├── README.md ├── access_schema.json ├── activity_schema.json ├── alternate_identifier_info_schema.json ├── anatomical_part_schema.json ├── annotation_schema.json ├── biological_entity_schema.json ├── category_values_pair_schema.json ├── consent_info_schema.json ├── data_acquisition_schema.json ├── data_analysis_schema.json ├── data_repository_schema.json ├── data_standard_schema.json ├── data_type_schema.json ├── data_use_condition.json ├── dataset_distribution_schema.json ├── dataset_schema.json ├── date_info_schema.json ├── dimension_schema.json ├── disease_schema.json ├── genome_location_schema.json ├── grant_schema.json ├── identifier_info_schema.json ├── instrument_schema.json ├── license_schema.json ├── material_schema.json ├── molecular_entity_schema.json ├── organization_schema.json ├── person_schema.json ├── place_schema.json ├── project_schema.json ├── provenance_schema.json ├── publication_schema.json ├── related_identifier_info_schema.json ├── software_schema.json ├── study_group_schema.json ├── study_schema.json ├── taxonomic_info_schema.json └── treatment_schema.json /README.md: -------------------------------------------------------------------------------- 1 | # DATS JSON schemas 2 | 3 | This repository contains [JSON schemas](http://json-schema.org/) for the DAta Tag Suite (DATS) model for describing datasets. 4 | 5 | The schemas can be accessed through the permanent identifiers with the following prefix: ```http://w3id.org/dats/schema/```. For example , the dataset schema is available at: http://w3id.org/dats/schema/dataset_schema.json 6 | 7 | ## Documentation 8 | 9 | The documentation about DATS is available at: https://datatagsuite.github.io/docs/html/ 10 | 11 | Previously, previous development of DATS can be found at this repository: https://github.com/datatagsuite/WG3-MetadataSpecifications 12 | 13 | DATS entities are represented in this overview diagram, including 'core entities' that allow to describe datasets irrespective of their domains and a set of entities that are specific for datasets in the biomedical domain. 14 | 15 | ![alt text](https://github.com/datatagsuite/docs/blob/master/source/_static/DATS-revised-overview.jpg "DATS overview") 16 | 17 | 18 | 19 | 20 | ## Publications 21 | - Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu; DataMed – an open source discovery index for finding biomedical datasets, Journal of the American Medical Informatics Association, Volume 25, Issue 3, 1 March 2018, Pages 300–308, https://doi.org/10.1093/jamia/ocx121 22 | - Alejandra N Gonzalez-Beltran, John Campbell, Patrick Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra; **Data discovery with DATS: exemplar adoptions and lessons learned**, *Journal of the American Medical Informatics Association*, Volume 25, Issue 1, 1 January 2018, Pages 13–16, [https://doi.org/10.1093/jamia/ocx119]( https://doi.org/10.1093/jamia/ocx119) 23 | - Lucila Ohno-Machado, Susanna-Assunta Sansone, George Alter, Ian Fore, Jeffrey Grethe, Hua Xu, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Anupama E Gururaj, Elizabeth Bell, Ergin Soysal, Nansu Zong & Hyeon-eui Kim; **Finding useful data across multiple biomedical data repositories using DataMed**; *Nature Genetics* 49, 816–819 (2017) [https://doi.org/10.1038/ng.3864](https://doi.org/10.1038/ng.3864) 24 | - Susanna-Assunta Sansone#, Alejandra Gonzalez-Beltran#, Philippe Rocca-Serra#, George Alter, Jeffrey S. Grethe, Hua Xu, Ian M. Fore, Jared Lyle, Anupama E. Gururaj, Xiaoling Chen, Hyeon-eui Kim, Nansu Zong, Yueling Li, Ruiling Liu, I. Burak Ozyurt & Lucila Ohno-Machado; **DATS, the data tag suite to enable discoverability of datasets**; Scientific Data volume 4, Article number: 170059 (2017) [DOI: 10.1038/sdata.2017.59](https://doi.org/10.1038/sdata.2017.59) #=equal contribution; Pre-print: [bioRxiv DOI: 10.1101/103143 ](https://doi.org/10.1101/103143). 25 | 26 | 27 | ## License 28 | 29 | These JSON schemas are distributed under [CC BY-SA 3.0](http://creativecommons.org/licenses/by-sa/3.0/) license. 30 | -------------------------------------------------------------------------------- /access_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/access_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS access schema", 5 | "description": "Information about resources that provide the means to obtain an asset (a dataset or other research object).", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", 25 | "format": "uri" 26 | }, 27 | "@type": { 28 | "description": "The JSON-LD type", 29 | "type": "string", 30 | "const": "Access" 31 | }, 32 | "identifier": { 33 | "description": "The identifier of the access entity.", 34 | "$ref": "identifier_info_schema.json#" 35 | }, 36 | "alternateIdentifiers": { 37 | "description": "Alternate identifiers for the access entity.", 38 | "type": "array", 39 | "items": { 40 | "$ref": "alternate_identifier_info_schema.json#" 41 | } 42 | }, 43 | "relatedIdentifiers": { 44 | "description": "Related identifiers for the access entity.", 45 | "type": "array", 46 | "items": { 47 | "$ref": "related_identifier_info_schema.json#" 48 | } 49 | }, 50 | "landingPage": { 51 | "description": "A web page that contains information about the associated dataset or other research object and a direct link to the object itself.", 52 | "type": "string", 53 | "format": "uri" 54 | }, 55 | "accessURL": { 56 | "description": "A URL from which the resource (dataset or other research object) can be retrieved, i.e. a direct link to the object itself.", 57 | "type": "string", 58 | "format": "uri" 59 | }, 60 | "types": { 61 | "description": "Method to obtain the resource, ideally specified from a controlled vocabulary or ontology.", 62 | "type": "array", 63 | "items": { 64 | "$ref": "annotation_schema.json#" 65 | } 66 | }, 67 | "authorizations": { 68 | "description": "Types of verification that accessing the resource is allowed. Authorization occurs before successful authentication and refers to the process of obtaining approval to use a data set. Ideally specified from a controlled vocabulary or ontology.", 69 | "type": "array", 70 | "items": { 71 | "$ref": "annotation_schema.json#" 72 | } 73 | }, 74 | "authentications": { 75 | "description": "Types of verification of the credentials for accessing the resource, it is the identification process at the time of access. ideally specified from a controlled vocabulary or ontology.", 76 | "type": "array", 77 | "items": { 78 | "$ref": "annotation_schema.json#" 79 | } 80 | }, 81 | "extraProperties": { 82 | "description": "Extra properties that do not fit in the previous specified attributes. ", 83 | "type": "array", 84 | "items": { 85 | "$ref" : "category_values_pair_schema.json#" 86 | } 87 | } 88 | }, 89 | "additionalProperties": false, 90 | "required": [ "landingPage" ] 91 | } 92 | -------------------------------------------------------------------------------- /activity_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/activity_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS activity (or process) schema.", 5 | "description": "A type of process scheduled in a study.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" }, 25 | "@type": { 26 | "description": "The JSON-LD type", 27 | "type": "string", 28 | "const": "Activity" 29 | }, 30 | "identifier": { 31 | "description": "The identifier of the activity.", 32 | "$ref": "identifier_info_schema.json#" 33 | }, 34 | "alternateIdentifiers": { 35 | "description": "Alternate identifiers for the activity.", 36 | "type": "array", 37 | "items": { 38 | "$ref": "alternate_identifier_info_schema.json#" 39 | } 40 | }, 41 | "relatedIdentifiers": { 42 | "description": "Related identifiers for the activity.", 43 | "type": "array", 44 | "items": { 45 | "$ref": "related_identifier_info_schema.json#" 46 | } 47 | }, 48 | "name": { 49 | "description": "The name of the activity, usually one sentece or short description of the activity.", 50 | "type" : "string" 51 | }, 52 | "description" : { 53 | "description": "A textual narrative comprised of one or more statements describing the activity.", 54 | "type" : "string" 55 | }, 56 | "startDate": { 57 | "description": "A timestamp to record the starting point of the activity.", 58 | "$ref": "date_info_schema.json#" 59 | }, 60 | "endDate": { 61 | "description": "A timestamp to record the end point of the activity.", 62 | "$ref": "date_info_schema.json#" 63 | }, 64 | "dates" : { 65 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 66 | "type" : "array", 67 | "items" : { 68 | "$ref" : "date_info_schema.json#" 69 | } 70 | }, 71 | "duration": { 72 | "description": "The time during which the activity takes place.", 73 | "type" : "string" 74 | }, 75 | "location" : { 76 | "description": "The location where the activity takes place.", 77 | "$ref" : "place_schema.json#" 78 | }, 79 | "performedBy" : { 80 | "description": "The person(s) or organisation(s) responsible for executing the process.", 81 | "type" : "array", 82 | "items" : { 83 | "anyOf": [ 84 | {"$ref" : "person_schema.json#"}, 85 | {"$ref" : "organization_schema.json#"} 86 | ] 87 | } 88 | }, 89 | "keywords": { 90 | "description": "Tags associated with the activity, which will help in its discovery.", 91 | "type": "array", 92 | "items": { 93 | "$ref" : "annotation_schema.json#" 94 | } 95 | }, 96 | "input" : { 97 | "description": "The entities used as input.", 98 | "type": "array", 99 | "items":{ 100 | "anyOf": [ 101 | {"$ref" : "dataset_schema.json#"}, 102 | {"$ref" : "material_schema.json#"} 103 | ] 104 | } 105 | }, 106 | "output" : { 107 | "description": "The entities resulting from applying the activity.", 108 | "type": "array", 109 | "items":{ 110 | "anyOf": [ 111 | {"$ref" : "dataset_schema.json#"}, 112 | {"$ref" : "material_schema.json#"} 113 | ] 114 | } 115 | }, 116 | "extraProperties": { 117 | "description": "Extra properties that do not fit in the previous specified attributes. ", 118 | "type": "array", 119 | "items": { 120 | "$ref" : "category_values_pair_schema.json#" 121 | } 122 | } 123 | }, 124 | "additionalProperties": false, 125 | "required": [ "name" ] 126 | } -------------------------------------------------------------------------------- /alternate_identifier_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/alternate_identifier_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS alternate identifier information schema", 5 | "description": "Information about an alternate identifier (other than the primary).", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "AlternateIdentifier" 30 | }, 31 | "identifier": { 32 | "description": "An identifier or identifiers other than the primary Identifier applied to the resource being registered. (definition from DataCite)", 33 | "type" : "string" 34 | }, 35 | "identifierSource": { 36 | "description": "The identifier source represents information about the organisation/namespace responsible for minting the identifiers. It must be provided if the identifier is provided.", 37 | "type" : "string" 38 | } 39 | }, 40 | "additionalProperties": false 41 | } -------------------------------------------------------------------------------- /anatomical_part_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/anatomical_part_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS anatomical part schema", 5 | "description": "A structure that is part of a multicellular organism.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" }, 25 | "@type": { 26 | "description": "The JSON-LD type", 27 | "type": "string", 28 | "const": "AnatomicalPart" 29 | }, 30 | "identifier": { 31 | "description": "The identifier of the anatomical part.", 32 | "$ref": "identifier_info_schema.json#" 33 | }, 34 | "alternateIdentifiers": { 35 | "description": "Alternate identifiers for the anatomical part.", 36 | "type": "array", 37 | "items": { 38 | "$ref": "alternate_identifier_info_schema.json#" 39 | } 40 | }, 41 | "relatedIdentifiers": { 42 | "description": "Related identifiers for the anatomical part.", 43 | "type": "array", 44 | "items": { 45 | "$ref": "related_identifier_info_schema.json#" 46 | } 47 | }, 48 | "name": { 49 | "description": "The name of the anatomical entity or anatomical part.", 50 | "type" : "string" 51 | }, 52 | "extraProperties": { 53 | "description": "Extra properties that do not fit in the previous specified attributes. ", 54 | "type": "array", 55 | "items": { 56 | "$ref" : "category_values_pair_schema.json#" 57 | } 58 | } 59 | }, 60 | "additionalProperties": false, 61 | "required" : [ "name" ] 62 | } -------------------------------------------------------------------------------- /annotation_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/annotation_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS annotation schema", 5 | "description": "A pair of value (string or numeric) with a corresponding ontology term (IRI), if applicable.