is part of the group 'Diagnosis'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :phenotypic_role_ ; 24 | sio:SIO_000300 "uid_000007"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498; 27 | sio:SIO_000228 :phenotypic_role_ ; 28 | sio:SIO_000008 :phenotypic_attribute_ . 29 | 30 | :phenotypic_role_ a obo:OBI_0000093, sio:SIO_000016 ; 31 | rdfs:label "Role: Phenotyping patient"^^xsd:string ; 32 | sio:SIO_000356 :phenotypic_process_ . 33 | 34 | :phenotypic_process_ a sio:SIO_000006, obo:OBI_0001546, obo:NCIT_C16205, obo:NCIT_C18020 ; 35 | rdfs:label "Process: Comparative phenotypic assessment"^^xsd:string ; 36 | sio:SIO_000680 :phenotypic_startdate_ ; 37 | sio:SIO_000681 :phenotypic_enddate_ ; 38 | sio:SIO_000229 :phenotypic_output_ . 39 | 40 | :phenotypic_output_ a sio:SIO_000015, obo:NCIT_C102741 ; 41 | rdfs:label "Output Type: Cerebellar ataxia"^^xsd:string ; 42 | sio:SIO_000628 :phenotypic_attribute_ . 43 | 44 | :phenotypic_attribute_ a sio:SIO_000614, sio:SIO_010056, obo:HP_0001251 ; 45 | rdfs:label "Attribute Type: Cerebellar ataxia"^^xsd:string . 46 | 47 | :phenotypic_startdate_ a sio:SIO_000031 ; 48 | rdfs:label "Startdate: 1998-08-12"^^xsd:string ; 49 | sio:SIO_000300 "1998-08-12"^^xsd:date . 50 | 51 | :phenotypic_enddate_ a sio:SIO_000032 ; 52 | rdfs:label "Enddate: 1998-08-12"^^xsd:string ; 53 | sio:SIO_000300 "1998-08-12"^^xsd:date . 54 | ``` 55 | 56 | *** 57 | ### Validation artifacts 58 | ##### ShEx figure 59 | 60 |

61 | 62 | 63 | 64 |

65 | 66 | *** 67 | ##### ShEx 68 | 69 | ``` ShEx 70 | PREFIX : 71 | PREFIX obo: 72 | PREFIX sio: 73 | PREFIX xsd: 74 | PREFIX rdfs: 75 | 76 | :identifierShape IRI { 77 | a [sio:SIO_000115] ; 78 | rdfs:label xsd:string? ; 79 | sio:SIO_000020 @:phenotypeRoleShape ; 80 | sio:SIO_000300 xsd:string 81 | } 82 | 83 | :personShape IRI { 84 | a [sio:SIO_000498] ; 85 | rdfs:label xsd:string? ; 86 | sio:SIO_000228 @:phenotypeRoleShape ; 87 | sio:SIO_000008 @:phenotypeAttributeShape 88 | } 89 | 90 | :phenotypeRoleShape IRI { 91 | a [obo:OBI_0000093] ; 92 | a [sio:SIO_000016] ; 93 | rdfs:label xsd:string? ; 94 | sio:SIO_000356 @:phenotypeProcessShape 95 | } 96 | 97 | :phenotypeProcessShape IRI { 98 | a [sio:SIO_000006] ; 99 | a [obo:OBI_0001546] ; 100 | a [obo:NCIT_C16205] ; 101 | a [obo:NCIT_C18020] ; 102 | rdfs:label xsd:string? ; 103 | sio:SIO_000680 @:phenotypeDateShape ; 104 | sio:SIO_000681 @:phenotypeDateShape ; 105 | sio:SIO_000229 @:phenotypeOutputShape 106 | } 107 | 108 | :phenotypeOutputShape IRI { 109 | a [sio:SIO_000015] ; 110 | a [obo:NCIT_C102741] ; 111 | rdfs:label xsd:string? ; 112 | sio:SIO_000628 @:phenotypeAttributeShape 113 | } 114 | 115 | :phenotypeAttributeShape IRI { 116 | a [sio:SIO_000614] ; 117 | a [sio:SIO_010056] ; 118 | a IRI /^http:\/\/purl.obolibrary.org\/obo\/HP_/ ; 119 | rdfs:label xsd:string? 120 | } 121 | 122 | :phenotypeDateShape IRI { 123 | a [sio:SIO_000031 sio:SIO_000032] ; 124 | rdfs:label xsd:string? ; 125 | sio:SIO_000300 xsd:date 126 | } 127 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/pseudonym.md: -------------------------------------------------------------------------------- 1 | ## Pseudonym 2 | 3 | ### Semantic model figure 4 | This module describes the data element pseudonym which is CDE 1.1'Pseudonym'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix obo: . 18 | @prefix sio: . 19 | @prefix xsd: . 20 | 21 | :person_ a sio:SIO_000498 ; 22 | sio:SIO_000228 :role_ . 23 | 24 | :role_ a obo:OBI_0000093 . 25 | 26 | :identifier_ a sio:SIO_000115 ; 27 | sio:SIO_000020 :role_ ; 28 | sio:SIO_000300 "uid_000008"^^xsd:string . 29 | ``` 30 | 31 | *** 32 | ### Validation artifacts 33 | ##### ShEx figure 34 | 35 |

36 | 37 | 38 | 39 |

40 | 41 | *** 42 | ##### ShEx 43 | 44 | ``` ShEx 45 | PREFIX : 46 | PREFIX obo: 47 | PREFIX sio: 48 | PREFIX xsd: 49 | PREFIX rdfs: 50 | 51 | :personShape IRI { 52 | a [sio:SIO_000498] ; 53 | rdfs:label xsd:string? ; 54 | sio:SIO_000228 @:personRoleShape 55 | } 56 | 57 | :personRoleShape IRI { 58 | rdfs:label xsd:string? ; 59 | a [obo:OBI_0000093] 60 | } 61 | 62 | :identifierShape IRI { 63 | a [sio:SIO_000115] ; 64 | rdfs:label xsd:string? ; 65 | sio:SIO_000020 @:personRoleShape ; 66 | sio:SIO_000300 xsd:string 67 | } 68 | 69 | ``` -------------------------------------------------------------------------------- /DEPRECATED/docs/undiagnosed.md: -------------------------------------------------------------------------------- 1 | ## Undiagnosed 2 | 3 | ### Semantic model figure 4 | This module describes the data element 6.2'Undiagnosed case' which is part of the group 'Diagnosis'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 5 |

6 | 7 | 8 | 9 |

10 | 11 | *** 12 | 13 | ### Example RDF (turtle) 14 | 15 | ```ttl 16 | @prefix : . 17 | @prefix sio: . 18 | @prefix obo: . 19 | @prefix xsd: . 20 | @prefix rdfs: . 21 | 22 | :identifier_ a sio:SIO_000115 ; 23 | sio:SIO_000020 :undiagnosed_role_ ; 24 | sio:SIO_000300 "uid_000008"^^xsd:string . 25 | 26 | :person_ a sio:SIO_000498 ; 27 | sio:SIO_000228 :undiagnosed_role_ ; 28 | sio:SIO_000008 :undiagnosed_attribute_ ; 29 | sio:SIO_000008 :phenotype_attribute_ ; 30 | sio:SIO_000008 :genotype_attribute_ . 31 | 32 | 33 | :undiagnosed_role_ a obo:OBI_0000093, sio:SIO_000016 ; 34 | rdfs:label "Role: Patient"^^xsd:string ; 35 | sio:SIO_000356 :undiagnosed_process_ . 36 | 37 | :undiagnosed_process_ a sio:SIO_000006, sio:SIO_001001 ; 38 | rdfs:label "Process: medical diagnosis"^^xsd:string ; 39 | sio:SIO_000680 :undiagnosed_startdate_ ; 40 | sio:SIO_000681 :undiagnosed_enddate_ ; 41 | sio:SIO_000230 :phenotype_input_ ; 42 | sio:SIO_000230 :genotype_input_ ; 43 | sio:SIO_000229 :undiagnosed_output_ . 44 | 45 | :undiagnosed_output_ a sio:SIO_000015 ; 46 | rdfs:label "Output Type: Undiagnosed label"^^xsd:string ; 47 | sio:SIO_000628 :undiagnosed_attribute_ ; 48 | sio:SIO_000300 "Undiagnosed"^^xsd:string . 49 | 50 | :undiagnosed_attribute_ a sio:SIO_000614, obo:NCIT_C113725 ; 51 | rdfs:label "Attribute Type: Undiagnosed"^^xsd:string . 52 | 53 | :phenotype_input_ a sio:SIO_000015 ; 54 | rdfs:label "Process input: information content entity - Type:HP_Phenotype"^^xsd:string ; 55 | sio:SIO_000628 :phenotype_attribute_ ; 56 | sio:SIO_000300 "Muscle weakness"^^xsd:string . 57 | 58 | :phenotype_attribute_ a sio:SIO_000614, ; 59 | rdfs:label "Attribute Type: Muscle weakness"^^xsd:string . 60 | 61 | :genotype_input_ a sio:SIO_000015, sio:SIO_001388 ; 62 | rdfs:label "Process input: Information content entity - Type:HGVS_genotype"^^xsd:string ; 63 | sio:SIO_000628 :genotype_attribute_ ; 64 | sio:SIO_000300 "NM_003977.4(AIP):c.40C>T (p.Gln14Ter)"^^xsd:string . 65 | 66 | :genotype_attribute_ a sio:SIO_000614, ; 67 | rdfs:label "Attribute Type: NM_003977.4(AIP):c.40C>T (p.Gln14Ter)"^^xsd:string . 68 | 69 | :undiagnosed_startdate_ a sio:SIO_000031 ; 70 | rdfs:label "Startdate: Medical diagnosis"^^xsd:string ; 71 | sio:SIO_000300 "2012-05-24"^^xsd:date . 72 | 73 | :undiagnosed_enddate_ a sio:SIO_000032 ; 74 | rdfs:label "Enddate: Medical diagnosis"^^xsd:string ; 75 | sio:SIO_000300 "2012-05-24"^^xsd:date . 76 | ``` 77 | 78 | *** 79 | ### Validation artifacts 80 | ##### ShEx figure 81 | 82 |

