Skip to content

update temporal extent branch from main #194

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
smrgeoinfo merged 5 commits into from
Dec 11, 2025
Merged

update temporal extent branch from main #194

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
bf463c9
Merge branch 'main' of https://github.com/isamplesorg/metadata
smrgeoinfo Apr 11, 2025
466db4e
brain examples
smrgeoinfo Apr 11, 2025
bee4996
django template for creating iSamples JSON
smrgeoinfo Apr 11, 2025
1ea7cbd
ODIS mapping
smrgeoinfo Apr 11, 2025
d5c266b
Merge pull request #189 from isamplesorg/develop
smrgeoinfo Jun 5, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
69 changes: 69 additions & 0 deletions examples/SESAR/test1.0Valid/SESARDjango-Template.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
{
"@schema": "iSamplesSchemaCore1.0.json",
"@id":"{{data.metadataid}}",
"label": "{{data.label}}",
"sample_identifier": "{{data.igsn}}",
"description": "{{data.description}}",
{% if data.featuretype %}
"has_context_category": [
{% for feat in data.featuretype %}
{"label":"","identifier":""},
{% endfor %}
],
{% endif %}
{% if data.materials %}
"has_material_category": [
{% for mat in data.materials %}
{"label":"","identifier":""},
{% endfor %}
],
{% endif %}
{% if data.objecttype %}
"has_sample_object_type": [
{% for obj in data.objecttype %}
{"label":"","identifier":""},
{% endfor %}
],
{% endif %}

{% endif %}
{% if data.keywords %}
"keywords": [
{% for word in data.kewords %}
{% if word.uri%}
{
"keyword": "{{word.label}}",
"keyword_uri": "{{word.uri}}",
{% if word.uri%}
"scheme_name": "{{word.schemename}}",
{% endif %}
{% if word.uri%}
"scheme_uri": "word.schemeuri"
}, {% endif %}
{% else %}
{"keyword":"{{word.label}"},
{% endif %}
{% endfor %}
],
{% endif %}

