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Merge pull request #189 from isamplesorg/develop
some support files
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‎examples/SESAR/test1.0Valid/SESARDjango-Template.json‎

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{
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"@schema": "iSamplesSchemaCore1.0.json",
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"@id":"{{data.metadataid}}",
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"label": "{{data.label}}",
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"sample_identifier": "{{data.igsn}}",
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"description": "{{data.description}}",
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{% if data.featuretype %}
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"has_context_category": [
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{% for feat in data.featuretype %}
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{"label":"","identifier":""},
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{% endfor %}
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],
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{% endif %}
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{% if data.materials %}
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"has_material_category": [
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{% for mat in data.materials %}
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{"label":"","identifier":""},
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{% endfor %}
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],
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{% endif %}
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{% if data.objecttype %}
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"has_sample_object_type": [
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{% for obj in data.objecttype %}
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{"label":"","identifier":""},
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{% endfor %}
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],
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{% endif %}
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{% endif %}
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{% if data.keywords %}
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"keywords": [
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{% for word in data.kewords %}
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{% if word.uri%}
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{
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"keyword": "{{word.label}}",
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"keyword_uri": "{{word.uri}}",
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{% if word.uri%}
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"scheme_name": "{{word.schemename}}",
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{% endif %}
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{% if word.uri%}
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"scheme_uri": "word.schemeuri"
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}, {% endif %}
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{% else %}
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{"keyword":"{{word.label}"},
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{% endif %}
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{% endfor %}
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],
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{% endif %}
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"produced_by": {
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"label": "",
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"description": "",
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"has_feature_of_interest": "{{data.locality_type}}",
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"responsibility": [{"role":"collector","name":"{{individual_name}}"}],
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"sampling_site": {
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"description": "{{locality_detail}}",
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"label": "",
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"sample_location": {
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"elevation": "",
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"latitude": 0,
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"longitude": 0
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},
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"place_name": [""]
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}
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},
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"registrant": {"name":"{{registrant}}"},
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"last_modified_time":"2024-09-13T09:20:00-07:00",
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"sampling_purpose": ""
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}

‎examples/brainExample1.json‎

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{
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"$schema": "../src/schemas/iSamplesSchemaCore1.0.json",
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"@id": "https://isamples.org/metadata/4327q543jh",
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"@context": "https://isamples.org/metadata",
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"@type": "schema:DigitalDocument",
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"dct:conformsTo": "https://isamples.org/metadata",
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"registrant": {
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"name": "name",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "role"
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},
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"about": {
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"@id":"xxx:metadataabout/NYBB-MS1",
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"@type":"schema:Thing",
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"sample_identifier": "NYBB-MS1",
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"label": "Brain, Spinal Cord from Male adult",
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"description": "Brain and spinal cord tissue from male adult, age 65 at death, affected by multiple sclerosis",
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"alternate_identifiers": [],
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"produced_by": {
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"identifier": "identifier",
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"label": "post-mortem analysis",
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"description": "description",
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"has_feature_of_interest": "Human Body",
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"project": "Brain inventory",
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"responsibility": [
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{
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"name": "Dr. Who did the dissection",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "role"
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}
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],
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"result_time": "2020-09-24",
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"sampling_site": {
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"description": "Post mortem dissection, St. Mary's hospital, Tucson, AZ",
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"label": "Post mortem dissection, patient MYBB-MS1",
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"place_name": ["St. Mary's Hospital, Tucson, AZ"]
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},
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"authorized_by": ["appropriate documentation authorizing collection of body parts for research"]
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},
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"sampling_purpose": "pathology analysis",
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"has_context_category": [
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{
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"label": "Human Body",
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"identifier": "http://example.com/resource/humanbody/brain",
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"scheme_name": "scheme_name"
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},
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{
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"label": "Biological entity",
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"identifier": "https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity",
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"scheme_name": "iSamples Sampled Feature Type vocabulary"
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}
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],
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"has_material_category": [
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{
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"label": "Organic material",
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"identifier": "https://w3id.org/isample/vocabulary/material/organicmaterial",
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"scheme_name": "iSamples Materials Vocabulary"
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}
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],
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"has_sample_object_type": [
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{
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"label": "Organism part",
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"identifier": "https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart",
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"scheme_name": "iSamples Material Sample Object Type Vocabulary"
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},
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{
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"label": "Human brain",
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"identifier": "\t\nhttp://purl.org/sig/ont/fma/fma50801",
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"scheme_name": "Foundational Model of Anatomy"
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},
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{
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"label": "Human spinal cord",
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"identifier": "http://purl.org/sig/ont/fma/fma7647",
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"scheme_name": "Foundational Model of Anatomy"
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}
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],
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"keywords": [
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{
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"keyword": "brain",
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"keyword_uri": "keyword_uri",
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"scheme_name": "scheme_name",
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"scheme_uri": "scheme_uri"
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},
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{
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"keyword": "spinal cord"
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},
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{
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"keyword": "Multiple Sclerosis"
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}
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],
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"related_resource": [
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{
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"description": "Tissue thin section from NYBB_MS1, BA9",
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"label": "SBB1.3",
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"relationship": "Child sample",
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"target": "http://medsamples.org/research/nybbms1/sbb1.3"
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},
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{
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"description": "many other child samples...."
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}
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],
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"complies_with": ["links or descriptions of protocols for collection and use of human body parts for research"],
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"curation": {
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"access_constraints": ["access_constraints0"],
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"curation_location": "curation_location",
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"description": "How and where is this tissue material preserverd; who to contact about access to sample?",
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"label": "label",
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"responsibility": [
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{
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"name": "name",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "role"
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}
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]
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}
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}
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}