83 | 84 | 85 | 86 |

87 | 88 | *** 89 | ##### ShEx 90 | 91 | ``` ShEx 92 | PREFIX : 93 | PREFIX obo: 94 | PREFIX sio: 95 | PREFIX rdfs: 96 | PREFIX xsd: 97 | 98 | :identifierShape IRI { 99 | a [sio:SIO_000115] ; 100 | rdfs:label xsd:string? ; 101 | sio:SIO_000020 @:undiagnosedRoleShape ; 102 | sio:SIO_000300 xsd:string 103 | } 104 | 105 | :personShape IRI { 106 | a [sio:SIO_000498] ; 107 | rdfs:label xsd:string? ; 108 | sio:SIO_000228 @:undiagnosedRoleShape ; 109 | sio:SIO_000008 @:undiagnosedAttributeShape ; 110 | sio:SIO_000008 @:phenotypeAttributeShape ; 111 | sio:SIO_000008 @:genotypeAttributeShape 112 | } 113 | 114 | :undiagnosedRoleShape IRI { 115 | a [obo:OBI_0000093] ; 116 | a [sio:SIO_000016] ; 117 | rdfs:label xsd:string? ; 118 | sio:SIO_000356 @:undiagnosedProcessShape 119 | } 120 | 121 | :undiagnosedProcessShape IRI { 122 | a [sio:SIO_000006] ; 123 | a [sio:SIO_001001] ; 124 | rdfs:label xsd:string? ; 125 | sio:SIO_000680 @:undiagnosedDateShape ; 126 | sio:SIO_000681 @:undiagnosedDateShape ; 127 | sio:SIO_000230 @:phenotypeInputShape ; 128 | sio:SIO_000230 @:genotypeInputShape ; 129 | sio:SIO_000229 @:undiagnosedOutputShape 130 | } 131 | 132 | :undiagnosedOutputShape IRI { 133 | a [sio:SIO_000015] ; 134 | rdfs:label xsd:string? ; 135 | sio:SIO_000300 xsd:string ; 136 | sio:SIO_000628 @:undiagnosedAttributeShape 137 | } 138 | 139 | :undiagnosedAttributeShape IRI { 140 | a [sio:SIO_000614] ; 141 | a [obo:NCIT_C113725] ; 142 | rdfs:label xsd:string? 143 | } 144 | 145 | :phenotypeInputShape IRI { 146 | a [sio:SIO_000015] ; 147 | rdfs:label xsd:string? ; 148 | sio:SIO_000628 @:phenotypeAttributeShape ; 149 | sio:SIO_000300 xsd:string 150 | } 151 | 152 | :phenotypeAttributeShape IRI { 153 | a [sio:SIO_000614] ; 154 | a IRI /^http:\/\/purl.obolibrary.org\/obo\/HP_/ ; 155 | rdfs:label xsd:string? 156 | } 157 | 158 | :genotypeInputShape IRI { 159 | a [sio:SIO_000015] ; 160 | a [sio:SIO_001388] ; 161 | rdfs:label xsd:string? ; 162 | sio:SIO_000628 @:genotypeAttributeShape ; 163 | sio:SIO_000300 xsd:string 164 | } 165 | 166 | :genotypeAttributeShape IRI { 167 | a [sio:SIO_000614] ; 168 | a IRI /^https:\/\/identifiers.org\// ; 169 | rdfs:label xsd:string? 170 | } 171 | 172 | :undiagnosedDateShape IRI { 173 | a [sio:SIO_000031 sio:SIO_000032] ; 174 | rdfs:label xsd:string? ; 175 | sio:SIO_000300 xsd:date 176 | } 177 | ``` -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/biobank.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | @prefix dc: . 7 | 8 | :identifier_ a sio:SIO_000115 ; 9 | sio:SIO_000020 :specimen_role_ ; 10 | sio:SIO_000300 "uid_000008"^^xsd:string . 11 | 12 | :person_ a sio:SIO_000498 ; 13 | sio:SIO_000228 :specimen_role_ . 14 | 15 | :specimen_role_ a obo:OBI_0000093, sio:SIO_000016 ; 16 | rdfs:label "Role: Patient for biobank sample collection"^^xsd:string ; 17 | sio:SIO_000356 :specimen_process_ . 18 | 19 | :specimen_process_ a sio:SIO_000006, obo:OBI_0000659 ; 20 | rdfs:label "Process: Sample collection"^^xsd:string ; 21 | sio:SIO_000229 :specimen_output_ . 22 | 23 | :specimen_output_ a sio:SIO_000015, obo:OBI_0100051 ; 24 | rdfs:label "Output Type: Specimen"^^xsd:string . 25 | 26 | :biobank_identifier_ a sio:SIO_000115 ; 27 | sio:SIO_000020 :biobank_role_ ; 28 | sio:SIO_000300 "biobankID_000008"^^xsd:string . 29 | 30 | :biobank_ a obo:OMIABIS_0000010 ; 31 | sio:SIO_000228 :biobank_role_ ; 32 | rdfs:label "UK Biobank"^^xsd:string . 33 | 34 | :biobank_role_ a obo:OBI_0000947, sio:SIO_000016; 35 | rdfs:label "Role: Biobank for sample storage"^^xsd:string ; 36 | sio:SIO_000356 :biobank_process_ . 37 | 38 | :biobank_process_ a sio:SIO_000006, obo:OBI_0302893 ; 39 | rdfs:label "Process: sample storage"^^xsd:string ; 40 | sio:SIO_000229 :specimen_output_ . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/bodyMeasurement.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix sio: . 3 | @prefix obo: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :body_measurement_role_ ; 9 | sio:SIO_000300 "uid_000008"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498 ; 12 | sio:SIO_000228 :body_measurement_role_ ; 13 | sio:SIO_000008 :body_measurement_attribute_ . 14 | 15 | :body_measurement_role_ a obo:OBI_0000093, sio:SIO_000016 ; 16 | rdfs:label "Patient role"^^xsd:string ; 17 | sio:SIO_000356 :body_measurement_process_ . 18 | 19 | :body_measurement_process_ a sio:SIO_000006, obo:NCIT_C25498 ; 20 | rdfs:label "Estimation process"^^xsd:string ; 21 | sio:SIO_000680 :body_measurement_startdate_ ; 22 | sio:SIO_000681 :body_measurement_enddate_ ; 23 | sio:SIO_000229 :body_measurement_output_ ; 24 | sio:CHEMINF_000047 . 25 | 26 | :body_measurement_output_ a sio:SIO_000015 ; 27 | rdfs:label "Measurement value output type"^^xsd:string ; 28 | sio:SIO_000300 "95"^^xsd:string ; 29 | rdfs:comment "Estimated by visual inspection"^^xsd:string ; 30 | sio:SIO_000221 :body_measurement_unit_ ; 31 | sio:SIO_000628 :body_measurement_attribute_ . 32 | 33 | :body_measurement_unit_ a obo:UO_0000009 ; 34 | rdfs:label "kg"^^xsd:string . 35 | 36 | :body_measurement_attribute_ a sio:SIO_000614, obo:NCIT_C81328 ; 37 | rdfs:label "Body weight attribute"^^xsd:string . 38 | 39 | a sio:SIO_000015, obo:NCIT_C42651 ; 40 | rdfs:label "Measurement protocol"^^xsd:string . 41 | 42 | :body_measurement_startdate_ a sio:SIO_000031 ; 43 | rdfs:label "Body measurement startdate"^^xsd:string ; 44 | sio:SIO_000300 "2019-02-28"^^xsd:date . 45 | 46 | :body_measurement_enddate_ a sio:SIO_000032 ; 47 | rdfs:label "Body measurement enddate"^^xsd:string ; 48 | sio:SIO_000300 "2019-02-28"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/carePathway.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :carepathway_role_ ; 9 | sio:SIO_000300 "uid_000007"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498; 12 | sio:SIO_000228 :carepathway_role_ . 13 | 14 | :carepathway_role_ a obo:OBI_0000093, sio:SIO_000016; 15 | rdfs:label "Role: First contact patient"^^xsd:string; 16 | sio:SIO_000356 :carepathway_process_ . 17 | 18 | :carepathway_process_ a sio:SIO_000006, obo:NCIT_C159705, obo:NCIT_C16205 ; 19 | rdfs:label "Process: First contact with specialized center"^^xsd:string; 20 | sio:SIO_000680 :carepathway_startdate_ ; 21 | sio:SIO_000681 :carepathway_enddate_ . 22 | 23 | :carepathway_startdate_ a sio:SIO_000031 ; 24 | rdfs:label "Startdate: 1991-02-12"^^xsd:string ; 25 | sio:SIO_000300 "1991-02-12"^^xsd:date . 26 | 27 | :carepathway_enddate_ a sio:SIO_000032 ; 28 | rdfs:label "Enddate: 1991-02-12"^^xsd:string ; 29 | sio:SIO_000300 "1991-02-12"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/diagnosis.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :diagnosis_role_ ; 9 | sio:SIO_000300 "uid_000007"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498; 12 | sio:SIO_000228 :diagnosis_role_ ; 13 | sio:SIO_000008 :diagnosis_attribute_ . 14 | 15 | :diagnosis_role_ a obo:OBI_0000093, sio:SIO_000016 ; 16 | rdfs:label "Role: Diagnosis patient"^^xsd:string; 17 | sio:SIO_000356 :diagnosis_process_ . 18 | 19 | :diagnosis_process_ a sio:SIO_000006, sio:SIO_001001 ; 20 | rdfs:label "Process: Medical diagnosis"^^xsd:string ; 21 | sio:SIO_000680 :diagnosis_startdate_ ; 22 | sio:SIO_000681 :diagnosis_enddate_ ; 23 | sio:SIO_000229 :diagnosis_output_ . 24 | 25 | :diagnosis_output_ a sio:SIO_000015, sio:SIO_001003 ; 26 | rdfs:label "Output Type: Diagnosis"^^xsd:string ; 27 | sio:SIO_000300 "Richards-Rundle syndrome is an extremely rare neurodegenerative disorder characterized by progressive spinocerebellar ataxia"^^xsd:string ; 28 | sio:SIO_000628 :diagnosis_attribute_ . 29 | 30 | :diagnosis_attribute_ a sio:SIO_000614, ; 31 | rdfs:label "Attribute Type: Richards-Rundle syndrome is an extremely rare neurodegenerative disorder characterized by progressive spinocerebellar ataxia"^^xsd:string . 32 | 33 | :diagnosis_startdate_ a sio:SIO_000031 ; 34 | rdfs:label "Startdate: 1996-02-12"^^xsd:string ; 35 | sio:SIO_000300 "1996-02-12"^^xsd:date . 36 | 37 | :diagnosis_enddate_ a sio:SIO_000032 ; 38 | rdfs:label "Enddate: 1996-02-12"^^xsd:string ; 39 | sio:SIO_000300 "1996-02-12"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/disability.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix sio: . 3 | @prefix obo: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :disability_role_ ; 9 | sio:SIO_000300 "uid_000002"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498 ; 12 | sio:SIO_000228 :disability_role_ . 13 | 14 | :disability_role_ a obo:OBI_0000093, sio:SIO_000016 ; 15 | rdfs:label "Role: Patient"^^xsd:string ; 16 | sio:SIO_000356 :assessment_test_ . 17 | 18 | :assessment_test_ a sio:SIO_000006, obo:NCIT_C20993, obo:NCIT_C107391 ; 19 | rdfs:label "Process: Edmonton symptom assessment system"^^xsd:string ; 20 | sio:SIO_000680 :disability_startdate_ ; 21 | sio:SIO_000681 :disability_enddate_ ; 22 | sio:SIO_000230 :question_answering_input_ ; 23 | sio:SIO_000229 :test_output_ . 24 | 25 | :test_output_ a sio:SIO_000015 ; 26 | rdfs:label "Output Type: disability score"^^xsd:string ; 27 | sio:SIO_000300 "12"^^xsd:string . 28 | 29 | :question_answering_input_ a sio:SIO_000015, obo:NCIT_C17048 ; 30 | rdfs:label "Process Input: Information content entity - Type: Questionnaire"^^xsd:string . 31 | 32 | :disability_startdate_ a sio:SIO_000031 ; 33 | rdfs:label "Startdate: 2019-11-12"^^xsd:string ; 34 | sio:SIO_000300 "2019-11-12"^^xsd:date . 35 | 36 | :disability_enddate_ a sio:SIO_000032 ; 37 | rdfs:label "Enddate: 2019-11-12"^^xsd:string ; 38 | sio:SIO_000300 "2019-11-12"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/diseaseHistory.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :symptom_onset_role_ ; 9 | sio:SIO_000020 :diagnosis_date_role_ ; 10 | sio:SIO_000300 "uid_000008"^^xsd:string . 11 | 12 | :person_ a sio:SIO_000498; 13 | sio:SIO_000228 :symptom_onset_role_ ; 14 | sio:SIO_000008 :symptom_onset_attribute_ ; 15 | sio:SIO_000228 :diagnosis_date_role_ ; 16 | sio:SIO_000008 :diagnosis_date_attribute_ . 17 | 18 | :symptom_onset_role_ a obo:OBI_0000093, sio:SIO_000016; 19 | rdfs:label "Role: Symptom onset patient"^^xsd:string; 20 | sio:SIO_000356 :symptom_onset_process_ . 21 | 22 | :symptom_onset_process_ a sio:SIO_000006, sio:SIO_001052 ; 23 | rdfs:label "Process: Data collection - symptom onset date recording process"^^xsd:string; 24 | sio:SIO_000229 :symptom_onset_output_ . 25 | 26 | :symptom_onset_output_ a sio:SIO_000015, obo:NCIT_C25164 ; 27 | rdfs:label "Output Type: Date of onset"^^xsd:string ; 28 | sio:SIO_000300 "1982-04-06"^^xsd:date ; 29 | sio:SIO_000628 :symptom_onset_attribute_ . 