diff --git a/bioschemasdrafts.json b/bioschemasdrafts.json index a4a4ac0..cc33ebb 100644 --- a/bioschemasdrafts.json +++ b/bioschemasdrafts.json @@ -21447,6 +21447,34 @@ } ] }, + { + "@id": "bioschemasdrafts:codeRepository", + "@type": "rdf:Property", + "rdfs:comment": "Link to the source code repository of the tool.", + "rdfs:label": "codeRepository", + "schema:domainIncludes": { + "@id": "bioschemasdrafts:ComputationalTool" + }, + "schema:rangeIncludes": [ + { + "@id": "schema:URL" + } + ] + }, + { + "@id": "bioschemasdrafts:programmingLanguage", + "rdfs:comment": "The main programming language(s) used to build or execute the tool. Please use terms from the ‘Programming language’ table in the Bio.Tools documentation.", + "@type": "rdf:Property", + "rdfs:label": "programmingLanguage", + "schema:domainIncludes": { + "@id": "bioschemasdrafts:ComputationalTool" + }, + "schema:rangeIncludes": [ + { + "@id": "schema:ComputerLanguage" + } + ] + }, { "@id": "bioschemasdrafts:applicationSubCategory", "@type": "rdf:Property", diff --git a/bioschemastypesdrafts.json b/bioschemastypesdrafts.json index 418eb83..83b779a 100644 --- a/bioschemastypesdrafts.json +++ b/bioschemastypesdrafts.json @@ -10,7 +10,7 @@ "bioschemastypesdrafts": "https://discovery.biothings.io/view/bioschemastypesdrafts/", "bioschemasdeprecated": "https://discovery.biothings.io/view/bioschemasdeprecated/", "dct": "http://purl.org/dc/terms/", - "@dateModified": "07/12/2023, 15:13:14" + "@dateModified": "12/14/2023, 09:09:05" }, "@graph": [ { @@ -23,8 +23,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/RNA/jsonld/type/RNA_v0.1-DRAFT-2019_06_21.json", - "https://bioschemas.org/types/RNA/0.1-DRAFT-2019_06_21" + "https://bioschemas.org/types/RNA/0.1-DRAFT-2019_06_21", + "https://github.com/BioSchemas/specifications/blob/master/RNA/jsonld/type/RNA_v0.1-DRAFT-2019_06_21.json" ] }, { @@ -37,8 +37,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/SequenceRange/jsonld/type/SequenceRange_v0.1-DRAFT-2019_06_21.json", - "https://bioschemas.org/types/SequenceRange/0.1-DRAFT-2019_06_21" + "https://bioschemas.org/types/SequenceRange/0.1-DRAFT-2019_06_21", + "https://github.com/BioSchemas/specifications/blob/master/SequenceRange/jsonld/type/SequenceRange_v0.1-DRAFT-2019_06_21.json" ] }, { @@ -51,8 +51,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/TaxonName/jsonld/type/TaxonName_v0.1-DRAFT.json", - "https://bioschemas.org/types/TaxonName/0.1-DRAFT-TYPE" + "https://bioschemas.org/types/TaxonName/0.1-DRAFT-TYPE", + "https://github.com/BioSchemas/specifications/blob/master/TaxonName/jsonld/type/TaxonName_v0.1-DRAFT.json" ] }, { @@ -79,22 +79,25 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/Study/jsonld/type/Study_v0.3-DRAFT.json", - "https://bioschemas.org/types/Study/0.3-DRAFT" + "https://bioschemas.org/types/Study/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/blob/master/Study/jsonld/type/Study_v0.3-DRAFT.json" ] }, { "@id": "bioschemastypesdrafts:LabProtocol", "@type": "rdfs:Class", - "rdfs:comment": "An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas. Version 0.3-DRAFT-2019_06_20", + "rdfs:comment": "An experimental lab protocol is a sequence of tasks and operations executed to perform experimental research in wet- or dry-labs. \n\nVersion: v0.3 \n\nChangelog: \n* Use HowTo as parent class rather than CreativeWork \n* Align properties to HowTo \n* Align properties from the previous version type (v0.3-DRAFT-2019_06_20) and current draft profile (v0.7-DRAFT) \n\nPrepared by: Leyla Jael Castro", "rdfs:label": "LabProtocol", "rdfs:subClassOf": { - "@id": "schema:CreativeWork" + "@id": "schema:HowTo" }, + "schemaVersion": [ + "https://schema.org/docs/releases.html#v23.0" + ], "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/LabProtocol/0.3-DRAFT-2019_06_20", - "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.3-DRAFT-2019_06_20.json" + "https://bioschemas.org/types/LabProtocol/0.4-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.4-DRAFT.jsonld" ] }, { @@ -107,8 +110,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/Phenotype/0.3-DRAFT-2020_06_07", - "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/type/Phenotype_v0.3-DRAFT-2020_06_07.json" + "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/type/Phenotype_v0.3-DRAFT-2020_06_07.json", + "https://bioschemas.org/types/Phenotype/0.3-DRAFT-2020_06_07" ] }, { @@ -135,8 +138,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/Taxon/0.4-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/type/Taxon_v0.4-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/type/Taxon_v0.4-DRAFT.json", + "https://bioschemas.org/types/Taxon/0.4-DRAFT" ] }, { @@ -214,8 +217,8 @@ "@type": "rdfs:Class", "rdfs:comment": "Protein is here used in its widest possible definition, as classes of amino acid based molecules. Amyloid-beta Protein in human (UniProt P05067), eukaryota (e.g. an OrthoDB group) or even a single molecule that one can point to are all of type schema:Protein. A protein can thus be a subclass of another protein, e.g. schema:Protein as a UniProt record can have multiple isoforms inside it which would also be schema:Protein. They can be imagined, synthetic, hypothetical or naturally occurring. This version has been added to schema.org as a pending type.", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/Protein/jsonld/type/Protein_v0.4-DRAFT.json", - "https://bioschemas.org/types/Protein/0.4-DRAFT" + "https://bioschemas.org/types/Protein/0.4-DRAFT", + "https://github.com/BioSchemas/specifications/blob/master/Protein/jsonld/type/Protein_v0.4-DRAFT.json" ], "rdfs:label": "Protein", "rdfs:subClassOf": { @@ -444,198 +447,202 @@ ] }, { - "@id": "bioschemastypesdrafts:executionTime", + "@id": "bioschemastypes:input", "@type": "rdf:Property", - "rdfs:comment": "The time it takes to actually carry out the protocol in ISO 8601 date format.", - "rdfs:label": "executionTime", + "rdfs:comment": "Specification of a consumed input.", + "rdfs:label": "input", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:Duration" + "@id": "bioschemastypes:FormalParameter" } ] }, { - "@id": "bioschemastypesdrafts:labEquipment", + "@id": "bioschemastypes:output", "@type": "rdf:Property", - "rdfs:comment": "For LabProtocols it would be a laboratory equipment use by a person to follow one or more steps described in this LabProtocol.", - "rdfs:label": "labEquipment", + "rdfs:comment": "Specification of a produced output.", + "rdfs:label": "output", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:DefinedTerm" - }, - { - "@id": "schema:Text" - }, - { - "@id": "schema:URL" + "@id": "bioschemastypes:FormalParameter" } ] }, { - "@id": "bioschemastypesdrafts:protocolAdvantage", + "@id": "bioschemastypesdrafts:intendedUse", "@type": "rdf:Property", - "rdfs:comment": "Situations where the Protocol has been successfully employed.", - "rdfs:label": "protocolAdvantage", + "rdfs:comment": "Purpose and intended use stated to enable users to make a decision as to the suitability of this creative work (e.g., lab protocol, machine learning model, software) to their experimental problem or own use case.", + "rdfs:label": "intendedUse", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:CreativeWork" + "@id": "schema:Text" + }, + { + "@id": "schema:URL" + }, + { + "@id": "schema:DefinedTerm" } ] }, { - "@id": "bioschemastypesdrafts:protocolApplication", + "@id": "bioschemastypesdrafts:ethicalLegalSocial", "@type": "rdf:Property", - "rdfs:comment": "Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc.", - "rdfs:label": "protocolApplication", + "rdfs:comment": "Considerations wrt ethical, legal and social aspects.", + "rdfs:label": "ethicalLegalSocial", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:CreativeWork" + "@id": "schema:Text" } ] }, { - "@id": "bioschemastypesdrafts:protocolLimitation", + "@id": "bioschemastypesdrafts:computationalTool", "@type": "rdf:Property", - "rdfs:comment": "Situations where the Protocol would be unreliable or otherwise unsuccessful.", - "rdfs:label": "protocolLimitation", + "rdfs:comment": "Computational tool or workflow used to complete a part of this protocol.", + "rdfs:label": "computationalTool", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:CreativeWork" + "@id": "bioschemastypes:ComputationalWorkflow" + }, + { + "@id": "schema:SoftwareApplication" + }, + { + "@id": "schema:SoftwareSourceCode" } ] }, { - "@id": "bioschemastypesdrafts:protocolOutcome", + "@id": "bioschemastypesdrafts:sample", "@type": "rdf:Property", - "rdfs:comment": "Outcome or expected result by a protocol execution.", - "rdfs:label": "protocolOutcome", + "rdfs:comment": "Sample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used.", + "rdfs:label": "sample", "schema:domainIncludes": { "@id": "bioschemastypesdrafts:LabProtocol" }, "schema:rangeIncludes": [ { - "@id": "schema:CreativeWork" + "@id": "schema:Thing" } ] }, { - "@id": "bioschemastypesdrafts:purpose", + "@id": "bioschemastypesdrafts:labEquipment", "@type": "rdf:Property", - "rdfs:comment": "A goal towards an action is taken. Can be concrete or abstract.", - "rdfs:label": "purpose", - "schema:domainIncludes": { - "@id": "bioschemastypesdrafts:LabProtocol" - }, + "rdfs:comment": "A laboratory equipment used by a person to follow one or more steps described in this LabProtocol.", + "rdfs:label": "labEquipment", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], "schema:rangeIncludes": [ { - "@id": "schema:MedicalDevicePurpose" + "@id": "schema:Text" }, { - "@id": "schema:Text" + "@id": "schema:URL" }, { - "@id": "schema:Thing" + "@id": "schema:DefinedTerm" } ] }, { - "@id": "bioschemastypesdrafts:reagent", + "@id": "bioschemastypesdrafts:protocolAdvantage", "@type": "rdf:Property", - "rdfs:comment": "Reagent used in the protocol. It can be a record in a Dataset describing the reagent or a BioChemEntity corresponding to the reagent or a URL pointing to the type of reagent used. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable (URL if possible).", - "rdfs:label": "reagent", - "schema:domainIncludes": { - "@id": "bioschemastypesdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:BioChemEntity" - }, + "rdfs:comment": "Situations where the LabProtocol has been successfully employed including advantageous elements (e.g. better yield, shorter running time).", + "rdfs:label": "protocolAdvantage", + "schema:domainIncludes": [ { - "@id": "schema:DefinedTerm" - }, + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], + "schema:rangeIncludes": [ { "@id": "schema:Text" }, { - "@id": "schema:URL" + "@id": "schema:CreativeWork" } ] }, { - "@id": "bioschemastypesdrafts:sampleUsed", + "@id": "bioschemastypesdrafts:protocolApplication", "@type": "rdf:Property", - "rdfs:comment": "Sample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used.", - "rdfs:label": "sampleUsed", - "schema:domainIncludes": { - "@id": "bioschemastypesdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ + "rdfs:comment": "Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc. ", + "rdfs:label": "protocolApplication", + "schema:domainIncludes": [ { - "@id": "schema:BioChemEntity" - }, + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], + "schema:rangeIncludes": [ { "@id": "schema:Text" }, { - "@id": "schema:URL" - }, - { - "@id": "schema:DefinedTerm" - }, - { - "@id": "bioschemastypes:BioSample" + "@id": "schema:CreativeWork" } ] }, { - "@id": "bioschemastypesdrafts:software", + "@id": "bioschemastypesdrafts:protocolLimitation", "@type": "rdf:Property", - "rdfs:comment": "Software or tool used as part of the lab protocol to complete a part of it.", - "rdfs:label": "software", - "schema:domainIncludes": { - "@id": "bioschemastypesdrafts:LabProtocol" - }, + "rdfs:comment": "Situations where the Protocol would be unreliable or otherwise unsuccessful", + "rdfs:label": "protocolLimitation", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], "schema:rangeIncludes": [ { - "@id": "schema:SoftwareApplication" + "@id": "schema:Text" + }, + { + "@id": "schema:CreativeWork" } ] }, { - "@id": "bioschemastypesdrafts:step", + "@id": "bioschemastypesdrafts:reagent", "@type": "rdf:Property", - "rdfs:comment": "A single step item (as HowToStep, text, document, video, etc.) or a HowToSection. Supersedes steps.", - "rdfs:label": "step", - "schema:domainIncludes": { - "@id": "bioschemastypesdrafts:LabProtocol" - }, + "rdfs:comment": "Reagents used in the protocol. DefinedTerm is preferred whenever possible, e.g., ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable. A reagent is defined as \u2018A substance used in a chemical reaction to detect, measure, examine, or produce other substances\u2019 in [CHEBI:33893](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33893).", + "rdfs:label": "reagent", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], "schema:rangeIncludes": [ { - "@id": "schema:CreativeWork" + "@id": "schema:BioChemEntity" }, { - "@id": "schema:HowToSection" + "@id": "schema:DefinedTerm" }, { - "@id": "schema:HowToStep" + "@id": "schema:Text" }, { - "@id": "schema:Text" + "@id": "schema:URL" } ] }, @@ -1134,96 +1141,64 @@ ] }, { - "@id": "bioschemastypesdrafts:additionalProperty", + "@id": "bioschemastypesdrafts:valueReference", "@type": "rdf:Property", - "rdfs:comment": "A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. https://schema.org/width, https://schema.org/color, https://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism. ", - "rdfs:label": "additionalProperty", + "rdfs:comment": "A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.", + "rdfs:label": "valueReference", "schema:domainIncludes": [ - { - "@id": "bioschemastypesdrafts:Study" - }, { "@id": "bioschemastypesdrafts:Phenotype" }, { - "@id": "bioschemastypesdrafts:Sample" + "@id": "bioschemastypesdrafts:SequenceAnnotation" } ], "schema:rangeIncludes": [ { - "@id": "schema:PropertyValue" - } - ] - }, - { - "@id": "bioschemastypesdrafts:hasSequenceAnnotation", - "@type": "rdf:Property", - "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity.", - "rdfs:label": "hasSequenceAnnotation", - "schema:domainIncludes": [ - { - "@id": "bioschemastypesdrafts:BioChemEntity" + "@id": "schema:DefinedTerm" }, { - "@id": "bioschemastypesdrafts:BioChemStructure" + "@id": "schema:Enumeration" }, { - "@id": "bioschemastypesdrafts:DNA" + "@id": "schema:PropertyValue" }, { - "@id": "bioschemastypesdrafts:Enzyme" - } - ], - "schema:rangeIncludes": [ - { - "@id": "schema:URL" + "@id": "schema:QualitativeValue" }, { - "@id": "bioschemastypesdrafts:SequenceAnnotation" - } - ] - }, - { - "@id": "bioschemastypesdrafts:creationMethod", - "@type": "rdf:Property", - "rdfs:comment": "Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.", - "rdfs:label": "creationMethod", - "schema:domainIncludes": [ - { - "@id": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "schema:QuantitativeValue" }, { - "@id": "bioschemastypesdrafts:BioChemStructure" - } - ], - "schema:rangeIncludes": [ - { - "@id": "schema:PropertyValue" + "@id": "schema:StructuredValue" }, { - "@id": "schema:Text" + "@id": "schema:URL" }, { - "@id": "schema:URL" + "@id": "schema:Text" } ] }, { - "@id": "bioschemastypesdrafts:sequenceLocation", + "@id": "bioschemastypesdrafts:encodesBioChemEntity", "@type": "rdf:Property", - "rdfs:comment": "A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.", - "rdfs:label": "sequenceLocation", + "rdfs:comment": "Another BioChemEntity encoded by this one. Inverse property: isEncodedByBioChemEntity.", + "rdfs:label": "encodesBioChemEntity", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "bioschemastypesdrafts:RNA" }, { - "@id": "bioschemastypesdrafts:BioChemStructure" + "@id": "bioschemastypesdrafts:DNA" + }, + { + "@id": "bioschemastypesdrafts:Gene" } ], "schema:rangeIncludes": [ { - "@id": "bioschemastypesdrafts:SequenceRange" + "@id": "bioschemastypes:BioChemEntity" } ] }, @@ -1247,42 +1222,43 @@ ] }, { - "@id": "bioschemastypesdrafts:valueReference", + "@id": "bioschemastypesdrafts:isMatchedBy", "@type": "rdf:Property", - "rdfs:comment": "A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.", - "rdfs:label": "valueReference", + "rdfs:comment": "A model matching this BioChemEntity.", + "rdfs:label": "isMatchedBy", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:Phenotype" + "@id": "bioschemastypesdrafts:BioChemStructure" }, { - "@id": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "bioschemastypesdrafts:Enzyme" } ], "schema:rangeIncludes": [ { - "@id": "schema:DefinedTerm" - }, - { - "@id": "schema:Enumeration" - }, - { - "@id": "schema:PropertyValue" - }, - { - "@id": "schema:QualitativeValue" - }, + "@id": "bioschemastypesdrafts:SequenceMatchingModel" + } + ] + }, + { + "@id": "bioschemastypesdrafts:additionalProperty", + "@type": "rdf:Property", + "rdfs:comment": "A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. https://schema.org/width, https://schema.org/color, https://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism. ", + "rdfs:label": "additionalProperty", + "schema:domainIncludes": [ { - "@id": "schema:QuantitativeValue" + "@id": "bioschemastypesdrafts:Study" }, { - "@id": "schema:StructuredValue" + "@id": "bioschemastypesdrafts:Phenotype" }, { - "@id": "schema:URL" - }, + "@id": "bioschemastypesdrafts:Sample" + } + ], + "schema:rangeIncludes": [ { - "@id": "schema:Text" + "@id": "schema:PropertyValue" } ] }, @@ -1309,35 +1285,69 @@ ] }, { - "@id": "bioschemastypesdrafts:isMatchedBy", + "@id": "bioschemastypesdrafts:taxonRank", "@type": "rdf:Property", - "rdfs:comment": "A model matching this BioChemEntity.", - "rdfs:label": "isMatchedBy", + "rdfs:comment": "The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary \u2013 (typically