diff --git a/examples/SESAR/test1.0Valid/SESARDjango-Template.json b/examples/SESAR/test1.0Valid/SESARDjango-Template.json new file mode 100644 index 0000000..cf5608c --- /dev/null +++ b/examples/SESAR/test1.0Valid/SESARDjango-Template.json @@ -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": "" +} \ No newline at end of file diff --git a/examples/brainExample1.json b/examples/brainExample1.json new file mode 100644 index 0000000..3075561 --- /dev/null +++ b/examples/brainExample1.json @@ -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" + } + ] + } + } +} \ No newline at end of file diff --git a/examples/brainSubSample1.json b/examples/brainSubSample1.json new file mode 100644 index 0000000..aa5aa19 --- /dev/null +++ b/examples/brainSubSample1.json @@ -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" + } + ] + } + } +} \ No newline at end of file diff --git a/schemaMapping/schema.org-iSamplesMapping-ODIS.docx b/schemaMapping/schema.org-iSamplesMapping-ODIS.docx new file mode 100644 index 0000000..faebfd1 Binary files /dev/null and b/schemaMapping/schema.org-iSamplesMapping-ODIS.docx differ