30 | 31 | :symptom_onset_attribute_ a sio:SIO_000614, obo:NCIT_C25279 ; 32 | rdfs:label "Attribute: Stage or date of onset"^^xsd:string . 33 | 34 | :diagnosis_date_role_ a obo:OBI_0000093, sio:SIO_000016 ; 35 | rdfs:label "Role: Diagnosis date patient"^^xsd:string ; 36 | sio:SIO_000356 :diagnosis_date_process_ . 37 | 38 | :diagnosis_date_process_ a sio:SIO_000006, sio:SIO_001052 ; 39 | rdfs:label "Process: Data collection - diagnosis date recording process"^^xsd:string ; 40 | sio:SIO_000229 :diagnosis_date_output_ . 41 | 42 | :diagnosis_date_output_ a sio:SIO_000015, obo:NCIT_C25164 ; 43 | rdfs:label "Output Type: Age at diagnosis"^^xsd:string ; 44 | sio:SIO_000300 "1992-04-06"^^xsd:date ; 45 | sio:SIO_000628 :diagnosis_date_attribute_ . 46 | 47 | :diagnosis_date_attribute_ a sio:SIO_000614, obo:NCIT_C156420 ; 48 | rdfs:label "Attribute Type: Stage or date of diagnosis"^^xsd:string . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/drugTreatment.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix rdfs: . 4 | @prefix sio: . 5 | @prefix xsd: . 6 | 7 | :Person a sio:SIO_000498 ; 8 | sio:SIO_000228 :Treatment_role . 9 | 10 | :ID a sio:SIO_000115 ; 11 | sio:SIO_000020 :Treatment_role ; 12 | sio:SIO_000300 "id_000007"^^xsd:string . 13 | 14 | a obo:NCIT_C1702, 15 | obo:NCIT_C177929 ; 16 | rdfs:label "Drug component: rituximab" ; 17 | sio:SIO_000313 :Drug . 18 | 19 | :Administration_input a obo:NCIT_C38288, 20 | sio:SIO_000015 ; 21 | rdfs:label "Route of administration: Oral Route of Administration" . 22 | 23 | :Dose a obo:NCIT_C25488 ; 24 | rdfs:label "Dose" ; 25 | sio:SIO_000221 :Unit ; 26 | sio:SIO_000900 :Frequency . 27 | 28 | :Drug_intake_process a obo:NCIT_C25538 ; 29 | rdfs:label "Process: Drug intake" ; 30 | sio:CHEMINF_000047 :Prescription_output ; 31 | sio:SIO_000139 :Drug ; 32 | sio:SIO_000230 :Administration_input ; 33 | sio:SIO_000680 :Treatment_startdate ; 34 | sio:SIO_000681 :Treatment_enddate . 35 | 36 | :Drug_prescription_process a obo:NCIT_C111077 ; 37 | rdfs:label "Process: Drug prescription" ; 38 | sio:SIO_000229 :Prescription_output . 39 | 40 | :Frequency a obo:NCIT_C66968 ; 41 | rdfs:label "Frequency: per day" ; 42 | sio:SIO_000300 "1"^^xsd:integer . 43 | 44 | :Treatment_enddate a sio:SIO_000032 ; 45 | rdfs:label "Enddate: 2021-08-08" ; 46 | sio:SIO_000300 "2021-08-08"^^xsd:date . 47 | 48 | :Treatment_startdate a sio:SIO_000031 ; 49 | rdfs:label "Startdate: 2019-04-05" ; 50 | sio:SIO_000300 "2019-04-05"^^xsd:date . 51 | 52 | :Unit a obo:UO_0000022 ; 53 | rdfs:label "Unit: miligram" . 54 | 55 | :Prescription_output a obo:NCIT_C28180, 56 | sio:SIO_000015 ; 57 | rdfs:label "Prescription" ; 58 | sio:SIO_000628 :Dose, 59 | :Drug ; 60 | rdfs:comment "60 miligrams 1 time per day of Rituximab via intramuscular "^^xsd:string . 61 | 62 | :Treatment_role a obo:OBI_0000093, 63 | sio:SIO_000016 ; 64 | rdfs:label "Role: Patient" ; 65 | sio:SIO_000356 :Drug_intake_process, 66 | :Drug_prescription_process . 67 | 68 | :Drug a sio:SIO_010038 ; 69 | rdfs:label "Drug" ; 70 | sio:SIO_000300 "60.0"^^xsd:float . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/geneticDiagnosis.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | @prefix edam: . 7 | 8 | :identifier_ a sio:SIO_000115 ; 9 | sio:SIO_000020 :genetic_role_ ; 10 | sio:SIO_000300 "uid_000008"^^xsd:string . 11 | 12 | :person_ a sio:SIO_000498 ; 13 | sio:SIO_000228 :genetic_role_ ; 14 | sio:SIO_000008 :hgvs_attribute_ ; 15 | sio:SIO_000008 ; 16 | sio:SIO_000008 . 17 | 18 | :genetic_role_ a obo:OBI_0000093, sio:SIO_000016 ; 19 | rdfs:label "Role: Genetic Diagnosis patient"^^xsd:string ; 20 | sio:SIO_000356 :hgvs_process_ ; 21 | sio:SIO_000356 :omim_process_ ; 22 | sio:SIO_000356 :hgnc_process_ . 23 | 24 | :hgvs_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 25 | rdfs:label "Process: HGVS genetic testing"^^xsd:string ; 26 | sio:SIO_000229 :hgvs_output_ . 27 | 28 | :hgvs_output_ a sio:SIO_000015, sio:SIO_001388 ; 29 | rdfs:label "Output Type: measurement-value"^^xsd:string ; 30 | sio:SIO_000300 "NM_004006.3:c.4375C>T"^^xsd:string ; 31 | sio:SIO_000628 :hgvs_attribute_ . 32 | 33 | :hgvs_attribute_ a sio:SIO_000614, sio:SIO_000015, obo:NCIT_C171178 ; 34 | xsd:label "NM_004006.3:c.4375C>T"^^xsd:string . 35 | 36 | :omim_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 37 | rdfs:label "Process: OMIM genetic testing"^^xsd:string ; 38 | sio:SIO_000229 :omim_output_ . 39 | 40 | :omim_output_ a sio:SIO_000015, sio:SIO_001381 ; 41 | rdfs:label "Output Type: OMIM genome sequence variant"^^xsd:string ; 42 | sio:SIO_000300 "https://www.omim.org/entry/192977"^^xsd:string ; 43 | sio:SIO_000628 . 44 | 45 | a sio:SIO_000614, sio:SIO_000015, edam:data_1153 ; 46 | rdfs:label "Attribute Type: https://www.omim.org/entry/192977"^^xsd:string . 47 | 48 | :hgnc_process_ a sio:SIO_000006, obo:NCIT_C15709 ; 49 | rdfs:label "Process: HGNC genetic testing"^^xsd:string ; 50 | sio:SIO_000229 :hgnc_output_ . 51 | 52 | :hgnc_output_ a sio:SIO_000015, sio:SIO_001381 ; 53 | rdfs:label "Output Type: HGNC genome sequence variant"^^xsd:string ; 54 | sio:SIO_000300 "https://identifiers.org/HGNC:12698"^^xsd:string ; 55 | sio:SIO_000628 . 56 | 57 | a sio:SIO_000614, sio:SIO_000015, edam:data_2298 ; 58 | rdfs:label "Attribute Type: https://identifiers.org/HGNC:12698"^^xsd:string . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/imaging.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix sio: . 3 | @prefix obo: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :imaging_role_ ; 9 | sio:SIO_000300 "uid_000008"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498 ; 12 | sio:SIO_000228 :imaging_role_ . 13 | 14 | :imaging_role_ a obo:OBI_0000093, sio:SIO_000016 ; 15 | rdfs:label "Patient role"^^xsd:string ; 16 | sio:SIO_000356 :imaging_process_ . 17 | 18 | :imaging_process_ a obo:NCIT_C48937, obo:NCIT_C18001 ; 19 | rdfs:label"Digital X-ray process"^^xsd:string ; 20 | sio:SIO_000680 :imaging_startdate_ ; 21 | sio:SIO_000681 :imaging_enddate_ ; 22 | sio:SIO_000229 :imaging_output_ ; 23 | sio:SIO_000291 :imaging_target_ ; 24 | sio:CHEMINF_000047 . 25 | 26 | :imaging_target_ a sio:SIO_000015, obo:NCIT_C12419 ; 27 | rdfs:label "Head process target"^^xsd:string . 28 | 29 | :imaging_output_ a sio:SIO_000015, ; 30 | rdfs:label "Measurement value output type"^^xsd:string ; 31 | rdfs:comment "A formula for estimating height based on ulnar length"^^xsd:string . 32 | 33 | a sio:SIO_000015, obo:NCIT_C42651 ; 34 | rdfs:label "Measurement protocol"^^xsd:string . 35 | 36 | :disability_startdate_ a sio:SIO_000031 ; 37 | rdfs:label "Imaging startdate"^^xsd:string ; 38 | sio:SIO_000300 "2019-02-28"^^xsd:date . 39 | 40 | :disability_enddate_ a sio:SIO_000032 ; 41 | rdfs:label "Imaging enddate"^^xsd:string ; 42 | sio:SIO_000300 "2019-02-28"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/labData.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix sio: . 3 | @prefix obo: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :lab_data_role_ ; 9 | sio:SIO_000300 "uid_000008"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498 ; 12 | sio:SIO_000228 :lab_data_role_ . 13 | 14 | :lab_data_role_ a obo:OBI_0000093, sio:SIO_000016 ; 15 | rdfs:label "Patient role"^^xsd:string ; 16 | sio:SIO_000356 :lab_data_process_ . 17 | 18 | :lab_data_process_ a obo:NCIT_C48937 ; 19 | rdfs:label "Quantitation process"^^xsd:string ; 20 | sio:SIO_000680 :lab_data_startdate_ ; 21 | sio:SIO_000681 :lab_data_enddate_ ; 22 | sio:SIO_000230 :lab_data_input_ ; 23 | sio:SIO_000229 :lab_data_output_ ; 24 | sio:SIO_000291 :lab_data_target_ ; 25 | sio:CHEMINF_000047 . 26 | 27 | :lab_data_input_ a sio:SIO_000015, obo:NCIT_C12434 ; 28 | rdfs:label "Blood process input"^^xsd:string . 29 | 30 | :lab_data_target_ a sio:SIO_000015, obo:NCIT_C16676 ; 31 | rdfs:label "Hemoglobin process target"^^xsd:string . 32 | 33 | :lab_data_output_ a sio:SIO_000015 ; 34 | rdfs:label "Measurement value output type"^^xsd:string ; 35 | sio:SIO_000300 "13"^^xsd:float ; 36 | rdfs:comment "Blood collected early morning"^^xsd:string ; 37 | sio:SIO_000221 :lab_data_unit_ . 38 | 39 | :lab_data_unit_ a obo:UO_0000208 ; 40 | rdfs:label "grams per decilitre"^^xsd:string . 41 | 42 | a sio:SIO_000015, obo:NCIT_C42651 ; 43 | rdfs:label " Measurement protocol"^^xsd:string . 44 | 45 | :lab_data_startdate_ a sio:SIO_000031 ; 46 | rdfs:label "Laboratory measuring startdate"^^xsd:string ; 47 | sio:SIO_000300 "2019-02-28"^^xsd:date . 48 | 49 | :lab_data_enddate_ a sio:SIO_000032 ; 50 | rdfs:label "Laboratory measuring enddate"^^xsd:string ; 51 | sio:SIO_000300 "2019-02-28"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/patientConsent.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :consent_role_ ; 9 | sio:SIO_000300 "uid_000010"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498 ; 12 | sio:SIO_000228 :consent_role_ ; 13 | sio:SIO_000008 :consent_attribute_ . 14 | 15 | :consent_role_ a obo:OBI_0000093, sio:SIO_000016; 16 | rdfs:label "Role: Patient for status recording"^^xsd:string; 17 | sio:SIO_000356 :consent_process_ . 18 | 19 | :consent_process_ a sio:SIO_000006, obo:OBI_0000810 ; 20 | rdfs:label "Process: Consenting"^^xsd:string; 21 | sio:SIO_000229 :consent_output_ ; 22 | sio:SIO_000230 :consent_input_ ; 23 | sio:SIO_000680 :consent_startdate_ ; 24 | sio:SIO_000681 :consent_enddate_ . 25 | 26 | :consent_output_ a sio:SIO_000015 ; 27 | rdfs:label "Output Type: Patient consent record"^^xsd:string ; 28 | sio:SIO_000300 "disease specific research"^^xsd:string ; 29 | sio:SIO_000628 :consent_attribute_ . 30 | 31 | :consent_input_ a sio:SIO_000015, obo:ICO_0000001 ; 32 | rdfs:label "Process Input: information content entity -Type: consent_document"^^xsd:string ; 33 | sio:SIO_000300 "http://example.org/my_consent_document_type2"^^xsd:string . 34 | 35 | :consent_attribute_ a sio:SIO_000614, obo:DUO_0000007 ; 36 | rdfs:label "Attribute Type: disease specific research"^^xsd:string . 37 | 38 | :consent_startdate_ a sio:SIO_000031 ; 39 | rdfs:label "Startdate: 1996-08-08"^^xsd:string ; 40 | sio:SIO_000300 "1996-08-08"^^xsd:date . 41 | 42 | :consent_enddate_ a sio:SIO_000032 ; 43 | rdfs:label "Enddate: 1996-08-08"^^xsd:string ; 44 | sio:SIO_000300 "1996-08-08"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/patientStatus.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix rdfs: . 4 | @prefix sio: . 5 | @prefix xsd: . 6 | 7 | :Person a sio:SIO_000498 ; 8 | sio:SIO_000008 :Death_information_Attribute, 9 | :Status_Attribute ; 10 | sio:SIO_000228 :Status_Role . 