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", 25 | "format": "uri" 26 | }, 27 | "@type": { 28 | "description": "The JSON-LD type", 29 | "type": "string", 30 | "const": "Annotation" 31 | }, 32 | "value": { 33 | "description": "The value of the annotation - it can be a string or a number (for coded values).", 34 | "oneOf": [ 35 | { 36 | "type": "string" 37 | }, 38 | { 39 | "type": "number" 40 | } 41 | ] 42 | }, 43 | "valueIRI": { 44 | "description": "The IRI of a concept or ontology term associated with the value. It can also be an empty string", 45 | "anyOf": [ 46 | { 47 | "type": "string", 48 | "format": "uri" 49 | }, 50 | { 51 | "type": "string", 52 | "maxLength": 0 53 | } 54 | ] 55 | } 56 | }, 57 | "additionalProperties": false 58 | } -------------------------------------------------------------------------------- /biological_entity_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/biological_entity_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS biological entity schema", 5 | "description": "A biological entity is a recognized entity covering biological process, molecular functions or cellular components (from: http://geneontology.org/).", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" }, 25 | "@type": { 26 | "description": "The JSON-LD type", 27 | "type": "string", 28 | "const": "BiologicalEntity" 29 | }, 30 | "identifier": { 31 | "description": "The identifier of the biological entity.", 32 | "$ref": "identifier_info_schema.json#" 33 | }, 34 | "alternateIdentifiers": { 35 | "description": "Alternate identifiers for the biological entity.", 36 | "type": "array", 37 | "items": { 38 | "$ref": "alternate_identifier_info_schema.json#" 39 | } 40 | }, 41 | "relatedIdentifiers": { 42 | "description": "Related identifiers for the biological entity.", 43 | "type": "array", 44 | "items": { 45 | "$ref": "related_identifier_info_schema.json#" 46 | } 47 | }, 48 | "name": { 49 | "description": "The name of the biological entity.", 50 | "type" : "string" 51 | }, 52 | "extraProperties": { 53 | "description": "Extra properties that do not fit in the previous specified attributes. ", 54 | "type": "array", 55 | "items": { 56 | "$ref" : "category_values_pair_schema.json#" 57 | } 58 | } 59 | }, 60 | "additionalProperties": false, 61 | "required" : [ "name" ] 62 | } 63 | -------------------------------------------------------------------------------- /category_values_pair_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/category_values_pair_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS extension mechanism", 5 | "description": "Extension mechanism for DATS, which allows to add extra properties to the entities. It should be used only for cases where there are no specific properties to deal with the desired property.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" }, 25 | "@type": { 26 | "description": "The JSON-LD type", 27 | "type": "string", 28 | "const": "CategoryValuesPair" 29 | }, 30 | "category": { 31 | "description": "A characteristic or property about the entity this object is associated with.", 32 | "type": "string" 33 | }, 34 | "categoryIRI": { 35 | "description": "The IRI corresponding to the category, if associated with an ontology term.", 36 | "anyOf": [ 37 | { 38 | "type": "string", 39 | "format": "uri" 40 | }, 41 | { 42 | "type": "string", 43 | "maxLength": 0 44 | } 45 | ] 46 | }, 47 | "values": { 48 | "description": "A set of (annotated) values associated with the cateogory.", 49 | "type": "array", 50 | "items": { 51 | "$ref" : "annotation_schema.json#" 52 | } 53 | } 54 | }, 55 | "additionalProperties": false 56 | } 57 | -------------------------------------------------------------------------------- /consent_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/consent_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS consent information schema", 5 | "description": "Information about a consent code. Consent information schema can refer to one or more License object(s) and can be used to annotate DATS.Material, for fine grained control, or DATS.StudyGroup for coarser annotation", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" }, 25 | "@type": { 26 | "description": "The JSON-LD type", 27 | "type": "string", 28 | "const": "ConsentInfo" 29 | }, 30 | "identifier": { 31 | "description": "The identifier of the consent information.", 32 | "$ref": "identifier_info_schema.json#" 33 | }, 34 | "alternateIdentifiers": { 35 | "description": "Alternate identifiers for the consent information.", 36 | "type": "array", 37 | "items": { 38 | "$ref": "alternate_identifier_info_schema.json#" 39 | } 40 | }, 41 | "relatedIdentifiers": { 42 | "description": "Related identifiers for the consent information.", 43 | "type": "array", 44 | "items": { 45 | "$ref": "related_identifier_info_schema.json#" 46 | } 47 | }, 48 | "name": { 49 | "description": "The name of the consent information, including a label and ideally an ontology term from resources such as DUO, ADA-M.", 50 | "$ref" : "annotation_schema.json#" 51 | }, 52 | "abbreviation": { 53 | "description": "An abbreviation of the consent information.", 54 | "type" : "string" 55 | }, 56 | "description": { 57 | "description": "A description of the consent information.", 58 | "type" : "string" 59 | }, 60 | "incorporatedIn": { 61 | "description": "A list of references to licences/ legal documents used as basis for extracting consent information summary and assigning one or more consent codes.", 62 | "type" : "array", 63 | "items": { 64 | "$ref": "license_schema.json#" 65 | } 66 | }, 67 | "participant": { 68 | "description": "The person providing the consent.", 69 | "$ref": "person_schema.json" 70 | }, 71 | "dates": { 72 | "description": "A set of dates indicating the temporal coverage of the consent information for dynamic consent.", 73 | "type": "array", 74 | "items": { 75 | "$ref": "date_info_schema.json" 76 | } 77 | }, 78 | "extraProperties": { 79 | "description": "Extra properties that do not fit in the previous specified attributes. ", 80 | "type": "array", 81 | "items": { 82 | "$ref" : "category_values_pair_schema.json#" 83 | } 84 | } 85 | }, 86 | "additionalProperties": false, 87 | "required": [ "name"] 88 | } 89 | -------------------------------------------------------------------------------- /data_acquisition_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_acquisition_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS data acquisition schema.", 5 | "description": "Process (or activity) of generating data through measurement made with specific techniques.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", 25 | "format": "uri" 26 | }, 27 | "@type": { 28 | "description": "The JSON-LD type", 29 | "type": "string", 30 | "const": "DataAcquisition" 31 | }, 32 | "identifier": { 33 | "description": "The identifier of the data acquisition.", 34 | "$ref": "identifier_info_schema.json#" 35 | }, 36 | "alternateIdentifiers": { 37 | "description": "Alternate identifiers for the activity.", 38 | "type": "array", 39 | "items": { 40 | "$ref": "alternate_identifier_info_schema.json#" 41 | } 42 | }, 43 | "relatedIdentifiers": { 44 | "description": "Related identifiers for the activity.", 45 | "type": "array", 46 | "items": { 47 | "$ref": "related_identifier_info_schema.json#" 48 | } 49 | }, 50 | "name": { 51 | "description": "The name of the activity, usually one sentece or short description of the data acquisition.", 52 | "type" : "string" 53 | }, 54 | "description" : { 55 | "description": "A textual narrative comprised of one or more statements describing the data acquisition.", 56 | "type" : "string" 57 | }, 58 | "startDate": { 59 | "description": "A timestamp to record the starting point of the activity.", 60 | "$ref": "date_info_schema.json#" 61 | }, 62 | "endDate": { 63 | "description": "A timestamp to record the end point of the activity.", 64 | "$ref": "date_info_schema.json#" 65 | }, 66 | "dates" : { 67 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 68 | "type" : "array", 69 | "items" : { 70 | "$ref" : "date_info_schema.json#" 71 | } 72 | }, 73 | "duration": { 74 | "description": "The time during which the activity takes place.", 75 | "type" : "string" 76 | }, 77 | "location" : { 78 | "description": "The location where the activity takes place.", 79 | "$ref" : "place_schema.json#" 80 | }, 81 | "performedBy" : { 82 | "description": "The person(s) or organisation(s) responsible for executing the process.", 83 | "type" : "array", 84 | "items" : { 85 | "anyOf": [ 86 | {"$ref" : "person_schema.json#"}, 87 | {"$ref" : "organization_schema.json#"} 88 | ] 89 | } 90 | }, 91 | "keywords": { 92 | "description": "Tags associated with the activity, which will help in its discovery.", 93 | "type": "array", 94 | "items": { 95 | "$ref" : "annotation_schema.json#" 96 | } 97 | }, 98 | "input" : { 99 | "description": "The entities used as input.", 100 | "type": "array", 101 | "items":{ 102 | "$ref" : "material_schema.json#" 103 | } 104 | }, 105 | "output" : { 106 | "description": "The entities resulting from applying the activity.", 107 | "type": "array", 108 | "items":{ 109 | "$ref" : "dataset_schema.json#" 110 | } 111 | }, 112 | "uses": { 113 | "description": "The instrument(s) or software(s) used to acquire the signal.", 114 | "type": "array", 115 | "items": { 116 | "anyOf": [ 117 | { 118 | "$ref": "instrument_schema.json#" 119 | }, 120 | { 121 | "$ref": "software_schema.json#" 122 | } 123 | ] 124 | } 125 | }, 126 | "measures": { 127 | "description": "The dimension(s) being acquired as signal.", 128 | "type": "array", 129 | "items": { 130 | "$ref": "dimension_schema.json#" 131 | } 132 | }, 133 | "extraProperties": { 134 | "description": "Extra properties that do not fit in the previous specified attributes. ", 135 | "type": "array", 136 | "items": { 137 | "$ref" : "category_values_pair_schema.json#" 138 | } 139 | } 140 | }, 141 | "additionalProperties": false, 142 | "required" : [ "name" ] 143 | } -------------------------------------------------------------------------------- /data_analysis_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_analysis_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS data analysis schema", 5 | "description": "Process (or activity) of transforming data and producing data.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DataAnalysis" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the data analysis.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the activity.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the activity.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the activity, usually one sentece or short description of the data analysis.", 51 | "type" : "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the data analysis.", 55 | "type" : "string" 56 | }, 57 | "startDate": { 58 | "description": "A timestamp to record the starting point of the activity.", 59 | "$ref": "date_info_schema.json#" 60 | }, 61 | "endDate": { 62 | "description": "A timestamp to record the end point of the activity.", 63 | "$ref": "date_info_schema.json#" 64 | }, 65 | "dates" : { 66 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 67 | "type" : "array", 68 | "items" : { 69 | "$ref" : "date_info_schema.json#" 70 | } 71 | }, 72 | "duration": { 73 | "description": "The time during which the activity takes place.", 74 | "type" : "string" 75 | }, 76 | "location" : { 77 | "description": "The location where the activity takes place.", 78 | "$ref" : "place_schema.json#" 79 | }, 80 | "performedBy" : { 81 | "description": "The person(s) or organisation(s) responsible for executing the process.", 82 | "type" : "array", 83 | "items" : { 84 | "anyOf": [ 85 | {"$ref" : "person_schema.json#"}, 86 | {"$ref" : "organization_schema.json#"} 87 | ] 88 | } 89 | }, 90 | "keywords": { 91 | "description": "Tags associated with the activity, which will help in its discovery.", 92 | "type": "array", 93 | "items": { 94 | "$ref" : "annotation_schema.json#" 95 | } 96 | }, 97 | "input" : { 98 | "description": "The entities used as input.", 99 | "type": "array", 100 | "items":{ 101 | "$ref" : "dataset_schema.json#" 102 | }, 103 | "minItems": 1 104 | }, 105 | "output" : { 106 | "description": "The entities resulting from applying the activity.", 107 | "type": "array", 108 | "items":{ 109 | "$ref" : "dataset_schema.json#" 110 | }, 111 | "minItems": 1 112 | }, 113 | "uses": { 114 | "description": "The instrument(s) or software(s) used to acquire the signal.", 115 | "type": "array", 116 | "items": { 117 | "anyOf": [ 118 | { 119 | "$ref": "instrument_schema.json#" 120 | }, 121 | { 122 | "$ref": "software_schema.json#" 123 | } 124 | ] 125 | } 126 | }, 127 | "measures": { 128 | "description": "The dimension(s) being acquired as signal.", 129 | "type": "array", 130 | "items": { 131 | "$ref": "dimension_schema.json#" 132 | } 133 | }, 134 | "extraProperties": { 135 | "description": "Extra properties that do not fit in the previous specified attributes. ", 136 | "type": "array", 137 | "items": { 138 | "$ref" : "category_values_pair_schema.json#" 139 | } 140 | } 141 | }, 142 | "additionalProperties": false, 143 | "required": [ "name" ] 144 | } -------------------------------------------------------------------------------- /data_repository_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_repository_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS data repository schema", 5 | "description": "A repository or catalog of datasets. It could be a primary repository or a repository that aggregates data existing in other repositories.