‎examples/brainSubSample1.json‎

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{
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"$schema": "../src/schemas/iSamplesSchemaCore1.0.json",
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"@id": "https://isamples.org/metadata/4327q543jh",
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"@context": "https://isamples.org/metadata",
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"@type": "schema:DigitalDocument",
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"dct:conformsTo": "https://isamples.org/metadata",
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"registrant": {
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"name": "name",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "role"
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},
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"about": {
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"@id":"xxx:metadataabout/NYBB-MS1/SBB5.1",
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"@type":"schema:Thing",
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"sample_identifier": "NYBB-MS1/SBB5.1",
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"label": "Hippocampal formation from Male adult",
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"description": "Hippocampal formation extracted from brain of male adult, age 65 at death, affected by multiple sclerosis",
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"alternate_identifiers": [],
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"produced_by": {
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"identifier": "identifier",
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"label": "label",
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"description": "Post mortem dissection",
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"has_feature_of_interest": "Human brain",
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"project": "Brain inventory",
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"responsibility": [
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{
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"name": "Dr. Who did the dissection",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "collector"
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}
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],
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"result_time": "2020-09-24",
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"sampling_site": {
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"description": "Hippocampal formation (HF), Post mortem dissection, St. Mary's hospital, Tucson, AZ",
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"label": "Hippocampal formation (HF)",
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"place_name": ["Hippocampal formation (HF)"]
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},
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"authorized_by": ["appropriate documentation authorizing collection of body parts for research"]
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},
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"sampling_purpose": "pathology analysis",
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"has_context_category": [
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{
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"label": "Human brain",
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"identifier": "\t\nhttp://purl.org/sig/ont/fma/fma50801",
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"scheme_name": "Foundational Model of Anatomy"
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},
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{
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"label": "Biological entity",
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"identifier": "https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity",
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"scheme_name": "iSamples Sampled Feature Type vocabulary"
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}
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],
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"has_material_category": [
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{
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"label": "Organic material",
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"identifier": "https://w3id.org/isample/vocabulary/material/organicmaterial",
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"scheme_name": "iSamples Materials Vocabulary"
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}
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],
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"has_sample_object_type": [
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{
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"label": "Organism part",
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"identifier": "https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart",
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"scheme_name": "iSamples Material Sample Object Type Vocabulary"
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}
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],
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"keywords": [
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{
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"keyword": "brain",
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"keyword_uri": "keyword_uri",
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"scheme_name": "scheme_name",
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"scheme_uri": "scheme_uri"
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},
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{
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"keyword": "Hippocampal formation"
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},
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{
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"keyword": "Multiple Sclerosis"
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}
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],
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"related_resource": [
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{
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"description": "Brain and spinal cord from MYBB_MS1",
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"label": "MYBB_MS1",
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"relationship": "Parent sample",
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"target": "http://medsamples.org/research/nybbms1"
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}
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],
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"complies_with": ["links or descriptions of protocols for collection and use of human body parts for research"],
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"curation": {
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"access_constraints": ["access_constraints0"],
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"curation_location": "curation_location",
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"description": "How and where is this tissue material preserverd; who to contact about access to sample?",
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"label": "label",
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"responsibility": [
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{
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"name": "name",
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"affiliation": "affiliation",
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"contact_information": "contact_information",
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"identifier": "identifier",
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"role": "role"
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}
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]
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}
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}
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}

‎schemaMapping/schema.org-iSamplesMapping-ODIS.docx‎

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