11 | 12 | :ID a sio:SIO_000115 ; 13 | sio:SIO_000020 :Status_Role ; 14 | sio:SIO_000300 "uid_000008"^^xsd:string . 15 | 16 | :Death_information_Output a sio:SIO_000015 ; 17 | rdfs:label "Output type: Patient death information" ; 18 | sio:SIO_000300 "2010-06-08"^^xsd:date ; 19 | sio:SIO_000628 :Death_information_Attribute . 20 | 21 | :Death_information_Process a sio:SIO_000006 ; 22 | rdfs:label "Process: Death information recording process" ; 23 | sio:SIO_000229 :Death_information_Output . 24 | 25 | :Status_Enddate a sio:SIO_000032 ; 26 | rdfs:label "Enddate: 2010-06-08" ; 27 | sio:SIO_000300 "2010-06-08"^^xsd:date . 28 | 29 | :Status_Output a sio:SIO_000015 ; 30 | rdfs:label "Output type: dead" ; 31 | sio:SIO_000300 "dead"^^xsd:string ; 32 | sio:SIO_000628 :Status_Attribute . 33 | 34 | :Status_Process a sio:SIO_000006, 35 | sio:SIO_001052 ; 36 | rdfs:label "Process: Status recording process" ; 37 | sio:SIO_000229 :Status_Output ; 38 | sio:SIO_000680 :Status_Startdate ; 39 | sio:SIO_000681 :Status_Enddate . 40 | 41 | :Status_Startdate a sio:SIO_000031 ; 42 | rdfs:label "Startdate: 2010-06-08" ; 43 | sio:SIO_000300 "2010-06-08"^^xsd:date . 44 | 45 | :Death_information_Attribute a obo:NCIT_C70810, 46 | sio:SIO_000614 ; 47 | rdfs:label "Attribute type: Date of death" . 48 | 49 | :Status_Attribute a obo:NCIT_C166244, 50 | sio:SIO_000614, 51 | sio:SIO_010059 ; 52 | rdfs:label "Attribute type: dead" . 53 | 54 | :Status_Role a obo:OBI_0000093, 55 | sio:SIO_000016 ; 56 | rdfs:label "Role: Patient for status recording" ; 57 | sio:SIO_000356 :Death_information_Process, 58 | :Status_Process . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/personalInformation.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :birthdate_role_ ; 9 | sio:SIO_000020 :sex_role_ ; 10 | sio:SIO_000300 "uid_000008"^^xsd:string . 11 | 12 | :person_ a sio:SIO_000498; 13 | sio:SIO_000228 :birthdate_role_ ; 14 | sio:SIO_000008 :birthdate_attribute_ ; 15 | sio:SIO_000228 :sex_role_ ; 16 | sio:SIO_000008 :sex_attribute_ . 17 | 18 | :birthdate_role_ a obo:OBI_0000093, sio:SIO_000016 ; 19 | rdfs:label "Role: Patient for age assessment"^^xsd:string ; 20 | sio:SIO_000356 :birthdate_process_ . 21 | 22 | :birthdate_process_ a sio:SIO_000006 ; 23 | rdfs:label "Process: Age measuring process"^^xsd:string ; 24 | sio:SIO_000229 :birthdate_output_ . 25 | 26 | :birthdate_output_ a sio:SIO_000015 ; 27 | rdfs:label "Output Type: Birth date"^^xsd:string ; 28 | sio:SIO_000300 "1991-02-12"^^xsd:date ; 29 | sio:SIO_000628 :birthdate_attribute_ . 30 | 31 | :birthdate_attribute_ a sio:SIO_000614, obo:NCIT_C68615 ; 32 | rdfs:label "Attribute Type: Birth date"^^xsd:string . 33 | 34 | :sex_role_ a obo:OBI_0000093, sio:SIO_000016 ; 35 | rdfs:label "Role: Patient for gender assessment"^^xsd:string ; 36 | sio:SIO_000356 :sex_process_ . 37 | 38 | :sex_process_ a sio:SIO_000006 ; 39 | rdfs:label "Process: sex measuring process"^^xsd:string ; 40 | sio:SIO_000229 :sex_output_ . 41 | 42 | :sex_output_ a sio:SIO_000015; 43 | rdfs:label "Output Type: Female"^^xsd:string ; 44 | sio:SIO_000300 "Female"^^xsd:string ; 45 | sio:SIO_000628 :sex_attribute_ . 46 | 47 | :sex_attribute_ a sio:SIO_000614, obo:NCIT_C28421, obo:NCIT_C16576 ; 48 | rdfs:label "Attribute Type: Female"^^xsd:string . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/phenotyping.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | @prefix rdfs: . 6 | 7 | :identifier_ a sio:SIO_000115 ; 8 | sio:SIO_000020 :phenotypic_role_ ; 9 | sio:SIO_000300 "uid_000007"^^xsd:string . 10 | 11 | :person_ a sio:SIO_000498; 12 | sio:SIO_000228 :phenotypic_role_ ; 13 | sio:SIO_000008 :phenotypic_attribute_ . 14 | 15 | :phenotypic_role_ a obo:OBI_0000093, sio:SIO_000016 ; 16 | rdfs:label "Role: Phenotyping patient"^^xsd:string ; 17 | sio:SIO_000356 :phenotypic_process_ . 18 | 19 | :phenotypic_process_ a sio:SIO_000006, obo:OBI_0001546, obo:NCIT_C16205, obo:NCIT_C18020 ; 20 | rdfs:label "Process: Comparative phenotypic assessment"^^xsd:string ; 21 | sio:SIO_000680 :phenotypic_startdate_ ; 22 | sio:SIO_000681 :phenotypic_enddate_ ; 23 | sio:SIO_000229 :phenotypic_output_ . 24 | 25 | :phenotypic_output_ a sio:SIO_000015, obo:NCIT_C102741 ; 26 | rdfs:label "Output Type: Cerebellar ataxia"^^xsd:string ; 27 | sio:SIO_000628 :phenotypic_attribute_ . 28 | 29 | :phenotypic_attribute_ a sio:SIO_000614, sio:SIO_010056, obo:HP_0001251 ; 30 | rdfs:label "Attribute Type: Cerebellar ataxia"^^xsd:string . 31 | 32 | :phenotypic_startdate_ a sio:SIO_000031 ; 33 | rdfs:label "Startdate: 1998-08-12"^^xsd:string ; 34 | sio:SIO_000300 "1998-08-12"^^xsd:date . 35 | 36 | :phenotypic_enddate_ a sio:SIO_000032 ; 37 | rdfs:label "Enddate: 1998-08-12"^^xsd:string ; 38 | sio:SIO_000300 "1998-08-12"^^xsd:date . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/pseudonym.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix sio: . 4 | @prefix xsd: . 5 | 6 | :person_ a sio:SIO_000498 ; 7 | sio:SIO_000228 :role_ . 8 | 9 | :role_ a obo:OBI_0000093 . 10 | 11 | :identifier_ a sio:SIO_000115 ; 12 | sio:SIO_000020 :role_ ; 13 | sio:SIO_000300 "uid_000008"^^xsd:string . -------------------------------------------------------------------------------- /DEPRECATED/example-data/turtle/unDiagnosis.ttl: -------------------------------------------------------------------------------- 1 | @prefix : . 2 | @prefix obo: . 3 | @prefix rdfs: . 4 | @prefix sio: . 5 | @prefix xsd: . 6 | 7 | :Person a sio:SIO_000498 ; 8 | sio:SIO_000008 :Phenotype_Attribute, 9 | :Undiagnosed_Attribute, 10 | ; 11 | sio:SIO_000228 :Undiagnosed_Role . 12 | 13 | :ID a sio:SIO_000115 ; 14 | sio:SIO_000020 :Undiagnosed_Role ; 15 | sio:SIO_000300 "uid_000002"^^xsd:string . 16 | 17 | :Genotype_Input a sio:SIO_000015, 18 | sio:SIO_001388 ; 19 | rdfs:label "Input type: HGVS_Genotype" ; 20 | sio:SIO_000300 "NM_003977.4(AIP):c.40C>T (p.Gln14Ter)"^^xsd:string ; 21 | sio:SIO_000628 . 22 | 23 | :Phenotype_Input a obo:NCIT_C102741, 24 | sio:SIO_000015 ; 25 | rdfs:label "Input type: HP_Phenotype" ; 26 | sio:SIO_000300 "Muscle Weakness"^^xsd:string ; 27 | sio:SIO_000628 :Phenotype_Attribute . 28 | 29 | :Undiagnosed_Enddate a sio:SIO_000032 ; 30 | rdfs:label "Enddate: 2012-05-24" ; 31 | sio:SIO_000300 "2012-05-24"^^xsd:date . 32 | 33 | :Undiagnosed_Output a sio:SIO_000015 ; 34 | rdfs:label "Output type: Undiagnosed label" ; 35 | sio:SIO_000300 "Undiagnosed" ; 36 | sio:SIO_000628 :Undiagnosed_Attribute . 37 | 38 | :Undiagnosed_Process a sio:SIO_000006, 39 | sio:SIO_001001 ; 40 | rdfs:label "Process: Medical diagnosis" ; 41 | sio:SIO_000229 :Undiagnosed_Output ; 42 | sio:SIO_000230 :Genotype_Input, 43 | :Phenotype_Input ; 44 | sio:SIO_000680 :Undiagnosed_Startdate ; 45 | sio:SIO_000681 :Undiagnosed_Enddate . 46 | 47 | :Undiagnosed_Startdate a sio:SIO_000031 ; 48 | rdfs:label "Startdate: 2012-05-24" ; 49 | sio:SIO_000300 "2012-05-24"^^xsd:date . 50 | 51 | :Phenotype_Attribute a obo:HP_0001324, 52 | sio:SIO_000614 ; 53 | rdfs:label "Attribute type: Muscle Weakness" . 54 | 55 | :Undiagnosed_Attribute a obo:NCIT_C113725, 56 | sio:SIO_000614 ; 57 | rdfs:label "Attribute type: Undiagnosed" . 58 | 59 | :Undiagnosed_Role a obo:OBI_0000093, 60 | sio:SIO_000016 ; 61 | rdfs:label "Role: Undiagnosed patient" ; 62 | sio:SIO_000356 :Undiagnosed_Process . 63 | 64 | a obo:NCIT_C171178, 65 | sio:SIO_000614 ; 66 | rdfs:label "Attribute type: NM_003977.4(AIP):c.40C>T (p.Gln14Ter)" . -------------------------------------------------------------------------------- /DEPRECATED/images/rdf/10_Disability.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ejp-rd-vp/CDE-semantic-model/65c044836b9b0e4c571a0ead48d4fbd59a464934/DEPRECATED/images/rdf/10_Disability.png 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https://raw.githubusercontent.com/ejp-rd-vp/CDE-semantic-model/65c044836b9b0e4c571a0ead48d4fbd59a464934/DEPRECATED/images/rdf/DCDE_lab_measurement.drawio.png -------------------------------------------------------------------------------- /DEPRECATED/images/rdf/complete_data_model_SIO.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ejp-rd-vp/CDE-semantic-model/65c044836b9b0e4c571a0ead48d4fbd59a464934/DEPRECATED/images/rdf/complete_data_model_SIO.png -------------------------------------------------------------------------------- /DEPRECATED/shex/biobank.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX dc: 6 | PREFIX rdfs: 7 | 8 | :identifierShape IRI { 9 | a [sio:SIO_000115] ; 10 | sio:SIO_000020 @:specimenRoleShape ; 11 | rdfs:label xsd:string? ; 12 | sio:SIO_000300 xsd:string 13 | } 14 | 15 | :personShape IRI { 16 | a [sio:SIO_000498] ; 17 | rdfs:label xsd:string? ; 18 | sio:SIO_000228 @:specimenRoleShape 19 | } 20 | 21 | :specimenRoleShape IRI { 22 | a [obo:OBI_0000093] ; 23 | a [sio:SIO_000016] ; 24 | rdfs:label xsd:string? ; 25 | sio:SIO_000356 @:specimenProcessShape 26 | } 27 | 28 | :specimenProcessShape IRI { 29 | a [sio:SIO_000006] ; 30 | a [obo:OBI_0000659] ; 31 | rdfs:label xsd:string? ; 32 | sio:SIO_000229 @:specimenOutputShape 33 | } 34 | 35 | :specimenOutputShape IRI { 36 | a [sio:SIO_000015] ; 37 | a [obo:OBI_0100051] ; 38 | rdfs:label xsd:string? 39 | } 40 | 41 | :biobankIdentifierShape IRI { 42 | a [sio:SIO_000115] ; 43 | sio:SIO_000020 @:biobankRoleShape ; 44 | rdfs:label xsd:string? ; 45 | sio:SIO_000300 xsd:string 46 | } 47 | 48 | :biobankShape IRI { 49 | a [obo:OMIABIS_0000010] ; 50 | rdfs:label xsd:string? ; 51 | sio:SIO_000228 @:biobankRoleShape 52 | } 53 | 54 | :biobankRoleShape IRI { 55 | a [obo:OBI_0000947] ; 56 | a [sio:SIO_000016] ; 57 | rdfs:label xsd:string? ; 58 | sio:SIO_000356 @:biobankProcessShape 59 | } 60 | 61 | :biobankProcessShape IRI { 62 | a [sio:SIO_000006] ; 63 | a [obo:OBI_0302893] ; 64 | rdfs:label xsd:string? ; 65 | sio:SIO_000230 @:specimenOutputShape 66 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/carePathwayShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | sio:SIO_000020 @:carePathwayRoleShape ; 10 | rdfs:label xsd:string? ; 11 | sio:SIO_000300 xsd:string 12 | } 13 | 14 | :personShape IRI { 15 | a [sio:SIO_000498] ; 16 | rdfs:label xsd:string? ; 17 | sio:SIO_000228 @:carePathwayRoleShape 18 | } 19 | 20 | :carePathwayRoleShape IRI { 21 | a [obo:OBI_0000093] ; 22 | a [sio:SIO_000016] ; 23 | rdfs:label xsd:string? ; 24 | sio:SIO_000356 @:carePathwayProcessShape 25 | } 26 | 27 | :carePathwayProcessShape IRI { 28 | a [sio:SIO_000006] ; 29 | a [obo:NCIT_C159705] ; 30 | a [obo:NCIT_C16205] ; 31 | rdfs:label xsd:string? ; 32 | sio:SIO_000680 @:carePathwayDateShape ; 33 | sio:SIO_000681 @:carePathwayDateShape 34 | } 35 | 36 | :carePathwayDateShape IRI { 37 | a [sio:SIO_000031 sio:SIO_000032] ; 38 | rdfs:label xsd:string? ; 39 | sio:SIO_000300 xsd:date 40 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/diagnosisShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | sio:SIO_000020 @:medicalDiagnosisRoleShape ; 10 | rdfs:label xsd:string? ; 11 | sio:SIO_000300 xsd:string 12 | } 13 | 14 | :personShape IRI { 15 | a [sio:SIO_000498] ; 16 | rdfs:label xsd:string? ; 17 | sio:SIO_000228 @:medicalDiagnosisRoleShape ; 18 | sio:SIO_000008 @:medicalDiagnosisAttributeShape 19 | } 20 | 21 | :medicalDiagnosisRoleShape IRI { 22 | a [obo:OBI_0000093] ; 23 | a [sio:SIO_000016] ; 24 | rdfs:label xsd:string? ; 25 | sio:SIO_000356 @:medicalDiagnosisProcessShape 26 | } 27 | 28 | :medicalDiagnosisProcessShape IRI { 29 | a [sio:SIO_000006] ; 30 | a [sio:SIO_001001] ; 31 | rdfs:label xsd:string? ; 32 | sio:SIO_000680 @:medicalDiagnosisDateShape ; 33 | sio:SIO_000681 @:medicalDiagnosisDateShape ; 34 | sio:SIO_000229 @:medicalDiagnosisOutputShape 35 | } 36 | 37 | :medicalDiagnosisOutputShape IRI { 38 | a [sio:SIO_000015] ; 39 | a [sio:SIO_001003] ; 40 | rdfs:label xsd:string? ; 41 | sio:SIO_000300 xsd:string ; 42 | sio:SIO_000628 @:medicalDiagnosisAttributeShape 43 | } 44 | 45 | :medicalDiagnosisAttributeShape IRI { 46 | a [sio:SIO_000614] ; 47 | a IRI /^http:\/\/www.orpha.net\/ORDO\/Orphanet_/ ; 48 | rdfs:label xsd:string? 