"produced_by": {
"label": "",
"description": "",
"has_feature_of_interest": "{{data.locality_type}}",
"responsibility": [{"role":"collector","name":"{{individual_name}}"}],
"sampling_site": {
"description": "{{locality_detail}}",
"label": "",
"sample_location": {
"elevation": "",
"latitude": 0,
"longitude": 0
},
"place_name": [""]
}
},
"registrant": {"name":"{{registrant}}"},
"last_modified_time":"2024-09-13T09:20:00-07:00",
"sampling_purpose": ""
}
123 changes: 123 additions & 0 deletions examples/brainExample1.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,123 @@
{
"$schema": "../src/schemas/iSamplesSchemaCore1.0.json",
"@id": "https://isamples.org/metadata/4327q543jh",
"@context": "https://isamples.org/metadata",
"@type": "schema:DigitalDocument",
"dct:conformsTo": "https://isamples.org/metadata",
"registrant": {
"name": "name",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "role"
},
"about": {
"@id":"xxx:metadataabout/NYBB-MS1",
"@type":"schema:Thing",
"sample_identifier": "NYBB-MS1",
"label": "Brain, Spinal Cord from Male adult",
"description": "Brain and spinal cord tissue from male adult, age 65 at death, affected by multiple sclerosis",
"alternate_identifiers": [],
"produced_by": {
"identifier": "identifier",
"label": "post-mortem analysis",
"description": "description",
"has_feature_of_interest": "Human Body",
"project": "Brain inventory",
"responsibility": [
{
"name": "Dr. Who did the dissection",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "role"
}
],
"result_time": "2020-09-24",
"sampling_site": {
"description": "Post mortem dissection, St. Mary's hospital, Tucson, AZ",
"label": "Post mortem dissection, patient MYBB-MS1",
"place_name": ["St. Mary's Hospital, Tucson, AZ"]
},
"authorized_by": ["appropriate documentation authorizing collection of body parts for research"]
},
"sampling_purpose": "pathology analysis",
"has_context_category": [
{
"label": "Human Body",
"identifier": "http://example.com/resource/humanbody/brain",
"scheme_name": "scheme_name"
},
{
"label": "Biological entity",
"identifier": "https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity",
"scheme_name": "iSamples Sampled Feature Type vocabulary"
}
],
"has_material_category": [
{
"label": "Organic material",
"identifier": "https://w3id.org/isample/vocabulary/material/organicmaterial",
"scheme_name": "iSamples Materials Vocabulary"
}
],
"has_sample_object_type": [
{
"label": "Organism part",
"identifier": "https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart",
"scheme_name": "iSamples Material Sample Object Type Vocabulary"
},
{
"label": "Human brain",
"identifier": "\t\nhttp://purl.org/sig/ont/fma/fma50801",
"scheme_name": "Foundational Model of Anatomy"
},
{
"label": "Human spinal cord",
"identifier": "http://purl.org/sig/ont/fma/fma7647",
"scheme_name": "Foundational Model of Anatomy"
}
],
"keywords": [
{
"keyword": "brain",
"keyword_uri": "keyword_uri",
"scheme_name": "scheme_name",
"scheme_uri": "scheme_uri"
},
{
"keyword": "spinal cord"
},
{
"keyword": "Multiple Sclerosis"
}
],
"related_resource": [
{
"description": "Tissue thin section from NYBB_MS1, BA9",
"label": "SBB1.3",
"relationship": "Child sample",
"target": "http://medsamples.org/research/nybbms1/sbb1.3"
},
{
"description": "many other child samples...."
}
],
"complies_with": ["links or descriptions of protocols for collection and use of human body parts for research"],
"curation": {
"access_constraints": ["access_constraints0"],
"curation_location": "curation_location",
"description": "How and where is this tissue material preserverd; who to contact about access to sample?",
"label": "label",
"responsibility": [
{
"name": "name",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "role"
}
]
}
}
}
110 changes: 110 additions & 0 deletions examples/brainSubSample1.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,110 @@
{
"$schema": "../src/schemas/iSamplesSchemaCore1.0.json",
"@id": "https://isamples.org/metadata/4327q543jh",
"@context": "https://isamples.org/metadata",
"@type": "schema:DigitalDocument",
"dct:conformsTo": "https://isamples.org/metadata",
"registrant": {
"name": "name",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "role"
},
"about": {
"@id":"xxx:metadataabout/NYBB-MS1/SBB5.1",
"@type":"schema:Thing",
"sample_identifier": "NYBB-MS1/SBB5.1",
"label": "Hippocampal formation from Male adult",
"description": "Hippocampal formation extracted from brain of male adult, age 65 at death, affected by multiple sclerosis",
"alternate_identifiers": [],
"produced_by": {
"identifier": "identifier",
"label": "label",
"description": "Post mortem dissection",
"has_feature_of_interest": "Human brain",
"project": "Brain inventory",
"responsibility": [
{
"name": "Dr. Who did the dissection",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "collector"
}
],
"result_time": "2020-09-24",
"sampling_site": {
"description": "Hippocampal formation (HF), Post mortem dissection, St. Mary's hospital, Tucson, AZ",
"label": "Hippocampal formation (HF)",
"place_name": ["Hippocampal formation (HF)"]
},
"authorized_by": ["appropriate documentation authorizing collection of body parts for research"]
},
"sampling_purpose": "pathology analysis",
"has_context_category": [
{
"label": "Human brain",
"identifier": "\t\nhttp://purl.org/sig/ont/fma/fma50801",
"scheme_name": "Foundational Model of Anatomy"
},
{
"label": "Biological entity",
"identifier": "https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity",
"scheme_name": "iSamples Sampled Feature Type vocabulary"
}
],
"has_material_category": [
{
"label": "Organic material",
"identifier": "https://w3id.org/isample/vocabulary/material/organicmaterial",
"scheme_name": "iSamples Materials Vocabulary"
}
],
"has_sample_object_type": [
{
"label": "Organism part",
"identifier": "https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart",
"scheme_name": "iSamples Material Sample Object Type Vocabulary"
}
],
"keywords": [
{
"keyword": "brain",
"keyword_uri": "keyword_uri",
"scheme_name": "scheme_name",
"scheme_uri": "scheme_uri"
},
{
"keyword": "Hippocampal formation"
},
{
"keyword": "Multiple Sclerosis"
}
],
"related_resource": [
{
"description": "Brain and spinal cord from MYBB_MS1",
"label": "MYBB_MS1",
"relationship": "Parent sample",
"target": "http://medsamples.org/research/nybbms1"
}
],
"complies_with": ["links or descriptions of protocols for collection and use of human body parts for research"],
"curation": {
"access_constraints": ["access_constraints0"],
"curation_location": "curation_location",
"description": "How and where is this tissue material preserverd; who to contact about access to sample?",
"label": "label",
"responsibility": [
{
"name": "name",
"affiliation": "affiliation",
"contact_information": "contact_information",
"identifier": "identifier",
"role": "role"
}
]
}
}
}
Binary file added schemaMapping/schema.org-iSamplesMapping-ODIS.docx
View file
Open in desktop
Binary file not shown.