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DataRepository" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the data repository.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the data repository.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the data repository.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the data repository.", 51 | "type": "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the data repository.", 55 | "type" : "string" 56 | }, 57 | "dates" : { 58 | "description": "Relevant dates for the data repository.", 59 | "type" : "array", 60 | "items" : { 61 | "$ref" : "date_info_schema.json#" 62 | } 63 | }, 64 | "scopes": { 65 | "description": "Information about the nature of the datasets in the repository, ideally from a controlled vocabulary or ontology (e.g. transcription profile, sequence reads, molecular structure, image, DNA sequence, NMR spectra).", 66 | "type": "array", 67 | "items": { 68 | "$ref": "annotation_schema.json#" 69 | } 70 | }, 71 | "types": { 72 | "description": "A descriptor (ideally from a controlled vocabulary) providing information about the type of repository, such as primary resource or aggregator.", 73 | "type": "array", 74 | "items": { 75 | "$ref": "annotation_schema.json#" 76 | } 77 | }, 78 | "licenses": { 79 | "description": "The terms of use of the data repository.", 80 | "type": "array", 81 | "items": { 82 | "$ref": "license_schema.json#" 83 | } 84 | }, 85 | "version": { 86 | "description": "A release point for the repository, when applicable.", 87 | "type": "string" 88 | }, 89 | "publishers": { 90 | "description": "The person(s) or organization(s) responsible for the repository and its availability.", 91 | "type": "array", 92 | "items": { 93 | "oneOf": [ 94 | { 95 | "$ref": "person_schema.json#" 96 | }, 97 | { 98 | "$ref": "organization_schema.json#" 99 | } 100 | ] 101 | } 102 | }, 103 | "aggregatorOf": { 104 | "description": "The DataRepositories aggregated by this repository. This property will be empty for primary repositories.", 105 | "type": "array", 106 | "items": { 107 | "$ref": "data_repository_schema.json#" 108 | } 109 | }, 110 | "access" : { 111 | "description": "The information about access modality for the data repository.", 112 | "type" : "array", 113 | "items" : { 114 | "$ref" : "access_schema.json#" 115 | } 116 | }, 117 | "extraProperties": { 118 | "description": "Extra properties that do not fit in the previous specified attributes. ", 119 | "type": "array", 120 | "items": { 121 | "$ref" : "category_values_pair_schema.json#" 122 | } 123 | } 124 | }, 125 | "additionalProperties": false, 126 | "required": [ "name" ] 127 | } 128 | -------------------------------------------------------------------------------- /data_standard_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_standard_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS data standard schema", 5 | "description": "A format, reporting guideline, terminology. It is used to indicate whether the dataset conforms to a particular community norm or specification.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DataStandard" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the data standard.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the standard.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the standard.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the standard (e.g. FASTQ, CDISC STDM, ISO8601).", 51 | "type" : "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the data standard.", 55 | "type" : "string" 56 | }, 57 | "type" : { 58 | "description": "The nature of the information resource, ideally specified with a controlled vocabulary or ontology (.e.g model or format, vocabulary, reporting guideline).", 59 | "$ref" : "annotation_schema.json#" 60 | }, 61 | "licenses" : { 62 | "description": "The terms of use of the data standard.", 63 | "type" : "array", 64 | "items" : { 65 | "$ref" : "license_schema.json#" 66 | } 67 | }, 68 | "version" : { 69 | "description": "A release point for the repository when applicable.", 70 | "type" : "string" 71 | }, 72 | "extraProperties": { 73 | "description": "Extra properties that do not fit in the previous specified attributes. ", 74 | "type": "array", 75 | "items": { 76 | "$ref" : "category_values_pair_schema.json#" 77 | } 78 | } 79 | }, 80 | "additionalProperties": false, 81 | "required":["name", "type"] 82 | } 83 | -------------------------------------------------------------------------------- /data_type_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_type_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS Data Type schema", 5 | "description": "The nature of the data, as determined for the information collected, the method used and the platform used.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DataType" 30 | }, 31 | "information": { 32 | "description": "The measurements or facts that the data is about.", 33 | "$ref" : "annotation_schema.json#" 34 | }, 35 | "method": { 36 | "description": "The procedure or technology used to generate the information.", 37 | "$ref" : "annotation_schema.json#" 38 | 39 | }, 40 | "platform": { 41 | "description": "The set of instruments, software and reagents that are needed to generated the data.", 42 | "$ref" : "annotation_schema.json#" 43 | 44 | }, 45 | "instrument": { 46 | "description": "The specific device used to generate the data.", 47 | "$ref" : "annotation_schema.json#" 48 | 49 | } 50 | }, 51 | "additionalProperties": false 52 | } -------------------------------------------------------------------------------- /data_use_condition.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/data_use_condition_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS data use condition schema", 5 | "description": "A legal document giving official permission to do something with a Resource. It is assumed that an external vocabulary will describe with sufficient granularity the permission for redistribution, modification, derivation, reuse, etc. and conditions for citation/acknowledgment.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DataUseCondition" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the data use condition.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the data use condition.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the data use condition.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the data use condition.", 51 | "type" : "string" 52 | }, 53 | "abbreviation": { 54 | "description": "An abbreviation of the data use condition such as a DUO short hand.", 55 | "type" : "string" 56 | }, 57 | "description" : { 58 | "description": "A textual narrative comprised of one or more statements describing the data use condition.", 59 | "type" : "string" 60 | }, 61 | "dates" : { 62 | "description": "Relevant dates, such as the date that data use condition was applied, may be provided.", 63 | "type" : "array", 64 | "items": { 65 | "$ref" : "date_info_schema.json#" 66 | } 67 | }, 68 | "condition_qualifier": { 69 | "description" : "Different entities (taxonomic information, disease, organisation, person, geographic location or others) qualifying this data use condition.", 70 | "type": "array", 71 | "items": { 72 | "anyOf": [ 73 | {"$ref" : "taxonomic_info_schema.json#"}, 74 | {"$ref" : "disease_schema.json#"}, 75 | {"$ref" : "organization_schema.json#"}, 76 | {"$ref" : "person_schema.json#"}, 77 | {"$ref" : "place_schema.json"}, 78 | {"$ref" : "category_values_pair_schema.json#"}, 79 | {"$ref" : "annotation_schema.json#"} 80 | ] 81 | } 82 | }, 83 | "restriction_type": { 84 | "description": "Indication of the type of the data use conditions - for example OBLIGATION or CONSTRAINED_PERMISSION.", 85 | "anyOf": [ 86 | { "type" : "string" }, 87 | { 88 | "$ref": "annotation_schema.json#" 89 | } 90 | ] 91 | }, 92 | "extraProperties": { 93 | "description": "Extra properties that do not fit in the previous specified attributes. ", 94 | "type": "array", 95 | "items": { 96 | "$ref" : "category_values_pair_schema.json#" 97 | } 98 | } 99 | }, 100 | "additionalProperties": false, 101 | "required": [ "name"] 102 | } 103 | -------------------------------------------------------------------------------- /dataset_distribution_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/dataset_distribution_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS dataset distribution schema", 5 | "description": "(From DCAT) Represents a specific available form of a dataset. Each dataset might be available in different forms, these forms might represent different formats of the dataset or different endpoints. Examples of distributions include a downloadable CSV file, an API or an RSS feed.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "DatasetDistribution" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the dataset distribution.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the dataset distribution.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the dataset distribution.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "title" : { 50 | "description" : "The name of the dataset, usually one sentece or short description of the dataset.", 51 | "type" : "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the dataset distribution.", 55 | "type" : "string" 56 | }, 57 | "storedIn" : { 58 | "description": "The data repository hosting the dataset distribution.", 59 | "$ref": "data_repository_schema.json#" 60 | }, 61 | "dates" : { 62 | "description": "Relevant dates for the datasets, e.g. creation date or last modification date may be added.", 63 | "type" : "array", 64 | "items" : { 65 | "$ref" : "date_info_schema.json#" 66 | } 67 | }, 68 | "version" : { 69 | "description": "A release point for the dataset when applicable.", 70 | "type" : "string" 71 | }, 72 | "licenses": { 73 | "description": "The terms of use of the dataset distribution.", 74 | "type": "array", 75 | "items": { 76 | "$ref": "license_schema.json#" 77 | } 78 | }, 79 | "access" : { 80 | "description": "The information about access modality for the dataset distribution.", 81 | "$ref" : "access_schema.json#" 82 | }, 83 | "curationStatus": { 84 | "description": "The level of curation of the dataset distribution.", 85 | "type": "array", 86 | "items": { 87 | "$ref": "annotation_schema.json#" 88 | } 89 | }, 90 | "conformsTo" : { 91 | "description": "A data standard whose requirements and constraints are met by the dataset.", 92 | "type" : "array", 93 | "items" : { 94 | "$ref": "data_standard_schema.json#" 95 | } 96 | }, 97 | "qualifiers": { 98 | "description": "One or more characteristics of the dataset distribution (e.g. how it relates to other distributions, if the data is raw or processed, compressed or encrypted).", 99 | "type" : "array", 100 | "items" : { 101 | "anyOf": [ 102 | { "$ref": "annotation_schema.json#"}, 103 | { "$ref": "category_values_pair_schema.json#"} 104 | ] 105 | } 106 | }, 107 | "formats" : { 108 | "description": "The technical format of the dataset distribution. Use the file extension or MIME type when possible. (Definition