├── 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 .
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/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 .
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/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 .
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/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 .
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/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 .
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/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 .
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/DEPRECATED/example-data/turtle/pseudonym.ttl:
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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 .
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/DEPRECATED/example-data/turtle/unDiagnosis.ttl:
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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)" .
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/DEPRECATED/shex/biobank.shex:
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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 | }
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/DEPRECATED/shex/carePathwayShape.shex:
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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 | }
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/DEPRECATED/shex/diagnosisShape.shex:
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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 | }
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/DEPRECATED/shex/disability.shex:
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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 | }
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/DEPRECATED/shex/diseaseHistoryShape.shex:
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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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/Images/Birthdate.png:
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/Images/Birthyear.png:
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/Images/Body_measurement.png:
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/Images/Clinical_trials.png:
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/Images/Consent.png:
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/README.md:
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1 |
2 | # Semantic data model of the set of common data elements for rare disease registration
3 | 
4 | 
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 | 
101 |
102 |
103 |
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/docs/Biobank.md:
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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 |
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/docs/Birthdate.md:
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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):
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/docs/Birthyear.md:
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1 | # Birthyear
2 |
3 |
4 |
5 |
6 |
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/docs/Body_measurement.md:
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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):
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/docs/Clinical_trials.md:
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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):
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/docs/Consent.md:
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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 |
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/docs/Deathdate.md:
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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):
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/docs/Diagnosis.md:
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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):
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/docs/Disability.md:
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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 |
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/docs/First_visit.md:
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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):
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/docs/Genotype.md:
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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):
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/docs/Imaging.md:
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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):
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/docs/Intervention.md:
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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):
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/docs/Laboratory.md:
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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):
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/docs/Medication.md:
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1 | # Medications
2 |
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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):
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/docs/Sex.md:
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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 |
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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):
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/docs/Status.md:
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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 |
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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):
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/docs/Symptoms.md:
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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 |
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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):
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/docs/Symptoms_onset.md:
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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 |
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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):
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/exemplar_rdf/Body_measurement.nt:
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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 |