the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs). ", + "rdfs:label": "taxonRank", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:TaxonName" + }, + { + "@id": "bioschemastypesdrafts:Taxon" + } + ], + "schema:rangeIncludes": [ + { + "@id": "schema:PropertyValue" + }, + { + "@id": "schema:Text" + }, + { + "@id": "schema:URL" + } + ] + }, + { + "@id": "bioschemastypesdrafts:hasSequenceAnnotation", + "@type": "rdf:Property", + "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity.", + "rdfs:label": "hasSequenceAnnotation", "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:BioChemEntity" + }, { "@id": "bioschemastypesdrafts:BioChemStructure" }, + { + "@id": "bioschemastypesdrafts:DNA" + }, { "@id": "bioschemastypesdrafts:Enzyme" } ], "schema:rangeIncludes": [ { - "@id": "bioschemastypesdrafts:SequenceMatchingModel" + "@id": "schema:URL" + }, + { + "@id": "bioschemastypesdrafts:SequenceAnnotation" } ] }, { - "@id": "bioschemastypesdrafts:taxonRank", + "@id": "bioschemastypesdrafts:creationMethod", "@type": "rdf:Property", - "rdfs:comment": "The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary \u2013 (typically the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs). ", - "rdfs:label": "taxonRank", + "rdfs:comment": "Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.", + "rdfs:label": "creationMethod", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:TaxonName" + "@id": "bioschemastypesdrafts:SequenceAnnotation" }, { - "@id": "bioschemastypesdrafts:Taxon" + "@id": "bioschemastypesdrafts:BioChemStructure" } ], "schema:rangeIncludes": [ @@ -1353,24 +1363,21 @@ ] }, { - "@id": "bioschemastypesdrafts:encodesBioChemEntity", + "@id": "bioschemastypesdrafts:sequenceLocation", "@type": "rdf:Property", - "rdfs:comment": "Another BioChemEntity encoded by this one. Inverse property: isEncodedByBioChemEntity.", - "rdfs:label": "encodesBioChemEntity", + "rdfs:comment": "A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.", + "rdfs:label": "sequenceLocation", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:RNA" - }, - { - "@id": "bioschemastypesdrafts:DNA" + "@id": "bioschemastypesdrafts:SequenceAnnotation" }, { - "@id": "bioschemastypesdrafts:Gene" + "@id": "bioschemastypesdrafts:BioChemStructure" } ], "schema:rangeIncludes": [ { - "@id": "bioschemastypes:BioChemEntity" + "@id": "bioschemastypesdrafts:SequenceRange" } ] }, diff --git a/draft_type_list.txt b/draft_type_list.txt index b926a64..de18d42 100644 --- a/draft_type_list.txt +++ b/draft_type_list.txt @@ -4,7 +4,7 @@ bioschemastypesdrafts SequenceRange schema:BioChemEntity Type 0.1-DRAFT-2019_06_ bioschemastypesdrafts TaxonName schema:CreativeWork Type 0.1-DRAFT-TYPE https://github.com/BioSchemas/specifications/blob/master/TaxonName/jsonld/type/TaxonName_v0.1-DRAFT.json issue542 BioChemEntity schema:BioChemEntity Type 0.8-DRAFT https://github.com/BioSchemas/specifications/blob/master/BioChemEntity/jsonld/type/BioChemEntity_v0.8-DRAFT.jsonld bioschemastypesdrafts Study schema:CreativeWork Type 0.3-DRAFT https://github.com/BioSchemas/specifications/blob/master/Study/jsonld/type/Study_v0.3-DRAFT.json -bioschemastypesdrafts LabProtocol schema:CreativeWork Type 0.3-DRAFT-2019_06_20 https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.3-DRAFT-2019_06_20.json +bioschemastypesdrafts LabProtocol schema:HowTo Type 0.4-DRAFT https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.4-DRAFT.jsonld bioschemastypesdrafts Phenotype schema:Thing Type 0.3-DRAFT-2020_06_07 https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/type/Phenotype_v0.3-DRAFT-2020_06_07.json bioschemastypesdrafts SequenceAnnotation schema:BioChemEntity Type 0.1-DRAFT-2019_06_21 https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/type/SequenceAnnotation_v0.1-DRAFT-2019_06_21.json bioschemastypesdrafts Taxon schema:Thing Type 0.4-DRAFT https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/type/Taxon_v0.4-DRAFT.json diff --git a/specification aggregator.ipynb b/specification aggregator.ipynb index 7efcb6a..8978c11 100644 --- a/specification aggregator.ipynb +++ b/specification aggregator.ipynb @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -549,7 +549,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -563,17 +563,32 @@ "name": "stderr", "output_type": "stream", "text": [ - "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['dct', 