49 | } 50 | 51 | :medicalDiagnosisDateShape IRI { 52 | a [sio:SIO_000031 sio:SIO_000032] ; 53 | rdfs:label xsd:string? ; 54 | sio:SIO_000300 xsd:date 55 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/disability.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000020 @:disabilityRoleShape ; 11 | sio:SIO_000300 xsd:string 12 | } 13 | 14 | :personShape IRI { 15 | a [sio:SIO_000498] ; 16 | rdfs:label xsd:string? ; 17 | sio:SIO_000228 @:disabilityRoleShape 18 | } 19 | 20 | :disabilityRoleShape IRI { 21 | a [obo:OBI_0000093] ; 22 | a [sio:SIO_000016] ; 23 | rdfs:label xsd:string? ; 24 | sio:SIO_000356 @:disabilityProcessShape 25 | } 26 | 27 | :disabilityProcessShape IRI { 28 | a [sio:SIO_000006] ; 29 | a [obo:NCIT_C20993] ; 30 | a IRI /^http:\/\/purl.obolibrary.org\/obo\// ; 31 | rdfs:label xsd:string? ; 32 | sio:SIO_000680 @:disabilityDateShape ; 33 | sio:SIO_000681 @:disabilityDateShape ; 34 | sio:SIO_000230 @:questionInputShape ; 35 | sio:SIO_000229 @:testOutputShape 36 | } 37 | 38 | :testOutputShape IRI { 39 | a [sio:SIO_000015] ; 40 | rdfs:label xsd:string? ; 41 | sio:SIO_000300 xsd:string 42 | } 43 | 44 | :questionInputShape IRI { 45 | a [sio:SIO_000015] ; 46 | a [obo:NCIT_C17048] ; 47 | rdfs:label xsd:string? 48 | } 49 | 50 | :disabilityDateShape IRI { 51 | a [sio:SIO_000031 sio:SIO_000032] ; 52 | rdfs:label xsd:string? ; 53 | sio:SIO_000300 xsd:date 54 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/diseaseHistoryShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000020 @:symptomOnsetRoleShape ; 11 | sio:SIO_000020 @:diagnosisDateRoleShape; 12 | sio:SIO_000300 xsd:string 13 | } 14 | 15 | :personShape IRI { 16 | a [sio:SIO_000498] ; 17 | rdfs:label xsd:string? ; 18 | sio:SIO_000228 @:symptomOnsetRoleShape ; 19 | sio:SIO_000008 @:symptomOnsetAttributeShape ; 20 | sio:SIO_000228 @:diagnosisDateRoleShape ; 21 | sio:SIO_000008 @:diagnosisDateAttributeShape 22 | } 23 | 24 | :symptomOnsetRoleShape IRI { 25 | a [obo:OBI_0000093] ; 26 | a [sio:SIO_000016] ; 27 | rdfs:label xsd:string? ; 28 | sio:SIO_000356 @:symptomOnsetProcessShape 29 | } 30 | 31 | :symptomOnsetProcessShape IRI { 32 | a [sio:SIO_000006] ; 33 | a [sio:SIO_001052] ; 34 | rdfs:label xsd:string? ; 35 | sio:SIO_000229 @:symptomOnsetOutputShape 36 | } 37 | 38 | :symptomOnsetOutputShape IRI { 39 | a [sio:SIO_000015] ; 40 | a [obo:HP_0410280 obo:HP_0003577 obo:HP_0030674 obo:HP_0003623 obo:HP_0003577 obo:NCIT_C124294 obo:NCIT_C25164] ; 41 | rdfs:label xsd:string? ; 42 | sio:SIO_000300 xsd:date? ; 43 | sio:SIO_000628 @:symptomOnsetAttributeShape 44 | } 45 | 46 | :symptomOnsetAttributeShape IRI { 47 | a [sio:SIO_000614] ; 48 | a [obo:NCIT_C25279] ; 49 | rdfs:label xsd:string? 50 | } 51 | 52 | :diagnosisDateRoleShape IRI { 53 | a [obo:OBI_0000093] ; 54 | a [sio:SIO_000016] ; 55 | rdfs:label xsd:string? ; 56 | sio:SIO_000356 @:diagnosisDateProcessShape 57 | } 58 | 59 | :diagnosisDateProcessShape IRI { 60 | a [sio:SIO_000006] ; 61 | a [sio:SIO_001052] ; 62 | rdfs:label xsd:string? ; 63 | sio:SIO_000229 @:diagnosisDateOutputShape 64 | } 65 | 66 | :diagnosisDateOutputShape IRI { 67 | a [sio:SIO_000015] ; 68 | a [obo:NCIT_C81318 obo:NCIT_C81317 obo:NCIT_C124294 obo:NCIT_C25164] ; 69 | rdfs:label xsd:string? ; 70 | sio:SIO_000300 xsd:date? ; 71 | sio:SIO_000628 @:diagnosisDateAttributeShape 72 | } 73 | 74 | :diagnosisDateAttributeShape IRI { 75 | a [sio:SIO_000614] ; 76 | a [obo:NCIT_C156420] ; 77 | rdfs:label xsd:string? 78 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/drugTreatment.shex: -------------------------------------------------------------------------------- 1 | PREFIX rdfs: 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX : 6 | 7 | :idShape IRI { 8 | sio:SIO_000020 @:treatmentRoleShape ; 9 | a [sio:SIO_000115] ; 10 | sio:SIO_000300 xsd:string 11 | } 12 | 13 | :personShape IRI { 14 | sio:SIO_000228 @:treatmentRoleShape ; 15 | a [sio:SIO_000498] 16 | } 17 | 18 | :treatmentRoleShape IRI { 19 | sio:SIO_000356 @:drugIntakeProcessShape ; 20 | sio:SIO_000356 @:drugPrescriptionProcessShape ; 21 | a [sio:SIO_000016] ; 22 | a [obo:OBI_0000093] ; 23 | rdfs:label xsd:string? 24 | } 25 | 26 | :drugIntakeProcessShape IRI { 27 | sio:CHEMINF_000047 @:prescriptionOutputShape ; 28 | sio:SIO_000680 @:treatmentEndStartdateShape ; 29 | sio:SIO_000681 @:treatmentEndStartdateShape ; 30 | sio:SIO_000230 @:administrationInputShape ; 31 | sio:SIO_000139 @:drugShape ; 32 | a [obo:NCIT_C25538] ; 33 | rdfs:label xsd:string? 34 | } 35 | 36 | :drugPrescriptionProcessShape IRI { 37 | sio:SIO_000229 @:prescriptionOutputShape ; 38 | a [obo:NCIT_C111077] ; 39 | rdfs:label xsd:string? 40 | } 41 | 42 | :prescriptionOutputShape IRI { 43 | sio:SIO_000628 @:drugShape ; 44 | sio:SIO_000628 @:doseShape ; 45 | a [sio:SIO_000015] ; 46 | a [obo:NCIT_C28180] ; 47 | rdfs:label xsd:string? ; 48 | rdfs:comment xsd:string 49 | } 50 | 51 | :doseShape IRI { 52 | sio:SIO_000221 @:unitShape ; 53 | sio:SIO_000900 @:frequencyShape ; 54 | a [obo:NCIT_C25488] ; 55 | rdfs:label xsd:string? 56 | } 57 | 58 | :medAtcUriShape IRI /^https:\/\/www.whocc.no\/atc_ddd_index\/?code=/ { 59 | sio:SIO_000313 @:drugShape ; 60 | a [obo:NCIT_C177929] ; 61 | a IRI /^http:\/\/purl.obolibrary.org\/obo\// ; 62 | rdfs:label xsd:string? 63 | } 64 | 65 | :treatmentEndStartdateShape IRI { 66 | a [sio:SIO_000031 sio:SIO_000032] ; 67 | rdfs:label xsd:string? ; 68 | sio:SIO_000300 xsd:date 69 | } 70 | 71 | :administrationInputShape IRI { 72 | a [sio:SIO_000015] ; 73 | a IRI /^http:\/\/purl.obolibrary.org\/obo\// ; 74 | rdfs:label xsd:string? 75 | } 76 | 77 | :unitShape IRI { 78 | a IRI ; 79 | rdfs:label xsd:string? 80 | } 81 | 82 | :drugShape IRI { 83 | a [sio:SIO_010038] ; 84 | rdfs:label xsd:string? ; 85 | sio:SIO_000300 xsd:float 86 | } 87 | 88 | :frequencyShape IRI { 89 | a IRI ; 90 | rdfs:label xsd:string? ; 91 | sio:SIO_000300 xsd:integer 92 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/geneticDiagnosisShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | PREFIX edam: 7 | 8 | :identifierShape IRI { 9 | a [sio:SIO_000115] ; 10 | rdfs:label xsd:string? ; 11 | sio:SIO_000020 @:geneticRoleShape ; 12 | sio:SIO_000300 xsd:string 13 | } 14 | 15 | :personShape IRI { 16 | a [sio:SIO_000498] ; 17 | rdfs:label xsd:string? ; 18 | sio:SIO_000228 @:geneticRoleShape ; 19 | sio:SIO_000008 @:hgvsAttributeShape ; 20 | sio:SIO_000008 @:omimAttributeShape ; 21 | sio:SIO_000008 @:hgncAttributeShape 22 | } 23 | 24 | :geneticRoleShape IRI { 25 | a [obo:OBI_0000093] ; 26 | a [sio:SIO_000016] ; 27 | rdfs:label xsd:string? ; 28 | sio:SIO_000356 @:hgvsProcessShape ; 29 | sio:SIO_000356 @:omimProcessShape ; 30 | sio:SIO_000356 @:hgncProcessShape 31 | } 32 | 33 | :hgvsProcessShape IRI { 34 | a [sio:SIO_000006] ; 35 | a [obo:NCIT_C15709] ; 36 | rdfs:label xsd:string? ; 37 | sio:SIO_000229 @:hgvsOutputShape 38 | } 39 | 40 | :hgvsOutputShape IRI { 41 | a [sio:SIO_000015] ; 42 | a [sio:SIO_001388] ; 43 | rdfs:label xsd:string? ; 44 | sio:SIO_000300 xsd:string ; 45 | sio:SIO_000628 @:hgvsAttributeShape 46 | } 47 | 48 | :hgvsAttributeShape IRI { 49 | a [sio:SIO_000614] ; 50 | a [obo:NCIT_C171178] ; 51 | a [sio:SIO_000015] ; 52 | rdfs:label xsd:string? 53 | } 54 | 55 | :omimProcessShape IRI { 56 | a [sio:SIO_000006] ; 57 | a [obo:NCIT_C15709] ; 58 | rdfs:label xsd:string? ; 59 | sio:SIO_000229 @:omimOutputShape 60 | } 61 | 62 | :omimOutputShape IRI { 63 | a [sio:SIO_000015] ; 64 | a [sio:SIO_001381] ; 65 | rdfs:label xsd:string? ; 66 | sio:SIO_000300 xsd:string ; 67 | sio:SIO_000628 @:omimAttributeShape 68 | } 69 | 70 | :omimAttributeShape IRI /^https:\/\/www.omim.org\/entry\// { 71 | a [sio:SIO_000614] ; 72 | a [edam:data_1153] ; 73 | a [sio:SIO_000015] ; 74 | rdfs:label xsd:string? 75 | } 76 | 77 | :hgncProcessShape IRI { 78 | a [sio:SIO_000006] ; 79 | a [obo:NCIT_C15709] ; 80 | rdfs:label xsd:string? ; 81 | sio:SIO_000229 @:hgncOutputShape 82 | } 83 | 84 | :hgncOutputShape IRI { 85 | a [sio:SIO_000015] ; 86 | a [sio:SIO_001381] ; 87 | rdfs:label xsd:string? ; 88 | sio:SIO_000300 xsd:string ; 89 | sio:SIO_000628 @:hgncAttributeShape 90 | } 91 | 92 | :hgncAttributeShape IRI /^https:\/\/identifiers.org\// { 93 | a [sio:SIO_000614] ; 94 | a [edam:data_2298] ; 95 | a [sio:SIO_000015] ; 96 | rdfs:label xsd:string? 