adapted from DataCite)", 109 | "type" : "array", 110 | "items" : { 111 | "anyOf": [ 112 | { "type" : "string" }, 113 | { 114 | "$ref": "annotation_schema.json#" 115 | } 116 | ] 117 | } 118 | }, 119 | "checksum": { 120 | "description": "The checksum to verify the integrity of the dataset after download", 121 | "type" : "string" 122 | }, 123 | "checksumAlgorithm": { 124 | "description": "The name of the algorithm used to generate the checksum, e.g. MD5 or SHA-256", 125 | "anyOf": [ 126 | { "type" : "string" }, 127 | { 128 | "$ref": "annotation_schema.json#" 129 | } 130 | ] 131 | }, 132 | "size": { 133 | "description": "The size of the dataset.", 134 | "type": "number" 135 | }, 136 | "unit": { 137 | "description": "The unit of measurement used to estimate the size of the dataset (e.g, petabyte). Ideally, the unit should be coming from a reference controlled terminology.", 138 | "$ref": "annotation_schema.json#" 139 | }, 140 | "extraProperties": { 141 | "description": "Extra properties that do not fit in the previous specified attributes. ", 142 | "type": "array", 143 | "items": { 144 | "$ref" : "category_values_pair_schema.json#" 145 | } 146 | } 147 | }, 148 | "additionalProperties": false, 149 | "required": [ "access" ] 150 | } 151 | -------------------------------------------------------------------------------- /dataset_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/dataset_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS Dataset Schema", 5 | "description": "A set of dimensions about an entity being observed. A collection of data, published or curated by a single agent, and available for access or download in one or more formats (from DCAT: http://www.w3.org/TR/vocab-dcat/#Class:_Dataset). A body of structured information describing some topic(s) of interest (from: http://schema.org/Dataset).", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Dataset" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the dataset.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the dataset.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the dataset.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "title" : { 50 | "description" : "The name of the dataset, usually one sentence or short description of the dataset.", 51 | "type" : "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the dataset.", 55 | "type" : "string" 56 | }, 57 | "dates" : { 58 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 59 | "type" : "array", 60 | "items" : { 61 | "$ref" : "date_info_schema.json#" 62 | } 63 | }, 64 | "storedIn" : { 65 | "description": "The data repository hosting the dataset.", 66 | "$ref": "data_repository_schema.json#" 67 | }, 68 | "spatialCoverage": { 69 | "description": "The geographical extension and span covered by the dataset and its measured dimensions/variables.", 70 | "type" : "array", 71 | "items" : { 72 | "$ref" : "place_schema.json#" 73 | } 74 | }, 75 | "types": { 76 | "description": "A term, ideally from a controlled terminology, identifying the dataset type or nature of the data, placing it in a typology", 77 | "type" : "array", 78 | "items" : { 79 | "$ref": "annotation_schema.json#" 80 | }, 81 | "minItems" : 1 82 | }, 83 | "availability": { 84 | "description": "A qualifier indicating the different types of availability for a dataset (available, unavailable, embargoed, available with restriction, information not available).", 85 | "type": "string" 86 | }, 87 | "refinement": { 88 | "description": "A qualifier to describe the level of data processing of the dataset and its distributions.", 89 | "type": "string" 90 | }, 91 | "aggregation": { 92 | "description": "A qualifier indicating if the entity represents an 'instance of dataset' or a 'collection of datasets'.", 93 | "type": "string" 94 | }, 95 | "privacy": { 96 | "description": "A qualifier to describe the data protection applied to the dataset. This is relevant for clinical data.", 97 | "type": "string" 98 | }, 99 | "distributions" : { 100 | "description": "The distribution(s) by which datasets are made available (for example: mySQL dump).", 101 | "type" : "array", 102 | "items" : { 103 | "$ref" : "dataset_distribution_schema.json#" 104 | } 105 | }, 106 | "dimensions" : { 107 | "description": "The different dimensions (granular components) making up a dataset.", 108 | "type" : "array", 109 | "items" : { 110 | "$ref" : "dimension_schema.json#" 111 | } 112 | }, 113 | "primaryPublications" : { 114 | "description": "The primary publication(s) associated with the dataset, usually describing how the dataset was produced.", 115 | "type" : "array", 116 | "items" : { 117 | "$ref" : "publication_schema.json#" 118 | } 119 | }, 120 | "citations" : { 121 | "description": "The publication(s) that cite this dataset.", 122 | "type" : "array", 123 | "items" : { 124 | "$ref" : "publication_schema.json#" 125 | } 126 | }, 127 | "citationCount": { 128 | "description": "The number of publications that cite this dataset (consterated in the citations property)", 129 | "type": "integer" 130 | }, 131 | "producedBy" : { 132 | "description": "A study process which generated a given dataset, if any.", 133 | "anyOf": [ 134 | {"$ref" : "study_schema.json#"}, 135 | {"$ref" : "data_acquisition_schema.json#"}, 136 | {"$ref" : "data_analysis_schema.json#"} 137 | ] 138 | }, 139 | "creators" : { 140 | "description": "The person(s) or organization(s) which contributed to the creation of the dataset.", 141 | "type" : "array", 142 | "items" : { 143 | "oneOf": [ 144 | {"$ref" : "person_schema.json#"}, 145 | {"$ref" : "organization_schema.json#"} 146 | ] 147 | }, 148 | "minItems" : 1 149 | }, 150 | "licenses": { 151 | "description": "The terms of use of the dataset.", 152 | "type": "array", 153 | "items": { 154 | "$ref": "license_schema.json#" 155 | } 156 | }, 157 | "dataUseConditions": { 158 | "description": "Types of data use conditions extracted from the license documents. Data Use Conditions may refer to restrictions, prohibition, research topics as granted by the dataset, dimension, software license. Ideally specified from a controlled vocabulary or ontology, such as GA4GH Data Use Ontology (DUO: http://www.obofoundry.org/ontology/duo.html) or ADA-M matrix (https://github.com/ga4gh/ADA-M).", 159 | "type": "array", 160 | "items": { 161 | "oneOf": [ 162 | {"$ref" : "data_use_condition.json#"}, 163 | {"$ref" : "annotation_schema.json#"} 164 | ] 165 | } 166 | }, 167 | "conformsTo" : { 168 | "description": "A data standard whose requirements and constraints are met by the dataset.", 169 | "type" : "array", 170 | "items" : { 171 | "$ref": "data_standard_schema.json#" 172 | } 173 | }, 174 | "isAbout": { 175 | "description" : "Different entities (biological entity, taxonomic information, disease, molecular entity, anatomical part, treatment) associated with this dataset.", 176 | "type": "array", 177 | "items": { 178 | "anyOf": [ 179 | {"$ref" : "biological_entity_schema.json#"}, 180 | {"$ref" : "taxonomic_info_schema.json#"}, 181 | {"$ref" : "disease_schema.json#"}, 182 | {"$ref" : "molecular_entity_schema.json#"}, 183 | {"$ref" : "anatomical_part_schema.json#"}, 184 | {"$ref" : "treatment_schema.json#"}, 185 | {"$ref" : "material_schema.json#"}, 186 | {"$ref" : "study_group_schema.json#"}, 187 | {"$ref" : "category_values_pair_schema.json#"}, 188 | {"$ref" : "annotation_schema.json#"} 189 | ] 190 | } 191 | }, 192 | "hasPart" : { 193 | "description": "A Dataset that is a subset of this Dataset; Datasets declaring the 'hasPart' relationship are considered a collection of Datasets, the aggregation criteria could be included in the 'description' field.", 194 | "type": "array", 195 | "items": { 196 | "$ref" : "dataset_schema.json#" 197 | } 198 | }, 199 | "acknowledges" : { 200 | "description": "The grant(s) which funded and supported the work reported by the dataset.", 201 | "type" : "array", 202 | "items" : { 203 | "$ref" : "grant_schema.json#" 204 | } 205 | }, 206 | "keywords" : { 207 | "description": "Tags associated with the dataset, which will help in its discovery.", 208 | "type": "array", 209 | "items": { 210 | "$ref" : "annotation_schema.json#" 211 | } 212 | }, 213 | "version" : { 214 | "description": "A release point for the dataset when applicable.", 215 | "type" : "string" 216 | }, 217 | "extraProperties": { 218 | "description": "Extra properties that do not fit in the previous specified attributes. ", 219 | "type": "array", 220 | "items": { 221 | "$ref" : "category_values_pair_schema.json#" 222 | } 223 | } 224 | }, 225 | "additionalProperties": false, 226 | "required" : [ "title", "types", "creators" ] 227 | } 228 | -------------------------------------------------------------------------------- /date_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/date_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS date information schema.", 5 | "description": "Information about a calendar date or timestamp indicating day, month, year and time of an event.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Date" 30 | }, 31 | "date": { 32 | "description": "A date following the ISO8601 standard.", 33 | "type" : "string", 34 | "format": "date-time" 35 | }, 36 | "type": { 37 | "description": "The type of date, used to specify the process which is being timestamped by the date attribute value, ideally comes from a controlled terminology.", 38 | "$ref" : "annotation_schema.json#" 39 | } 40 | }, 41 | "additionalProperties": false, 42 | "required": ["date","type"] 43 | } -------------------------------------------------------------------------------- /dimension_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/dimension_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS dimension schema", 5 | "description": "A feature of an entity, i.e. an individual measurable property (both quantitative or qualitative) of the entity being observed.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Dimension" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the dimension.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the dimension.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the dimension.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name" : { 50 | "description": "The name of the dimension measured or observed during the data acquisition process, ideally from a controlled terminology.", 51 | "$ref" : "annotation_schema.json#" 52 | }, 53 | "description": { 54 | "description": "A textual narrative comprised of one or more statements describing the dimension.", 55 | "type": "string" 56 | }, 57 | "types": { 58 | "description": "A term, ideally from a controlled terminology, identifying the nature of the dimension, placing it in a typology.", 59 | "type": "array", 60 | "items": { 61 | "$ref": "annotation_schema.json#" 62 | } 63 | }, 64 | "datatype": { 65 | "description": "The type of data for this dimension, as described with the DataType entity.", 66 | "$ref": "data_type_schema.json#" 67 | }, 68 | "values": { 69 | "description": "The actual collections of values collected for that dimension.", 70 | "type": "array", 71 | "items": { 72 | "anyOf": [ 73 | {"$ref" : "annotation_schema.json#"}, 74 | {"$ref" : "category_values_pair_schema.json#"} 75 | ] 76 | } 77 | }, 78 | "unit": { 79 | "description": "A reference measurement unit associated with scalar dimensions, ideally from a reference controlled terminology.", 80 | "$ref" : "annotation_schema.json#" 81 | }, 82 | "isAbout" : { 83 | "description": "A material or a dataset, which is the object of this dimension (this dimension is about the material - e.g. the heights of the patients - or the dataset - e.g. the standard deviation or the set of outliers or a quality indicator of a dataset).", 84 | "type" : "array", 85 | "items" : { 86 | "oneOf": [ 87 | {"$ref" : "material_schema.json#"}, 88 | {"$ref" : "dataset_schema.json#"} 89 | ] 90 | } 91 | }, 92 | "consentInformation": { 93 | "description": "The consent information related to this dimennsion.", 94 | "type": "array", 95 | "items" : { 96 | "$ref" : "consent_info_schema.json#" 97 | } 98 | }, 99 | "partOf" : { 100 | "description": "The dataset(s) this dimension belongs to.", 101 | "type" : "array", 102 | "items" : { 103 | "$ref": "dataset_schema.json#" 104 | } 105 | }, 106 | "extraProperties": { 107 | "description": "Extra properties that do not fit in the previous specified attributes. ", 108 | "type": "array", 109 | "items": { 110 | "$ref" : "category_values_pair_schema.json#" 111 | } 112 | } 113 | }, 114 | "additionalProperties": false, 115 | "required": [ "name" ] 116 | } -------------------------------------------------------------------------------- /disease_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/disease_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS disease schema", 5 | "description": "A disorder of structure or function in a human, animal, or plant, that produces specific symptoms or that affects a specific location.