97 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/patientConsentShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000020 @:consentRoleShape ; 11 | sio:SIO_000300 xsd:string 12 | } 13 | 14 | :personShape IRI { 15 | a [sio:SIO_000498] ; 16 | rdfs:label xsd:string? ; 17 | sio:SIO_000228 @:consentRoleShape ; 18 | sio:SIO_000008 @:consentAttributeShape 19 | } 20 | 21 | :consentRoleShape IRI { 22 | a [obo:OBI_0000093] ; 23 | a [sio:SIO_000016] ; 24 | rdfs:label xsd:string? ; 25 | sio:SIO_000356 @:consentProcessShape 26 | } 27 | 28 | :consentProcessShape IRI { 29 | a [obo:OBI_0000810] ; 30 | a [sio:SIO_000006] ; 31 | rdfs:label xsd:string? ; 32 | sio:SIO_000680 @:consentDateShape ; 33 | sio:SIO_000681 @:consentDateShape ; 34 | sio:SIO_000229 @:patientconsentOutputShape ; 35 | sio:SIO_000230 @:consentInputShape 36 | } 37 | 38 | :patientconsentOutputShape IRI { 39 | a [sio:SIO_000015] ; 40 | rdfs:label xsd:string? ; 41 | sio:SIO_000300 xsd:string ; 42 | sio:SIO_000628 @:consentAttributeShape 43 | } 44 | 45 | :consentInputShape IRI { 46 | a [sio:SIO_000015] ; 47 | a [obo:ICO_0000001] ; 48 | rdfs:label xsd:string? ; 49 | sio:SIO_000300 xsd:string 50 | } 51 | 52 | :consentAttributeShape IRI { 53 | a [sio:SIO_000614] ; 54 | a IRI ; 55 | rdfs:label xsd:string? ; 56 | } 57 | 58 | :consentDateShape IRI { 59 | a [sio:SIO_000031 sio:SIO_000032] ; 60 | rdfs:label xsd:string? ; 61 | sio:SIO_000300 xsd:date 62 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/patientStatusShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX rdfs: 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX : 6 | 7 | :idShape IRI { 8 | sio:SIO_000020 @:statusRoleShape ; 9 | a [sio:SIO_000115] ; 10 | sio:SIO_000300 xsd:string 11 | } 12 | 13 | :personShape IRI { 14 | sio:SIO_000228 @:statusRoleShape ; 15 | sio:SIO_000008 @:statusAttributeShape ; 16 | sio:SIO_000008 @:deathInformationAttributeShape ; 17 | a [sio:SIO_000498] 18 | } 19 | 20 | :statusRoleShape IRI { 21 | sio:SIO_000356 @:statusProcessShape ; 22 | sio:SIO_000356 @:deathInformationProcessShape ; 23 | a [sio:SIO_000016] ; 24 | a [obo:OBI_0000093] ; 25 | rdfs:label xsd:string? 26 | } 27 | 28 | :statusProcessShape IRI { 29 | sio:SIO_000229 @:statusOutputShape ; 30 | sio:SIO_000680 @:statusStartdateShape ; 31 | sio:SIO_000681 @:statusEnddateShape ; 32 | a [sio:SIO_001052] ; 33 | a [sio:SIO_000006] ; 34 | rdfs:label xsd:string? 35 | } 36 | 37 | :statusOutputShape IRI { 38 | sio:SIO_000628 @:statusAttributeShape ; 39 | a [sio:SIO_000015] ; 40 | rdfs:label xsd:string? ; 41 | sio:SIO_000300 xsd:string 42 | } 43 | 44 | :deathInformationProcessShape IRI { 45 | sio:SIO_000229 @:deathInformationOutputShape ; 46 | a [sio:SIO_000006] ; 47 | rdfs:label xsd:string? 48 | } 49 | 50 | :deathInformationOutputShape IRI { 51 | sio:SIO_000628 @:deathInformationAttributeShape ; 52 | a [sio:SIO_000015] ; 53 | rdfs:label xsd:string? ; 54 | sio:SIO_000300 xsd:date 55 | } 56 | 57 | :statusAttributeShape IRI { 58 | a [sio:SIO_000614] ; 59 | a [obo:NCIT_C166244] ; 60 | a [sio:SIO_010059 sio:SIO_010058 obo:NCIT_C70740 obo:NCIT_C124784] ; 61 | rdfs:label xsd:string? 62 | } 63 | 64 | :statusStartdateShape IRI { 65 | a [sio:SIO_000031] ; 66 | rdfs:label xsd:string? ; 67 | sio:SIO_000300 xsd:date 68 | } 69 | 70 | :statusEnddateShape IRI { 71 | a [sio:SIO_000032] ; 72 | rdfs:label xsd:string? ; 73 | sio:SIO_000300 xsd:date 74 | } 75 | 76 | :deathInformationAttributeShape IRI { 77 | a [sio:SIO_000614] ; 78 | a [obo:NCIT_C70810] ; 79 | rdfs:label xsd:string? 80 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/personalInformationShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115]; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000020 @:birthdateRoleShape ; 11 | sio:SIO_000020 @:sexRoleShape ; 12 | sio:SIO_000300 xsd:string 13 | } 14 | 15 | :personShape IRI { 16 | a [sio:SIO_000498] ; 17 | rdfs:label xsd:string? ; 18 | sio:SIO_000228 @:birthdateRoleShape ; 19 | sio:SIO_000008 @:birthdateAttributeShape ; 20 | sio:SIO_000228 @:sexRoleShape ; 21 | sio:SIO_000008 @:sexAttributeShape 22 | } 23 | 24 | :birthdateRoleShape IRI { 25 | a [obo:OBI_0000093] ; 26 | a [sio:SIO_000016] ; 27 | rdfs:label xsd:string? ; 28 | sio:SIO_000356 @:birthdateProcessShape 29 | } 30 | 31 | :birthdateProcessShape IRI { 32 | a [sio:SIO_000006] ; 33 | rdfs:label xsd:string? ; 34 | sio:SIO_000229 @:birthdateOutputShape 35 | } 36 | 37 | :birthdateOutputShape IRI { 38 | a [sio:SIO_000015] ; 39 | rdfs:label xsd:string? ; 40 | sio:SIO_000300 xsd:date ; 41 | sio:SIO_000628 @:birthdateAttributeShape 42 | } 43 | 44 | :birthdateAttributeShape IRI { 45 | a [sio:SIO_000614] ; 46 | a [obo:NCIT_C68615] ; 47 | rdfs:label xsd:string? 48 | } 49 | 50 | :sexRoleShape IRI { 51 | a [obo:OBI_0000093] ; 52 | a [sio:SIO_000016] ; 53 | rdfs:label xsd:string? ; 54 | sio:SIO_000356 @:sexProcessShape 55 | } 56 | 57 | :sexProcessShape IRI { 58 | a [sio:SIO_000006] ; 59 | rdfs:label xsd:string? ; 60 | sio:SIO_000229 @:sexOutputShape 61 | } 62 | 63 | :sexOutputShape IRI { 64 | a [sio:SIO_000015] ; 65 | rdfs:label xsd:string? ; 66 | sio:SIO_000300 xsd:string ; 67 | sio:SIO_000628 @:sexAttributeShape 68 | } 69 | 70 | :sexAttributeShape IRI { 71 | a [sio:SIO_000614] ; 72 | a [obo:NCIT_C28421] ; 73 | a [obo:NCIT_C16576 obo:NCIT_C20197 obo:NCIT_C124294 obo:NCIT_C17998] ; 74 | rdfs:label xsd:string? 75 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/phenotypingShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :identifierShape IRI { 8 | a [sio:SIO_000115] ; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000020 @:phenotypeRoleShape ; 11 | sio:SIO_000300 xsd:string 12 | } 13 | 14 | :personShape IRI { 15 | a [sio:SIO_000498] ; 16 | rdfs:label xsd:string? ; 17 | sio:SIO_000228 @:phenotypeRoleShape ; 18 | sio:SIO_000008 @:phenotypeAttributeShape 19 | } 20 | 21 | :phenotypeRoleShape IRI { 22 | a [obo:OBI_0000093] ; 23 | a [sio:SIO_000016] ; 24 | rdfs:label xsd:string? ; 25 | sio:SIO_000356 @:phenotypeProcessShape 26 | } 27 | 28 | :phenotypeProcessShape IRI { 29 | a [sio:SIO_000006] ; 30 | a [obo:OBI_0001546] ; 31 | a [obo:NCIT_C16205] ; 32 | a [obo:NCIT_C18020] ; 33 | rdfs:label xsd:string? ; 34 | sio:SIO_000680 @:phenotypeDateShape ; 35 | sio:SIO_000681 @:phenotypeDateShape ; 36 | sio:SIO_000229 @:phenotypeOutputShape 37 | } 38 | 39 | :phenotypeOutputShape IRI { 40 | a [sio:SIO_000015] ; 41 | a [obo:NCIT_C102741] ; 42 | rdfs:label xsd:string? ; 43 | sio:SIO_000628 @:phenotypeAttributeShape 44 | } 45 | 46 | :phenotypeAttributeShape IRI { 47 | a [sio:SIO_000614] ; 48 | a [sio:SIO_010056] ; 49 | a IRI /^http:\/\/purl.obolibrary.org\/obo\/HP_/ ; 50 | rdfs:label xsd:string? 51 | } 52 | 53 | :phenotypeDateShape IRI { 54 | a [sio:SIO_000031 sio:SIO_000032] ; 55 | rdfs:label xsd:string? ; 56 | sio:SIO_000300 xsd:date 57 | } -------------------------------------------------------------------------------- /DEPRECATED/shex/pseudonymShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX : 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX rdfs: 6 | 7 | :personShape IRI { 8 | a [sio:SIO_000498] ; 9 | rdfs:label xsd:string? ; 10 | sio:SIO_000228 @:personRoleShape 11 | } 12 | 13 | :personRoleShape IRI { 14 | rdfs:label xsd:string? ; 15 | a [obo:OBI_0000093] 16 | } 17 | 18 | :identifierShape IRI { 19 | a [sio:SIO_000115] ; 20 | rdfs:label xsd:string? ; 21 | sio:SIO_000020 @:personRoleShape ; 22 | sio:SIO_000300 xsd:string 23 | } 24 | -------------------------------------------------------------------------------- /DEPRECATED/shex/undiagnosedShape.shex: -------------------------------------------------------------------------------- 1 | PREFIX rdfs: 2 | PREFIX obo: 3 | PREFIX sio: 4 | PREFIX xsd: 5 | PREFIX : 6 | 7 | :idShape IRI { 8 | sio:SIO_000020 @:undiagnosedRoleShape ; 9 | a [sio:SIO_000115] ; 10 | sio:SIO_000300 xsd:string ; 11 | rdfs:label xsd:string? 12 | } 13 | 14 | :personShape IRI { 15 | sio:SIO_000228 @:undiagnosedRoleShape ; 16 | sio:SIO_000008 @:genotypeAttributeShape ; 17 | sio:SIO_000008 @:phenotypeAttributeShape ; 18 | sio:SIO_000008 @:undiagnosedAttributeShape ; 19 | a [sio:SIO_000498] ; 20 | rdfs:label xsd:string? 21 | } 22 | 23 | :undiagnosedRoleShape IRI { 24 | sio:SIO_000356 @:undiagnosedProcessShape ; 25 | a [obo:OBI_0000093] ; 26 | a [sio:SIO_000016] ; 27 | rdfs:label xsd:string? 28 | } 29 | 30 | :undiagnosedProcessShape IRI { 31 | sio:SIO_000680 @:undiagnosedEndStartdateShape ; 32 | sio:SIO_000681 @:undiagnosedEndStartdateShape ; 33 | sio:SIO_000229 @:undiagnosedOutputShape ; 34 | sio:SIO_000230 @:genotypeInputShape ; 35 | sio:SIO_000230 @:phenotypeInputShape ; 36 | a [sio:SIO_001001] ; 37 | a [sio:SIO_000006] ; 38 | rdfs:label xsd:string? 39 | } 40 | 41 | :undiagnosedOutputShape IRI { 42 | sio:SIO_000628 @:undiagnosedAttributeShape ; 43 | a [sio:SIO_000015] ; 44 | rdfs:label xsd:string? ; 45 | sio:SIO_000300 xsd:string 46 | } 47 | 48 | :phenotypeInputShape IRI { 49 | sio:SIO_000628 @:phenotypeAttributeShape ; 50 | a [obo:NCIT_C102741] ; 51 | a [sio:SIO_000015] ; 52 | rdfs:label xsd:string? ; 53 | sio:SIO_000300 xsd:string 54 | } 55 | 56 | :genotypeInputShape IRI { 57 | sio:SIO_000628 @:genotypeAttributeShape ; 58 | a [sio:SIO_001388] ; 59 | a [sio:SIO_000015] ; 60 | rdfs:label xsd:string? ; 61 | sio:SIO_000300 xsd:string 62 | } 63 | 64 | :undiagnosedEndStartdateShape IRI { 65 | a [sio:SIO_000031 sio:SIO_000032] ; 66 | rdfs:label xsd:string? ; 67 | sio:SIO_000300 xsd:date 68 | } 69 | 70 | :undiagnosedAttributeShape IRI { 71 | a [obo:NCIT_C113725] ; 72 | a [sio:SIO_000614] ; 73 | rdfs:label xsd:string? 74 | } 75 | 76 | :phenotypeAttributeShape IRI { 77 | a [sio:SIO_000614] ; 78 | a IRI /^http:\/\/purl.obolibrary.org\/obo\/HP_/ ; 79 | rdfs:label xsd:string? 80 | } 81 | 82 | :genotypeAttributeShape IRI /^https:\/\/identifiers.org\// { 83 | a [obo:NCIT_C171178] ; 84 | a [sio:SIO_000614] ; 85 | rdfs:label xsd:string? 86 | } -------------------------------------------------------------------------------- /Images/Biobank.png: -------------------------------------------------------------------------------- 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Affirmer understands and acknowledges that Creative Commons is not a 112 | party to this document and has no duty or obligation with respect to this 113 | CC0 or use of the Work. 114 | 115 | For more information, please see 116 | 117 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | # Semantic data model of the set of common data elements for rare disease registration 3 | ![GitHub](https://img.shields.io/github/license/ejp-rd-vp/CDE-semantic-model) 4 | ![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/ejp-rd-vp/CDE-semantic-model) 5 | 6 | > To make rare disease registry data Interoperable (the I in FAIR). 7 | 8 | In this work we present a semantic data model for [the set of common data elements for rare diseases registration](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf) recommended by the European commission Joint Research Centre. We proposed a semantic data model for these data elements. 9 | 10 | 11 | # *IMPORTANT ANNOUNCEMENT!* 12 | This Github repository is currently deprecated, The new stable version of this semantic model is maintained as Clinical And Registry Entries (CARE) Semantic Model. This model is maintained at this different [Github registry](https://github.com/ejp-rd-vp/CARE-Semantic-Model) 13 | 14 | 15 | ## CDE modules overview 16 | 17 | The figure below gives an overview of upper level concepts and properties used in our cde model. 18 | 19 |

20 | 21 |

Figure 1: Common data element overall semantic model

22 | 23 |

24 |
25 | 26 |

27 | 28 |

Figure 2: Observation context metadata layer

29 | 30 |

31 |
32 | 33 | You can browse different CDE modules by visiting the links below. 34 | 35 | Patient personal information: 36 | * [Birthyear](docs/Birthyear.md) - describes patient year of birth 37 | * [Birthdate](docs/Birthdate.md) - describes patient date of birth 38 | * [Sex](docs/Sex.md) - describes patient sex at birth 39 | * [Body measurement](docs/Body_measurement.md) - describes patient physical measurement of the body. 40 | 41 | Participation status: 42 | * [Status](docs/Status.md) - describes patient alive or dead status 43 | * [Deathdate](docs/Deathdate.md) - describes patient date of death 44 | 45 | Medical history: 46 | * [First confirmed visit](docs/First_visit.md) - describes patient first contact with specialized center 47 | * [Symptoms onset](docs/Symptoms_onset.md) - describes patient signs/symptoms onset 48 | 49 | Conditions and medical findings: 50 | * [Diagnosis](docs/Diagnosis.md) - describes patient disease diagnosis 51 | * [Symptoms and phenotype assessment](docs/Symptoms.md) - describes patient date of signs/symptoms and its onset 52 | * [Genetic information](docs/Genotype.md) - describes genetic diagnosis retained by the specialized center 53 | * [Disability](docs/Disability.md) - describes patient disability score 54 | * [Laboratory Measurement](docs/Laboratory.md) - describes patient laboratory measurements. 55 | * [Imaging](docs/Imaging.md) - capture any patient medical imaging data. 56 | 57 | Research availability and consent: 58 | * [Biobank](docs/Biobank.md) - describes availability of subject's samples in a biobank 59 | * [Consent](docs/Consent.md) - describes consent given by a subject 60 | 61 | Treatment-related interventions: 62 | * [Medications](docs/Medication.md) - describes patient medications based on a prescription. 63 | * [Treatment/Therapy](docs/Intervention.md) - describes any component presented in treatment and therapy procedures. 64 | 65 | Clinical trials: 66 | * [Clinical Trials](docs/Clinical_trials.md) - describes patient participation in clinical trials. 67 | 68 | ## Moving to the new version 2.0.0 69 | 70 | While considerable time was spent on the first generation of CDE models, the final published set remained inconsistent in a number of ways: 71 | 72 | 1) Nodes had different numbers of ontological annotations, with no justification 73 | 2) The CDE models adopted the high-level CDEs defined by the RD Platform, which were often aggregations of individual data elements. As a consequence: 74 | 75 | a) Registries did not always have all of the individual subcomponents to fulfil the model 76 | 77 | b) It was unclear what to do when a model couldn't be filled 78 | 79 | c) This led to data loss, when those data elements were not FAIR-transformed 80 | 81 | 3) Date/time were sometimes included in the model, and sometimes not 82 | 4) The CSV files all had a distinct structure, meaning each one needed fairly specialized code to generate. For more information about how to implement our CDE semantic model, click [here](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations). 83 | 5) There was no easy way to aggregate various observations together that might be related (e.g. the observations/interventions made during the course of a COVID infection) 84 | 85 | ## Features of the new version: 86 | 87 | 1) The overall model is identical to the original Core CDE model ([Figure 1](/Images/0.Unified_CDE_model.png)). 88 | 2) Only one data element is modeled at a time; if you do not have that element, you do not use that model 89 | 3) Every element of the model has an "upper ontology" type (e.g. "process") and a domain-specific type (e.g. "blood pressure measurement process"). Exactly two types per node. 90 | 4) Date/Time is now considered metadata of the data model. Even in the case where date/time are the core observation of the model (e.g. date of symptom onset) Thus, all models are identical in structure and metadata ([Figure 2](/Images/context_metadata.png)). 91 | 5) This metadata takes the form of a "context" node (i.e. an RDF Quad, rather than an RDF Triple), which is annotated with various things. In addition, the context node becomes "part of" a patient's overall timeline, which itself is modeled in RDF and creates a larger grouping of all observations about a patient. 92 | 6) In addition to being "part of" a patient's timeline, context nodes _can be_ grouped into other arbitrary collections reflecting other kinds of groupings (like the COVID-19 infection scenario described above). Its not mandatory to implement this in your model - it is merely made possible by this new model, which was not the case with the Version 1 models. 93 | 94 | 95 | ## Cite us 96 | To cite this model please use this publication [Semantic modeling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data](https://doi.org/10.1186/s13326-022-00264-6). 97 | 98 | ## Acknowledgement 99 | This work was done in the [European Joint Programme on Rare Diseases (EJP RD)](https://www.ejprarediseases.org/) project which has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement N°82557. 100 | ![EU logo](https://github.com/ejp-rd-vp/smart-guidance/blob/main/images/eu-flag.png?raw=true) 101 | 102 | 103 | -------------------------------------------------------------------------------- /docs/Biobank.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements related to biological samples stored in a biobank. It specifically covers the CDE elements 7.3.'Biological Sample' and 7.4.'Link to a biobank'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | #### RDF representation: 11 | 12 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Biobank.nt) 13 | 14 | #### CDE implementation: 15 | 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#biobank): 17 | -------------------------------------------------------------------------------- /docs/Birthdate.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements in the CDE 'Personal information' group. It specifically covers the CDE elements 2.1.'Date of Birth'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 | 5 |