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Disease" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the disease.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the disease.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the disease.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the disease.", 51 | "type" : "string" 52 | }, 53 | "dates" : { 54 | "description": "Relevant dates, such as the diagnosis date of the disease, may be provided.", 55 | "type": "array", 56 | "items": { 57 | "$ref": "date_info_schema.json#" 58 | } 59 | }, 60 | "diseaseStatus": { 61 | "description": "A value (and ideally also an ontology annotation provided as a valueIRI) for the disease status.", 62 | "$ref": "annotation_schema.json#" 63 | }, 64 | "extraProperties": { 65 | "description": "Extra properties that do not fit in the previous specified attributes. ", 66 | "type": "array", 67 | "items": { 68 | "$ref" : "category_values_pair_schema.json#" 69 | } 70 | } 71 | }, 72 | "additionalProperties": false, 73 | "required" : [ "name" ] 74 | } 75 | -------------------------------------------------------------------------------- /genome_location_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/genome_location_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema#", 4 | "title": "DATS genome location schema", 5 | "description": "Location of a sequence object used both by display, and by jbrowse to render a browser. The addition to DATS uses the genomeLocation as defined by AGR [https://github.com/alliance-genome/agr_schemas/blob/develop/gene/genomeLocation.json]", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "GenomeLocation" 30 | }, 31 | "assembly": { 32 | "type" : "string", 33 | "description" : "The assembly on which the position and chromosome are based." 34 | }, 35 | "startPosition":{ 36 | "type": "number", 37 | "description": "the start position of the location." 38 | }, 39 | "endPosition":{ 40 | "type": "number", 41 | "description": "the end position of the location." 42 | }, 43 | "chromosome":{ 44 | "type": "string", 45 | "description": "the chromosome of the genomic feature. Note: whatever loaded here, will be used in JBrowse." 46 | }, 47 | "strand":{ 48 | "enum": ["+","-","."], 49 | "description": "strand of the genome location." 50 | } 51 | }, 52 | "additionalProperties": false, 53 | "required": [ "assembly","chromosome" ] 54 | } -------------------------------------------------------------------------------- /grant_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/grant_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS grant schema", 5 | "description": "An allocated sum of funds given by a government or other organization for a particular purpose.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Grant" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the grant.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the grant.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the grant.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the grant and its funding program.", 51 | "type" : "string" 52 | }, 53 | "funds" : { 54 | "description": "The study or dataset supported by the grant.", 55 | "type" : "array", 56 | "items" : { 57 | "oneOf": [ 58 | {"$ref" : "study_schema.json#"}, 59 | {"$ref" : "dataset_schema.json#"} 60 | ] 61 | } 62 | }, 63 | "funders" : { 64 | "description": "The person(s) or organization(s) which has awarded the funds supporting the project.", 65 | "type" : "array", 66 | "items" : { 67 | "oneOf": [ 68 | {"$ref" : "person_schema.json#"}, 69 | {"$ref" : "organization_schema.json#"} 70 | ] 71 | }, 72 | "minItems" : 1 73 | }, 74 | "awardees" : { 75 | "description": "The person(s) or organization(s) which received the funds supporting the project.", 76 | "type" : "array", 77 | "items" : { 78 | "oneOf": [ 79 | {"$ref" : "person_schema.json#"}, 80 | {"$ref" : "organization_schema.json#"} 81 | ] 82 | } 83 | }, 84 | "dates" : { 85 | "description": "Relevant dates, such as the date when the grant was awarded, may be provided.", 86 | "type" : "array", 87 | "items": { 88 | "$ref" : "date_info_schema.json#" 89 | } 90 | }, 91 | "extraProperties": { 92 | "description": "Extra properties that do not fit in the previous specified attributes. ", 93 | "type": "array", 94 | "items": { 95 | "$ref" : "category_values_pair_schema.json#" 96 | } 97 | } 98 | }, 99 | "additionalProperties": false, 100 | "required": [ "name"] 101 | } 102 | -------------------------------------------------------------------------------- /identifier_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/identifier_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS identifier information schema", 5 | "description": "Information about the primary identifier.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Identifier" 30 | }, 31 | "identifier": { 32 | "description": "A code uniquely identifying an entity locally to a system or globally.", 33 | "type" : "string" 34 | }, 35 | "identifierSource": { 36 | "description": "The identifier source represents information about the organisation/namespace responsible for minting the identifiers. It must be provided if the identifier is provided.", 37 | "type" : "string" 38 | } 39 | }, 40 | "additionalProperties": false 41 | } -------------------------------------------------------------------------------- /instrument_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/instrument_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS instrument schema", 5 | "description": "An entity that helps an agent perform an activity.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Instrument" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the instrument.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the instrument.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the instrument.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the instrument.", 51 | "type" : "string" 52 | }, 53 | "type": { 54 | "description": "The type of the instrument/technology.", 55 | "$ref" : "annotation_schema.json#" 56 | }, 57 | "isUsedBy" : { 58 | "description": "The data acquisition activity that makes use of this instrument.", 59 | "type" : "array", 60 | "items" : { 61 | "$ref": "data_acquisition_schema.json#" 62 | } 63 | }, 64 | "manufacturer" : { 65 | "description": "The person or organisation that produced the instrument.", 66 | "oneOf": [ 67 | {"$ref" : "person_schema.json#"}, 68 | {"$ref" : "organization_schema.json#"} 69 | ] 70 | }, 71 | "extraProperties": { 72 | "description": "Extra properties that do not fit in the previous specified attributes. ", 73 | "type": "array", 74 | "items": { 75 | "$ref" : "category_values_pair_schema.json#" 76 | } 77 | } 78 | }, 79 | "additionalProperties": false, 80 | "required":[ "name" ] 81 | } -------------------------------------------------------------------------------- /license_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/license_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS license schema", 5 | "description": "A legal document giving official permission to do something with a Resource. It is assumed that an external vocabulary will describe with sufficient granularity the permission for redistribution, modification, derivation, reuse, etc. and conditions for citation/acknowledgment.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "License" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the license.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the license.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the license.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the license.", 51 | "type" : "string" 52 | }, 53 | "version": { 54 | "description": "The version of the license.", 55 | "type" : "string" 56 | }, 57 | "dates" : { 58 | "description": "Relevant dates, such as the date of the license was issued, may be provided.", 59 | "type" : "array", 60 | "items": { 61 | "$ref" : "date_info_schema.json#" 62 | } 63 | }, 64 | "licensingAuthority": { 65 | "description": "The person(s) or organization(s) responsible for granting access to the data by approving the license.", 66 | "type" : "array", 67 | "items" : { 68 | "oneOf": [ 69 | {"$ref" : "person_schema.json#"}, 70 | {"$ref" : "organization_schema.json#"} 71 | ] 72 | } 73 | }, 74 | "creators" : { 75 | "description": "The person(s) or organization(s) responsible for writing the license.", 76 | "type" : "array", 77 | "items" : { 78 | "oneOf": [ 79 | {"$ref" : "person_schema.json#"}, 80 | {"$ref" : "organization_schema.json#"} 81 | ] 82 | } 83 | }, 84 | "consentInformation": { 85 | "description": "Types of consent given by study participant extracted from the terms of use documents. Ideally specified from a controlled vocabulary or ontology, such as GA4GH Data Use Ontology (DUO: http://www.obofoundry.org/ontology/duo.html) or ADA-M matrix (https://github.com/ga4gh/ADA-M).", 86 | "type": "array", 87 | "items": { 88 | "$ref": "annotation_schema.json#" 89 | } 90 | }, 91 | "dataUseConditions": { 92 | "description": "Types of data use conditions extracted from the license documents. Data Use Conditions may refer to restrictions, prohibition, research topics as granted by the dataset, dimension, software license. Ideally specified from a controlled vocabulary or ontology, such as GA4GH Data Use Ontology (DUO: http://www.obofoundry.org/ontology/duo.html) or ADA-M matrix (https://github.com/ga4gh/ADA-M).", 93 | "type": "array", 94 | "items": { 95 | "oneOf": [ 96 | {"$ref" : "data_use_condition.json#"}, 97 | {"$ref" : "annotation_schema.json#"} 98 | ] 99 | } 100 | }, 101 | "extraProperties": { 102 | "description": "Extra properties that do not fit in the previous specified attributes. ", 103 | "type": "array", 104 | "items": { 105 | "$ref" : "category_values_pair_schema.json#" 106 | } 107 | } 108 | }, 109 | "additionalProperties": false, 110 | "required": [ "name"] 111 | } 112 | -------------------------------------------------------------------------------- /material_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/material_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS material schema", 5 | "description": "A physical entity.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", 25 | "format": "uri" 26 | }, 27 | "@type": { 28 | "description": "The JSON-LD type", 29 | "type": "string", 30 | "const": "Material" 31 | }, 32 | "identifier": { 33 | "description": "The identifier of the material.", 34 | "$ref": "identifier_info_schema.json#" 35 | }, 36 | "alternateIdentifiers": { 37 | "description": "Alternate identifiers for the material.", 38 | "type": "array", 39 | "items": { 40 | "$ref": "alternate_identifier_info_schema.json#" 41 | } 42 | }, 43 | "relatedIdentifiers": { 44 | "description": "Related identifiers for the material.", 45 | "type": "array", 46 | "items": { 47 | "$ref": "related_identifier_info_schema.json#" 48 | } 49 | }, 50 | "name": { 51 | "description": "The name of the material.", 52 | "type": "string" 53 | }, 54 | "description": { 55 | "description": "A textual narrative comprised of one or more statements describing the material.", 56 | "type": "string" 57 | }, 58 | "types": { 59 | "description": "The types of material (e.g. cell line, tissue sample), ideally from a controlled vocabulary.", 60 | "type": "array", 61 | "items": { 62 | "$ref": "annotation_schema.json#" 63 | } 64 | }, 65 | "derivesFrom": { 66 | "description": "A material from which this material originated.", 67 | "type": "array", 68 | "items": { 69 | "anyOf": [ 70 | { 71 | "$ref": "material_schema.json#" 72 | }, 73 | { 74 | "$ref": "anatomical_part_schema.json#" 75 | } 76 | ] 77 | } 78 | }, 79 | "spatialCoverage": { 80 | "description": "The spatial coordinates denoting the geospatial origin of the material used to produce measurements part of the dataset.", 81 | "type": "array", 82 | "items": { 83 | "$ref": "place_schema.json#" 84 | } 85 | }, 86 | "bearerOfDisease": { 87 | "description": "The pathology affecting the material used in the study or refered to in the dataset (ideally from a controlled vocabulary/ontology).", 88 | "type": "array", 89 | "items": { 90 | "$ref": "disease_schema.json#" 91 | } 92 | }, 93 | "taxonomy": { 94 | "description": "The taxonomic information for this material (ideally specified from a controlled vocabulary/ontology).", 95 | "type": "array", 96 | "items": { 97 | "$ref": "taxonomic_info_schema.json#" 98 | } 99 | }, 100 | "involvedInBiologicalEntity": { 101 | "description": "A biological process (ideally specified from a controlled vocabulary/ontology) in which the material is involved.", 102 | "type": "array", 103 | "items": { 104 | "$ref": "biological_entity_schema.json#" 105 | } 106 | }, 107 | "characteristics": { 108 | "description": "The characteristic information or attributes denoting the material.", 109 | "type": "array", 110 | "items": { 111 | "oneOf": [ 112 | { 113 | "$ref": "dimension_schema.json#" 114 | }, 115 | { 116 | "$ref": "material_schema.json#" 117 | } 118 | ] 119 | } 120 | }, 121 | "consentInformation": { 122 | "description": "The consent information related to this material.", 123 | "type": "array", 124 | "items" : { 125 | "$ref" : "consent_info_schema.json#" 126 | } 127 | }, 128 | "roles" : { 129 | "description": "The roles played by a material.", 130 | "type": "array", 131 | "items": { 132 | "$ref": "annotation_schema.json#" 133 | } 134 | }, 135 | "dates": { 136 | "description": "Relevant dates, such as the date when the material was harvested, may be provided.", 137 | "type": "array", 138 | "items": { 139 | "$ref": "date_info_schema.json#" 140 | } 141 | }, 142 | "extraProperties": { 143 | "description": "Extra properties that do not fit in the previous specified attributes. ", 144 | "type": "array", 145 | "items": { 146 | "$ref": "category_values_pair_schema.json#" 147 | } 148 | } 149 | }, 150 | "additionalProperties": false, 151 | "required": ["name"] 152 | } 153 | -------------------------------------------------------------------------------- /molecular_entity_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/molecular_entity_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS molecular entity schema", 5 | "description": "A physical entity of molecular scales such as proteins, nucleic acids, chemical materials. They can be abiotic, biological or synthetic origin.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "MolecularEntity" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the molecular entity.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the molecular entity.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the molecular entity.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the molecular entity.", 51 | "type" : "string" 52 | }, 53 | "description": { 54 | "description": "A textual narrative comprised of one or more statements describing the molecular entity.", 55 | "type": "string" 56 | }, 57 | "taxonomy" : { 58 | "description": "The taxonomic information for this material (ideally specified from a controlled vocabulary/ontology).", 59 | "type": "array", 60 | "items": { 61 | "$ref": "taxonomic_info_schema.json#" 62 | } 63 | }, 64 | "characteristics" : { 65 | "description": "The characteristic information or attributes denoting the material.", 66 | "type" : "array", 67 | "items" : { 68 | "oneOf": [ 69 | {"$ref": "dimension_schema.json#"}, 70 | {"$ref": "material_schema.json#"} 71 | ] 72 | } 73 | }, 74 | "genomeLocations" : { 75 | "description": "The set of location information of a genetic element in a genome.", 76 | "type" : "array", 77 | "items" : { 78 | "$ref": "genome_location_schema.json#" 79 | } 80 | }, 81 | "structure": { 82 | "description": "The primary sequence of the molecular entity (e.g. inchi code;DNA sequence in FASTA format)", 83 | "type" : "string" 84 | }, 85 | "roles" : { 86 | "description": "The roles played by the molecular entity.", 87 | "type" : "array", 88 | "items" : { 89 | "$ref": "annotation_schema.json#" 90 | } 91 | }, 92 | "involvedInProcess" : { 93 | "description": "The molecular processes where the molecular entity is known to be involved in.", 94 | "type": "array", 95 | "items":{ 96 | "$ref" : "activity_schema.json#" 97 | } 98 | }, 99 | "relatedEntities": { 100 | "description": "Entities that are related to this molecular entity.", 101 | "type": "array", 102 | "items": { 103 | "type": "object", 104 | "properties": { 105 | "object": { 106 | "description": "The object of the relationship, i.e. the representation or identifier of the related enttity", 107 | "anyOf": [ 108 | { 109 | "type": "object" 110 | }, 111 | { 112 | "type": "string" 113 | } 114 | ] 115 | }, 116 | "relation": { 117 | "description": "The type of the relationship corresponding to this molecular entity.", 118 | "$ref": "annotation_schema.json#" 119 | }, 120 | "resultingFrom": { 121 | "description": "The activity (or process) that gave origin at the relationship between this molecular entity and the external entity.", 122 | "$ref": "activity_schema.json#" 123 | }, 124 | "relationEvidence": { 125 | "type": "array", 126 | "items": { 127 | "type": "object", 128 | "properties": { 129 | "evidenceCodes": { 130 | "description": "An array of labels and ideally an ontology term IRI (e.g. for the Evidence & Conclusion Ontology - ECO) indicating the evidence for the relationship between the molecular entity and the external entity", 131 | "type": "array", 132 | "items": { 133 | "$ref": "annotation_schema.json#" 134 | } 135 | }, 136 | "publications": { 137 | "description": "The list of publications providing evidence of the relationship.", 138 | "type": "array", 139 | "items": { 140 | "$ref": "publication_schema.json#" 141 | } 142 | }, 143 | "dateEstablished": { 144 | "description": "The date in which the evidence of the relationship was established.", 145 | "$ref": "date_info_schema.json#" 146 | } 147 | } 148 | } 149 | } 150 | } 151 | } 152 | }, 153 | "dates" : { 154 | "description": "Relevant dates for the molecular entity, a date must be added, e.g. creation date, annotation date or last modification date should be added. a type should always be provided", 155 | "type" : "array", 156 | "items" : { 157 | "$ref" : "date_info_schema.json#" 158 | } 159 | }, 160 | "extraProperties": { 161 | "description": "Extra properties that do not fit in the previous specified attributes. ", 162 | "type": "array", 163 | "items": { 164 | "$ref" : "category_values_pair_schema.json#" 165 | } 166 | } 167 | }, 168 | "additionalProperties": false, 169 | "required": [ "name" ] 170 | } 171 | -------------------------------------------------------------------------------- /organization_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/organization_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS organization schema", 5 | "description": "Legal or physical entity corresponding to a business or administration.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Organization" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the organization.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the organization.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the organization.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the organization.", 51 | "type" : "string" 52 | }, 53 | "abbreviation": { 54 | "description": "The shortname, abbreviation associated to the organization.", 55 | "type" : "string" 56 | }, 57 | "email": { 58 | "description": "An electronic mail address for the organization.", 59 | "type" : "string", 60 | "format": "email" 61 | }, 62 | "phoneNumber": { 63 | "description": "A phone number for the organization.", 64 | "type" : "string" 65 | }, 66 | "location": { 67 | "description": "The place where the organization is located.", 68 | "$ref" : "place_schema.json#" 69 | }, 70 | "roles" : { 71 | "description": "The roles of the organization (ideally from a controlled vocabulary/ontology).", 72 | "type" : "array", 73 | "items" : { 74 | "$ref" : "annotation_schema.json#" 75 | } 76 | }, 77 | "extraProperties": { 78 | "description": "Extra properties that do not fit in the previous specified attributes. ", 79 | "type": "array", 80 | "items": { 81 | "$ref" : "category_values_pair_schema.json#" 82 | } 83 | } 84 | }, 85 | "additionalProperties": false, 86 | "required": [ "name" ] 87 | } -------------------------------------------------------------------------------- /person_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/person_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS person schema", 5 | "description": "A human being", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Person" 30 | }, 31 | "identifier": { 32 | "description": "Primary identifier for the person.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the person.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the person.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "fullName": { 50 | "description": "The first name, any middle names, and surname of a person.", 51 | "type" : "string" 52 | }, 53 | "firstName": { 54 | "description": "The given name of the person.", 55 | "type" : "string" 56 | }, 57 | "middleInitial": { 58 | "description": "The first letter of the person's middle name.", 59 | "type" : "string" 60 | }, 61 | "lastName": { 62 | "description": "The person's family name.", 63 | "type" : "string" 64 | }, 65 | "title": { 66 | "description": "The person's title, usually a professional designation such as Dr or Prof.", 67 | "type": "string" 68 | }, 69 | "email": { 70 | "description": "An electronic mail address for the person.", 71 | "type" : "string", 72 | "format": "email" 73 | }, 74 | "phoneNumber": { 75 | "description": "A phone number for the person.", 76 | "type" : "string" 77 | }, 78 | "affiliations" : { 79 | "description": "The organizations to which the person is associated with.", 80 | "type" : "array", 81 | "items" : { 82 | "$ref" : "organization_schema.json#" 83 | } 84 | }, 85 | "location": { 86 | "description": "The place where the person is located.", 87 | "$ref" : "place_schema.json#" 88 | }, 89 | "roles" : { 90 | "description": "The roles assumed by a person, ideally from a controlled vocabulary/ontology.", 91 | "type" : "array", 92 | "items" : { 93 | "$ref" : "annotation_schema.json#" 94 | } 95 | }, 96 | "extraProperties": { 97 | "description": "Extra properties that do not fit in the previous specified attributes. ", 98 | "type": "array", 99 | "items": { 100 | "$ref" : "category_values_pair_schema.json#" 101 | } 102 | } 103 | }, 104 | "additionalProperties": false, 105 | "required" : [ "fullName" ] 106 | } -------------------------------------------------------------------------------- /place_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/place_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS place schema", 5 | "description": "A spatially bounded entity.", 6 | "comment": "It corresponds to Feature in GeoJSON, https://tools.ietf.org/html/rfc7946, geoLocation in DataCite,http://schema.datacite.org/meta/kernel-4.0/ and Place in schema.org", 7 | "type": "object", 8 | "definitions": { 9 | "position": { 10 | "description": "A GeoJSON Position", 11 | "type": "array", 12 | "minItems": 2, 13 | "items": { "type": "number" } 14 | } 15 | 16 | }, 17 | "properties": { 18 | "@context": { 19 | "description": "The JSON-LD context", 20 | "anyOf": [ 21 | { 22 | "type": "string" 23 | }, 24 | { 25 | "type": "object" 26 | }, 27 | { 28 | "type": "array" 29 | } 30 | ] 31 | }, 32 | "@id": { 33 | "description": "The JSON-LD identifier", 34 | "type": "string", "format": "uri" 35 | }, 36 | "@type": { 37 | "description": "The JSON-LD type", 38 | "type": "string", 39 | "const": "Place" 40 | }, 41 | "identifier": { 42 | "description": "Primary identifier for the place.", 43 | "$ref": "identifier_info_schema.json#" 44 | }, 45 | "alternateIdentifiers": { 46 | "description": "Alternate identifiers for the place.", 47 | "type": "array", 48 | "items": { 49 | "$ref": "alternate_identifier_info_schema.json#" 50 | } 51 | }, 52 | "relatedIdentifiers": { 53 | "description": "Related identifiers for the place.", 54 | "type": "array", 55 | "items": { 56 | "$ref": "related_identifier_info_schema.json#" 57 | } 58 | }, 59 | "name": { 60 | "description": "The name of the place.", 61 | "type": "string" 62 | }, 63 | "description": { 64 | "description": "A textual narrative comprised of one or more statements describing the place.", 65 | "type": "string" 66 | }, 67 | "postalAddress": { 68 | "description": "A physical street address.", 69 | "type": "string" 70 | }, 71 | "geometry": { 72 | "description": "A region of a space.", 73 | "type": "string", 74 | "comment": "It follows GeoJSON specification https://tools.ietf.org/html/rfc7946", 75 | "enum": [ "Point", "MultiPoint", "LineString", "MultiLineString", "Polygon", "MultiPolygon", "GeometryCollection"] 76 | }, 77 | "coordinates": { 78 | "description": "A non-empty list of GeoJSON positions.", 79 | "type": "array", 80 | "minItems": 1, 81 | "items": { "$ref": "#/definitions/position" } 82 | } 83 | }, 84 | "additionalProperties": false 85 | } -------------------------------------------------------------------------------- /project_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/project_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS project schema", 5 | "description": "An object to describe an research program supported investigation and studies through funding tools", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Project" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the project.