6 | 7 | 8 | 9 |

10 | 11 | 12 | 13 | #### RDF representation: 14 | 15 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Birthdate.nt) 16 | 17 | #### CDE implementation: 18 | 19 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#birthdate): -------------------------------------------------------------------------------- /docs/Birthyear.md: -------------------------------------------------------------------------------- 1 | # Birthyear 2 |

3 | 4 | 5 | 6 |

-------------------------------------------------------------------------------- /docs/Body_measurement.md: -------------------------------------------------------------------------------- 1 | # Body measurement 2 | 3 |

4 | 5 | 6 | 7 |

8 | 9 | #### RDF representation: 10 | 11 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Body_measurement.nt) 12 | 13 | #### CDE implementation: 14 | 15 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#body-measurement): -------------------------------------------------------------------------------- /docs/Clinical_trials.md: -------------------------------------------------------------------------------- 1 | # Clinical trials 2 |

3 | 4 | 5 | 6 |

7 | 8 | 9 | #### CDE implementation: 10 | 11 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#clinical-trials): -------------------------------------------------------------------------------- /docs/Consent.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements related to consent from the group 'Research'. It specifically covers the CDE elements 7.1.'Agreement to be contacted for research purposes' and 7.2.'Consent to the reuse of data'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | 11 | #### RDF representation: 12 | 13 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Consent.nt) 14 | 15 | #### CDE implementation: 16 | 17 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#consent-for-being-contacted): 18 | -------------------------------------------------------------------------------- /docs/Deathdate.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements in the module 'Patient's status'. It specifically covers the CDE elements 3.1.'Patient's status'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | 11 | #### RDF representation: 12 | 13 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Deathdate.nt) 14 | 15 | #### CDE implementation: 16 | 17 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#deathdate): -------------------------------------------------------------------------------- /docs/Diagnosis.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements related to the diagnosis combining elements from the group 'Diagnosis'. It specifically covers the CDE elements 6.1.'Diagnosis of the rare disease'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf)." 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | #### RDF representation: 11 | 12 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Diagnosis.nt) 13 | 14 | #### CDE implementation: 15 | 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#diagnosis): -------------------------------------------------------------------------------- /docs/Disability.md: -------------------------------------------------------------------------------- 1 | This module describes the data element 8.1'Classification of functioning/disability' which is part of the group 'Disability'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 2 | 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | #### RDF representation: 11 | 12 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Disability.nt) 13 | 14 | #### CDE implementation: 15 | 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#disability): 17 | -------------------------------------------------------------------------------- /docs/First_visit.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements related to the 'Care pathway'. It specifically covers the CDE element 4.1.'First contact with specialised centre'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | #### RDF representation: 11 | 12 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/First_visit.nt) 13 | 14 | #### CDE implementation: 15 | 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#first-confirmed-visit): -------------------------------------------------------------------------------- /docs/Genotype.md: -------------------------------------------------------------------------------- 1 | This module describes the data element 6.2'Genetic Diagnosis' which is part of the group 'Diagnosis'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | 11 | #### RDF representation: 12 | 13 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Genotype.nt) 14 | 15 | #### CDE implementation: 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#genetic-information): -------------------------------------------------------------------------------- /docs/Imaging.md: -------------------------------------------------------------------------------- 1 | # Medical Imaging 2 |

3 | 4 | 5 | 6 |

7 | 8 | #### RDF representation: 9 | 10 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Imaging.nt) 11 | 12 | #### CDE implementation: 13 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#imaging): -------------------------------------------------------------------------------- /docs/Intervention.md: -------------------------------------------------------------------------------- 1 | # Clinical Treatment/Therapies 2 |

3 | 4 | 5 | 6 |

7 | 8 | #### RDF representation: 9 | 10 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Intervention.nt) 11 | 12 | #### CDE implementation: 13 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#intervention-surgery): -------------------------------------------------------------------------------- /docs/Laboratory.md: -------------------------------------------------------------------------------- 1 | # Laboratory measurement 2 | 3 |

4 | 5 | 6 | 7 |

8 | 9 | #### RDF representation: 10 | 11 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Lab_measurement.nt) 12 | 13 | #### CDE implementation: 14 | 15 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#laboratory-measurement): -------------------------------------------------------------------------------- /docs/Medication.md: -------------------------------------------------------------------------------- 1 | # Medications 2 | 3 |

4 | 5 | 6 | 7 |

8 | 9 | #### RDF representation: 10 | 11 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Medications.nt) 12 | 13 | #### CDE implementation: 14 | 15 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#medications-and-therapies): -------------------------------------------------------------------------------- /docs/Sex.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements in the CDE 'Personal information' group. It specifically covers the CDE elements 2.2.'Sex'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | 11 | #### RDF representation: 12 | 13 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Sex.nt) 14 | 15 | #### CDE implementation: 16 | 17 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#sex): -------------------------------------------------------------------------------- /docs/Status.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements in the module 'Patient's status'. It specifically covers the CDE elements 3.2.'Date of death'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 | 5 |

6 | 7 | 8 | 9 |

10 | 11 | #### RDF representation: 12 | 13 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Status.nt) 14 | 15 | #### CDE implementation: 16 | 17 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#status): -------------------------------------------------------------------------------- /docs/Symptoms.md: -------------------------------------------------------------------------------- 1 | This module describes the data element 6.2 'Phenotype' in undiagnosed case which is part of the group 'Diagnosis'. These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 2 | 3 |

4 | 5 | 6 | 7 |

8 | 9 | #### RDF representation: 10 | 11 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Symptoms.nt) 12 | 13 | #### CDE implementation: 14 | 15 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#symptoms-or-signs): -------------------------------------------------------------------------------- /docs/Symptoms_onset.md: -------------------------------------------------------------------------------- 1 | This module describes the data elements related to the diagnosis combining elements from the groups 'Disease history'. It specifically covers the CDE elements 5.1.'Age at onset'. 2 | These elements, defined by the JRC, can be found on the EU RD Platform at [this link](https://eu-rd-platform.jrc.ec.europa.eu/sites/default/files/CDS/EU_RD_Platform_CDS_Final.pdf). 3 | 4 |

5 | 6 | 7 | 8 |

9 | 10 | #### RDF representation: 11 | 12 | You can check an exemplar RDF-based representation for this Common data Element [here](../exemplar_rdf/Symptoms_onset.nt) 13 | 14 | #### CDE implementation: 15 | 16 | If you're interested in implmenting this model on data, you can information around data requirements at our [Github implementation repo](https://github.com/ejp-rd-vp/CDE-semantic-model-implementations/blob/master/CDE_version_2.0.0/CSV_docs/glossary.md#symptoms-onset): -------------------------------------------------------------------------------- /exemplar_rdf/Body_measurement.nt: -------------------------------------------------------------------------------- 1 | "Body_measurement agent"^^ . 2 | . 3 | "Body_measurement route"^^ . 4 | . 5 | "50012001"^^ . 6 | . 7 | "Identifier"^^ . 8 | . 9 | . 10 | . 11 | . 12 | . 13 | . 14 | "Body_measurement measurement process"^^ . 15 | . 16 | . 17 | . 18 | . 19 | "50012001"^^. 20 | . 21 | . 22 | . 23 | . 24 | "Patient role"^^ . 25 | "Body_measurement enddate: 2011-03-15"^^ . 26 | . 27 | "2011-03-15"^^ . 28 | . 29 | "20230618170934156313"^^. 30 | . 31 | . 32 | . 33 | . 34 | . 35 | . 36 | "Body_measurement unit of measurement"^^ . 37 | . 38 | . 39 | . 40 | . 41 | "Person"^^ . 42 | . 43 | . 44 | "Body_measurement target"^^ . 45 | . 46 | . 47 | "29.3"^^ . 48 | . 49 | "Body_measurement measurement output"^^ . 50 | . 51 | . 52 | . 53 | "2011-03-15"^^ . 54 | . 55 | "Body_measurement startdate: 2011-03-15"^^ . 56 | . 57 | "Body_measurement frequency"^^ . 58 | . 59 | "Body_measurement input"^^ . 60 | "Body_measurement attribute"^^ . 61 | . 62 | . 63 | . 64 | -------------------------------------------------------------------------------- /exemplar_rdf/Genotype.nt: -------------------------------------------------------------------------------- 1 | . 2 | . 3 | "Identifier" . 4 | "50012001" . 5 | . 6 | . 7 | . 8 | "Person" . 9 | . 10 | . 11 | . 12 | "Patient role" . 13 | . 14 | . 15 | . 16 | . 17 | . 18 | . 19 | . 20 | . 21 | "Genetic measurement process" . 22 | . 23 | . 24 | . 25 | . 26 | . 27 | "Genetic measurement output" . 28 | "601556.0" . 29 | . 30 | "Genetic input" . 31 | . 32 | "Genetic target" . 33 | . 34 | "Genetic route" . 35 | . 36 | . 37 | "Genetic attribute" . 38 | . 39 | "Genetic unit of measurement" . 40 | . 41 | "Genetic frequency" . 42 | . 43 | "Genetic startdate: 1998-06-30" . 44 | "1998-06-30"^^ . 45 | . 46 | "Genetic enddate: 1998-06-30" . 47 | "1998-06-30"^^ . 48 | . 49 | . 50 | . 51 | . 52 | "20230627143140442450". 53 | . 54 | . 55 | . 56 | . 57 | . 58 | . 59 | . 60 | . 61 | . 62 | . 63 | "50012001". 64 | -------------------------------------------------------------------------------- /exemplar_rdf/Imaging.nt: -------------------------------------------------------------------------------- 1 | . 2 | . 3 | "Identifier" . 4 | "50012001" . 5 | . 6 | . 7 | . 8 | "Person" . 9 | . 10 | . 11 | . 12 | "Patient role" . 13 | . 14 | . 15 | . 16 | . 17 | . 18 | . 19 | . 20 | . 21 | "Imaging measurement process" . 22 | . 23 | . 24 | . 25 | . 26 | . 27 | "Imaging measurement output" . 28 | . 29 | "Imaging input" . 30 | . 31 | "Imaging target" . 32 | . 33 | "Imaging route" . 34 | . 35 | . 36 | "Imaging attribute" . 37 | . 38 | "Imaging unit of measurement" . 39 | . 40 | "Imaging frequency" . 41 | . 42 | "Imaging startdate: 2006-12-10" . 43 | "2006-12-10"^^ . 44 | . 45 | "Imaging enddate: 2006-12-10" . 46 | "2006-12-10"^^ . 47 | . 48 | . 49 | . 50 | . 51 | "20230627143140442491". 52 | . 53 | . 54 | . 55 | . 56 | . 57 | . 58 | . 59 | . 60 | . 61 | . 62 | "50012001". 63 | -------------------------------------------------------------------------------- /exemplar_rdf/Intervention.nt: -------------------------------------------------------------------------------- 1 | "Identifier"^^ . 2 | . 3 | . 4 | "50012001"^^ . 5 | "Intervention target"^^ . 6 | . 7 | . 8 | . 9 | . 10 | . 11 | "Intervention measurement output"^^ . 12 | . 13 | "Intervention input"^^ . 14 | . 15 | . 16 | . 17 | . 18 | "Intervention frequency"^^ . 19 | . 20 | . 21 | . 22 | . 23 | "20230618170934156320"^^. 24 | "Intervention agent"^^ . 25 | . 26 | . 27 | . 28 | "50012001"^^. 29 | . 30 | "1998-06-30"^^ . 31 | "Intervention enddate: 1998-06-30"^^ . 32 | "1998-06-30"^^ . 33 | "Intervention startdate: 1998-06-30"^^ . 34 | . 35 | . 36 | . 37 | . 38 | . 39 | . 40 | . 41 | . 42 | . 43 | "Intervention measurement process"^^ . 44 | "Intervention unit of measurement"^^ . 45 | . 46 | . 47 | "Intervention attribute"^^ . 48 | . 49 | . 50 | . 51 | . 52 | . 53 | "Intervention route"^^ . 54 | . 55 | . 56 | . 57 | . 58 | "Person"^^ . 59 | . 60 | . 61 | . 62 | "Patient role"^^ . 63 | --------------------------------------------------------------------------------