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the project.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the project.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "title": { 50 | "description": "The name of the project.", 51 | "type": "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the project.", 55 | "type" : "string" 56 | }, 57 | "acronym": { 58 | "description": "The short form of the project name.", 59 | "type": "string" 60 | }, 61 | "types": { 62 | "description": "The types of project (e.g. safety assessment, drug discovery, innovative action), see IMI document for more examples.", 63 | "type": "array", 64 | "items": { 65 | "$ref": "annotation_schema.json#" 66 | } 67 | }, 68 | "startDate": { 69 | "description": "A timestamp to record the starting point of the activity.", 70 | "$ref": "date_info_schema.json#" 71 | }, 72 | "endDate": { 73 | "description": "A timestamp to record the end point of the activity.", 74 | "$ref": "date_info_schema.json#" 75 | }, 76 | "dates" : { 77 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 78 | "type" : "array", 79 | "items" : { 80 | "$ref" : "date_info_schema.json#" 81 | } 82 | }, 83 | "projectAssets":{ 84 | "description": "The person(s) or organisation(s) responsible for executing the project.", 85 | "type": "array", 86 | "items": { 87 | "anyOf": [ 88 | { 89 | "$ref": "study_schema.json#" 90 | }, 91 | { 92 | "$ref": "dataset_schema.json#" 93 | } 94 | ] 95 | } 96 | }, 97 | 98 | "projectLeads": { 99 | "description": "The person(s) or organisation(s) responsible for executing the project.", 100 | "type": "array", 101 | "items": { 102 | "anyOf": [ 103 | { 104 | "$ref": "person_schema.json#" 105 | }, 106 | { 107 | "$ref": "organization_schema.json#" 108 | } 109 | ] 110 | } 111 | }, 112 | "keywords": { 113 | "description": "Tags associated with the activity, which will help in its discovery.", 114 | "type": "array", 115 | "items": { 116 | "$ref": "annotation_schema.json#" 117 | } 118 | }, 119 | "fundedBy" : { 120 | "description": "The grant(s) which funded and supported the work reported by the dataset.", 121 | "type" : "array", 122 | "items" : { 123 | "$ref" : "grant_schema.json#" 124 | } 125 | }, 126 | "projectWebsite" : { 127 | "description": "The URL of the project website", 128 | "type": "string", 129 | "format": "uri" 130 | }, 131 | "primaryPublications" : { 132 | "description": "The primary publication(s) associated with the project.", 133 | "type" : "array", 134 | "items" : { 135 | "$ref" : "publication_schema.json#" 136 | } 137 | }, 138 | "citations" : { 139 | "description": "The publication(s) that cite this project.", 140 | "type" : "array", 141 | "items" : { 142 | "$ref" : "publication_schema.json#" 143 | } 144 | }, 145 | "citationCount": { 146 | "description": "The number of publications that cite this project", 147 | "type": "integer" 148 | }, 149 | "extraProperties": { 150 | "description": "Extra properties that do not fit in the previous specified attributes. ", 151 | "type": "array", 152 | "items": { 153 | "$ref" : "category_values_pair_schema.json#" 154 | } 155 | } 156 | }, 157 | "additionalProperties": false, 158 | "required" : [ "title", "types", "projectLeads" ] 159 | } 160 | 161 | -------------------------------------------------------------------------------- /provenance_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/provenance_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "Internal DATS provenance schema", 5 | "description": "The provenance information kept in DataMed. This schema is for internal use in DataMed and not to be implemented by repositories.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Provenance" 30 | }, 31 | "transformationFile": { 32 | "description": "The DataMed transformation file describing the mapping between the original repository and DATS.", 33 | "type": "string" 34 | }, 35 | "ingestMethod": { 36 | "description": "The method used to ingest the dataset from the repository into DataMed.", 37 | "type": "string" 38 | }, 39 | "ingestTarget": { 40 | "description": "The location where the source files can be found, using the ingestMethod, to produce this DATS intance ingested in DataMed.", 41 | "type": "string" 42 | }, 43 | "filePattern": { 44 | "description": "A regular expression indicating the pattern of files considered during the ingestion process.", 45 | "type": "string" 46 | }, 47 | "ingestTimestamp": { 48 | "description": "A timestamp reporting when the ingestion occurred.", 49 | "type": "string" 50 | } 51 | }, 52 | "additionalProperties": false 53 | } 54 | -------------------------------------------------------------------------------- /publication_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/publication_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title" : "DATS publication schema", 5 | "description" : "A (digital) document made available by a publisher.", 6 | "type" : "object", 7 | "properties" : { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Publication" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the publication.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the publication.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the publication.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "title": { 50 | "description": "The name of the publication, usually one sentence or short description of the publication.", 51 | "type" : "string" 52 | }, 53 | "type" : { 54 | "description": "Publication type, ideally delegated to an external vocabulary/resource.", 55 | "$ref" : "annotation_schema.json#" 56 | }, 57 | "publicationVenue": { 58 | "description": "The name of the publication venue where the document is published if applicable.", 59 | "type": "string" 60 | }, 61 | "dates" : { 62 | "description": "Relevant dates, the date of the publication must be provided.", 63 | "type" : "array", 64 | "items": { 65 | "$ref" : "date_info_schema.json#" 66 | } 67 | }, 68 | "authors" : { 69 | "description": "The person(s) and/or organisation(s) responsible for the publication.", 70 | "type" : "array", 71 | "items" : { 72 | "oneOf": [ 73 | {"$ref" : "person_schema.json#"}, 74 | {"$ref" : "organization_schema.json#"} 75 | ] 76 | }, 77 | "minItems" : 1 78 | }, 79 | "authorsList": { 80 | "description": "The list of authors made available as a string (does not allow disambiguation).", 81 | "type": "string" 82 | }, 83 | "acknowledges" : { 84 | "description": "The grant(s) which funded and supported the work reported by the publication.", 85 | "type" : "array", 86 | "items" : { 87 | "$ref" : "grant_schema.json#" 88 | } 89 | }, 90 | "licenses" : { 91 | "description": "The terms of use of the publication.", 92 | "type" : "array", 93 | "items" : { 94 | "$ref" : "license_schema.json#" 95 | } 96 | }, 97 | "extraProperties": { 98 | "description": "Extra properties that do not fit in the previous specified attributes. ", 99 | "type": "array", 100 | "items": { 101 | "$ref" : "category_values_pair_schema.json#" 102 | } 103 | } 104 | }, 105 | "additionalProperties": false 106 | } 107 | -------------------------------------------------------------------------------- /related_identifier_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/related_identifier_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS related identifier information schema", 5 | "description": "Information about an idenfier of related resources.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "RelatedIdentifier" 30 | }, 31 | "identifier": { 32 | "description": "An identifier of a related resource.", 33 | "type" : "string" 34 | }, 35 | "identifierSource": { 36 | "description": "The identifier source represents information about the organisation/namespace responsible for minting the identifiers. It must be provided if the identifier is provided.", 37 | "type" : "string" 38 | }, 39 | "relationType": { 40 | "description": "The type of the relationship corresponding to this identifier.", 41 | "anyOf": [ 42 | { "type" : "string" }, 43 | { "type": "string", 44 | "format": "uri" 45 | }, 46 | { 47 | "$ref": "annotation_schema.json#" 48 | } 49 | ] 50 | } 51 | }, 52 | "additionalProperties": false 53 | } 54 | -------------------------------------------------------------------------------- /software_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/software_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS software schema", 5 | "description": "A digital entity containing sets of instructions and operation, which allows computation and operation of and by computer.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Software" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the software.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the software.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the software.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the software.", 51 | "type" : "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the software.", 55 | "type" : "string" 56 | }, 57 | "licenses" : { 58 | "description": "The terms of use of the software.", 59 | "type" : "array", 60 | "items" : { 61 | "$ref" : "license_schema.json#" 62 | } 63 | }, 64 | "version" : { 65 | "description": "A release point for the software.", 66 | "type" : "string" 67 | }, 68 | "dates" : { 69 | "description": "Relevant dates, e.g. the release date of the software, may be provided.", 70 | "type" : "array", 71 | "items": { 72 | "$ref" : "date_info_schema.json#" 73 | } 74 | }, 75 | "isUsedBy" : { 76 | "description": "The data acquisition activity that makes use of this software.", 77 | "type" : "array", 78 | "items" : { 79 | "oneOf": [ 80 | {"$ref": "data_acquisition_schema.json#"}, 81 | {"$ref": "data_analysis_schema.json#"} 82 | ] 83 | } 84 | }, 85 | "manufacturer" : { 86 | "description": "The person or organisation that produced the software.", 87 | "type" : "array", 88 | "items" : { 89 | "oneOf": [ 90 | {"$ref" : "person_schema.json#"}, 91 | {"$ref" : "organization_schema.json#"} 92 | ] 93 | } 94 | }, 95 | "extraProperties": { 96 | "description": "Extra properties that do not fit in the previous specified attributes. ", 97 | "type": "array", 98 | "items": { 99 | "$ref" : "category_values_pair_schema.json#" 100 | } 101 | } 102 | }, 103 | "additionalProperties": false, 104 | "required":[ "name" ] 105 | } 106 | -------------------------------------------------------------------------------- /study_group_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/study_group_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS study group schema", 5 | "description": "A collection of entities known as study subjects based on a set of specified criteria and rules; synonyms: population, cohort.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "StudyGroup" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the study group.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the study group.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the study group", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the study group.", 51 | "type" : "string" 52 | }, 53 | "keywords": { 54 | "description": "a set of annotations to characterize the study group.", 55 | "type": "array", 56 | "items": { 57 | "$ref": "annotation_schema.json#" 58 | } 59 | }, 60 | "size": { 61 | "description": "The number of members in the group.", 62 | "oneOf": [ 63 | { 64 | "type": "string" 65 | }, 66 | { 67 | "type": "number", 68 | "minimum": 0 69 | } 70 | ] 71 | }, 72 | "members" : { 73 | "description": "The entities making up the study group.", 74 | "type" : "array", 75 | "items" : { 76 | "$ref" : "material_schema.json#" 77 | } 78 | }, 79 | "characteristics" : { 80 | "description": "The characteristic information or attributes associated with the study group.", 81 | "type" : "array", 82 | "items" : { 83 | "$ref": "dimension_schema.json#" 84 | } 85 | }, 86 | "selectionCriteria": { 87 | "description": "The attributes and values that the material should meet in order to be part of the group.", 88 | "type": "array", 89 | "items": { 90 | "anyOf": [ 91 | { "$ref": "annotation_schema.json#"}, 92 | { "$ref": "category_values_pair_schema.json#"} 93 | ] 94 | } 95 | }, 96 | "consentInformation": { 97 | "description": "The consent information related to this study group.", 98 | "type": "array", 99 | "items" : { 100 | "$ref" : "consent_info_schema.json#" 101 | } 102 | }, 103 | "extraProperties": { 104 | "description": "Extra properties that do not fit in the previous specified attributes. ", 105 | "type": "array", 106 | "items": { 107 | "$ref" : "category_values_pair_schema.json#" 108 | } 109 | } 110 | }, 111 | "additionalProperties": false, 112 | "required": [ "name" ] 113 | } -------------------------------------------------------------------------------- /study_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/study_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS study schema", 5 | "description": "Process to acquire data on a sample and attempt to draw conclusions about the population the sample has been selected from, executing a plan and design.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "Study" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the study.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the activity.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the activity.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The name of the activity, usually one sentece or short description of the study.", 51 | "type": "string" 52 | }, 53 | "description" : { 54 | "description": "A textual narrative comprised of one or more statements describing the study.", 55 | "type" : "string" 56 | }, 57 | "acronym": { 58 | "description": "The short form of the study, usually related to the project name.", 59 | "type": "string" 60 | }, 61 | "types": { 62 | "description": "The types of study (e.g. intervention or observation or meta-analysis or clinical trials, or behavioural study, or the study design).", 63 | "type": "array", 64 | "items": { 65 | "$ref": "annotation_schema.json#" 66 | } 67 | }, 68 | "startDate": { 69 | "description": "A timestamp to record the starting point of the activity.", 70 | "$ref": "date_info_schema.json#" 71 | }, 72 | "endDate": { 73 | "description": "A timestamp to record the end point of the activity.", 74 | "$ref": "date_info_schema.json#" 75 | }, 76 | "dates" : { 77 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 78 | "type" : "array", 79 | "items" : { 80 | "$ref" : "date_info_schema.json#" 81 | } 82 | }, 83 | "duration": { 84 | "description": "The time during which the activity takes place.", 85 | "type": "string" 86 | }, 87 | "location": { 88 | "description": "The location where the activity takes place.", 89 | "$ref": "place_schema.json#" 90 | }, 91 | "performedBy": { 92 | "description": "The person(s) or organisation(s) responsible for executing the process.", 93 | "type": "array", 94 | "items": { 95 | "anyOf": [ 96 | { 97 | "$ref": "person_schema.json#" 98 | }, 99 | { 100 | "$ref": "organization_schema.json#" 101 | } 102 | ] 103 | } 104 | }, 105 | "keywords": { 106 | "description": "Tags associated with the activity, which will help in its discovery.", 107 | "type": "array", 108 | "items": { 109 | "$ref": "annotation_schema.json#" 110 | } 111 | }, 112 | "input": { 113 | "description": "The entities used as input.", 114 | "type": "array", 115 | "items": { 116 | "anyOf": [ 117 | { 118 | "$ref": "dataset_schema.json#" 119 | }, 120 | { 121 | "$ref": "material_schema.json#" 122 | } 123 | ] 124 | } 125 | }, 126 | "output": { 127 | "description": "The entities resulting from applying the activity.", 128 | "type": "array", 129 | "items": { 130 | "anyOf": [ 131 | { 132 | "$ref": "dataset_schema.json#" 133 | }, 134 | { 135 | "$ref": "material_schema.json#" 136 | } 137 | ] 138 | } 139 | }, 140 | "schedulesActivity": { 141 | "description": "The activities scheduled by the study.", 142 | "type": "array", 143 | "items": { 144 | "anyOf":[ 145 | {"$ref": "activity_schema.json#"}, 146 | {"$ref": "data_acquisition_schema.json#"}, 147 | {"$ref": "data_analysis_schema.json#"} 148 | ] 149 | } 150 | }, 151 | "schedulesDataAcquisition": { 152 | "description": "The kind of techniques and response variables used during a study for acquiring data.", 153 | "type": "array", 154 | "items": { 155 | "$ref": "data_acquisition_schema.json#" 156 | }, 157 | "minItems": 1 158 | }, 159 | "selectionCriteria": { 160 | "description": "The attributes and values that the material should meet in order to be part of the group.", 161 | "type": "array", 162 | "items": { 163 | "anyOf": [ 164 | { "$ref": "annotation_schema.json#"}, 165 | { "$ref": "category_values_pair_schema.json#"} 166 | ] 167 | } 168 | }, 169 | "studyGroups": { 170 | "description": "The different study groups associated with a study.", 171 | "type": "array", 172 | "items": { 173 | "$ref": "study_group_schema.json#" 174 | } 175 | }, 176 | "characteristics" : { 177 | "description": "The characteristic information or attributes associated with the study.", 178 | "type" : "array", 179 | "items" : { 180 | "$ref": "dimension_schema.json#" 181 | } 182 | }, 183 | "usesReagent": { 184 | "description": "The materials that are used as reagents (but not subjects) of the study.", 185 | "type": "array", 186 | "items": { 187 | "$ref": "material_schema.json#" 188 | } 189 | }, 190 | "isAboutBiologicalEntity": { 191 | "description": "The biological entities relevant to the study, ideally from a controlled vocabulary/ontology such as Gene Ontology.", 192 | "type": "array", 193 | "items": { 194 | "$ref": "biological_entity_schema.json#" 195 | } 196 | }, 197 | "extraProperties": { 198 | "description": "Extra properties that do not fit in the previous specified attributes. ", 199 | "type": "array", 200 | "items": { 201 | "$ref" : "category_values_pair_schema.json#" 202 | } 203 | } 204 | }, 205 | "additionalProperties": false, 206 | "required": ["name"] 207 | 208 | } -------------------------------------------------------------------------------- /taxonomic_info_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/taxonomic_info_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS organism schema", 5 | "description": "A living entity.", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", "format": "uri" 25 | }, 26 | "@type": { 27 | "description": "The JSON-LD type", 28 | "type": "string", 29 | "const": "TaxonomicInformation" 30 | }, 31 | "identifier": { 32 | "description": "The identifier of the taxonomic information.", 33 | "$ref": "identifier_info_schema.json#" 34 | }, 35 | "alternateIdentifiers": { 36 | "description": "Alternate identifiers for the organism.", 37 | "type": "array", 38 | "items": { 39 | "$ref": "alternate_identifier_info_schema.json#" 40 | } 41 | }, 42 | "relatedIdentifiers": { 43 | "description": "Related identifiers for the organism.", 44 | "type": "array", 45 | "items": { 46 | "$ref": "related_identifier_info_schema.json#" 47 | } 48 | }, 49 | "name": { 50 | "description": "The scientific name of an organism.", 51 | "type" : "string" 52 | }, 53 | "extraProperties": { 54 | "description": "Extra properties that do not fit in the previous specified attributes. ", 55 | "type": "array", 56 | "items": { 57 | "$ref" : "category_values_pair_schema.json#" 58 | } 59 | } 60 | }, 61 | "additionalProperties": false, 62 | "required" : ["name"] 63 | } -------------------------------------------------------------------------------- /treatment_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$id": "https://w3id.org/dats/schema/treatment_schema.json", 3 | "$schema": "http://json-schema.org/draft-07/schema", 4 | "title": "DATS treatment schema", 5 | "description": "Process, part of a study, consisting in exposing participants to the study to different conditions or group those participants into different categories based on specific criteria and compare their outcomes", 6 | "type": "object", 7 | "properties": { 8 | "@context": { 9 | "description": "The JSON-LD context", 10 | "anyOf": [ 11 | { 12 | "type": "string" 13 | }, 14 | { 15 | "type": "object" 16 | }, 17 | { 18 | "type": "array" 19 | } 20 | ] 21 | }, 22 | "@id": { 23 | "description": "The JSON-LD identifier", 24 | "type": "string", 25 | "format": "uri" 26 | }, 27 | "@type": { 28 | "description": "The JSON-LD type", 29 | "type": "string", 30 | "const": "Treatment" 31 | }, 32 | "identifier": { 33 | "description": "The identifier of the treatment.", 34 | "$ref": "identifier_info_schema.json#" 35 | }, 36 | "alternateIdentifiers": { 37 | "description": "Alternate identifiers for the activity.", 38 | "type": "array", 39 | "items": { 40 | "$ref": "alternate_identifier_info_schema.json#" 41 | } 42 | }, 43 | "relatedIdentifiers": { 44 | "description": "Related identifiers for the activity.", 45 | "type": "array", 46 | "items": { 47 | "$ref": "related_identifier_info_schema.json#" 48 | } 49 | }, 50 | "name": { 51 | "description": "The name of the activity, usually one sentece or short description of the treatment.", 52 | "type" : "string" 53 | }, 54 | "description" : { 55 | "description": "A textual narrative comprised of one or more statements describing the treatment.", 56 | "type" : "string" 57 | }, 58 | "startDate": { 59 | "description": "A timestamp to record the starting point of the activity.", 60 | "$ref": "date_info_schema.json#" 61 | }, 62 | "endDate": { 63 | "description": "A timestamp to record the end point of the activity.", 64 | "$ref": "date_info_schema.json#" 65 | }, 66 | "dates" : { 67 | "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.", 68 | "type" : "array", 69 | "items" : { 70 | "$ref" : "date_info_schema.json#" 71 | } 72 | }, 73 | "duration": { 74 | "description": "The time during which the activity takes place.", 75 | "type" : "string" 76 | }, 77 | "location" : { 78 | "description": "The location where the activity takes place.", 79 | "$ref" : "place_schema.json#" 80 | }, 81 | "performedBy" : { 82 | "description": "The person(s) or organisation(s) responsible for executing the process.", 83 | "type" : "array", 84 | "items" : { 85 | "anyOf": [ 86 | {"$ref" : "person_schema.json#"}, 87 | {"$ref" : "organization_schema.json#"} 88 | ] 89 | } 90 | }, 91 | 92 | "keywords": { 93 | "description": "Tags associated with the activity, which will help in its discovery.", 94 | "type": "array", 95 | "items": { 96 | "$ref" : "annotation_schema.json#" 97 | } 98 | }, 99 | "input" : { 100 | "description": "The entities used as input.", 101 | "type": "array", 102 | "items":{ 103 | "$ref" : "study_group_schema.json#" 104 | }, 105 | "minItems": 1 106 | }, 107 | "output" : { 108 | "description": "The entities resulting from applying the activity.", 109 | "type": "array", 110 | "items":{ 111 | "$ref" : "study_group_schema.json#" 112 | } 113 | }, 114 | "agent": { 115 | "description": "The nature of the perturbation or intervention used in the treatment.", 116 | "oneOf": [ 117 | {"$ref": "molecular_entity_schema.json#"}, 118 | {"$ref": "material_schema.json#"}, 119 | {"$ref": "activity_schema.json#"}, 120 | { 121 | "type": "string", 122 | "format": "uri" 123 | } 124 | ] 125 | }, 126 | "intensity": { 127 | "description": "A measurement about how acute the perturbation is.", 128 | "type": "array", 129 | "items": { 130 | "oneOf": [ 131 | {"type": "string"}, 132 | {"type": "number"} 133 | ] 134 | } 135 | }, 136 | "concomitance": { 137 | "description": "A boolean value to indicate if more that one perturbations are applied at the same time to the same subject.", 138 | "type": "boolean" 139 | }, 140 | "order": { 141 | "description": "The rank in which perturbations are being applied to study subjects.", 142 | "type": "number" 143 | }, 144 | "extraProperties": { 145 | "description": "Extra properties that do not fit in the previous specified attributes. ", 146 | "type": "array", 147 | "items": { 148 | "$ref" : "category_values_pair_schema.json#" 149 | } 150 | } 151 | }, 152 | "additionalProperties": false, 153 | "required": [ "name", "input" ] 154 | } 155 | --------------------------------------------------------------------------------