'bioschemastypes']\n", + "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['bioschemastypes', 'dct']\n", " warnings.warn(f\"Found multiple namespace prefixes defined in the schema: f{namespace_set}\")\n", - "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['dct', 'bioschemastypesdrafts']\n", + "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['bioschemastypesdrafts', 'bioschemastypes', 'dct']\n", " warnings.warn(f\"Found multiple namespace prefixes defined in the schema: f{namespace_set}\")\n", "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['dwc', 'dct', 'bioschemas']\n", " warnings.warn(f\"Found multiple namespace prefixes defined in the schema: f{namespace_set}\")\n", - "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['dwc', 'bioschemasdrafts', 'ppeo', 'rdf', 'dct']\n", - " warnings.warn(f\"Found multiple namespace prefixes defined in the schema: f{namespace_set}\")\n", - "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['bioschemasdeprecated', 'bioschemasdrafts', 'rdf', 'dct']\n", + "C:\\Users\\gtsueng\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py:281: UserWarning: Found multiple namespace prefixes defined in the schema: f['dct', 'rdf', 'ppeo', 'bioschemasdrafts', 'dwc']\n", " warnings.warn(f\"Found multiple namespace prefixes defined in the schema: f{namespace_set}\")\n" ] + }, + { + "ename": "SchemaValidationError", + "evalue": "field \"codeRepository\" in \"$validation\" is not defined in this class or any of its parent classes", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mSchemaValidationError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m~\\AppData\\Local\\Temp/ipykernel_22324/2112215399.py\u001b[0m in \u001b[0;36m\u001b[1;34m\u001b[0m\n\u001b[0;32m 12\u001b[0m \u001b[1;31m#### Main\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 13\u001b[0m \u001b[0mscript_path\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m''\u001b[0m \u001b[1;31m#pathlib.Path(__file__).parent.absolute()\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 14\u001b[1;33m \u001b[0mrun_update\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mscript_path\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;32mTrue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\bioschemas\\bioschemas-dde\\src\\common.py\u001b[0m in \u001b[0;36mrun_update\u001b[1;34m(script_path, updateall)\u001b[0m\n\u001b[0;32m 413\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 414\u001b[0m \u001b[0mbioschemasfile\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mos\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mscript_path\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;34m'bioschemas.json'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 415\u001b[1;33m \u001b[0msc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mSchema\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mcleandict\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 416\u001b[0m \u001b[0msc\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidation\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 417\u001b[0m \u001b[1;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mbioschemasfile\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;34m'w'\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0moutfile\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py\u001b[0m in \u001b[0;36m__init__\u001b[1;34m(self, schema, context, base_schema, validator_options, base_schema_loader)\u001b[0m\n\u001b[0;32m 186\u001b[0m \u001b[0mbase_schema\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbase_schema\u001b[0m \u001b[1;32mor\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_base_schema_list\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0m_schema\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 187\u001b[0m \u001b[1;31m# print(self.namespace, base_schema)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 188\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mload_schema\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mschema\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0m_schema\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mbase_schema\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mbase_schema\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 189\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 190\u001b[0m \u001b[1;33m@\u001b[0m\u001b[0mproperty\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\schema.py\u001b[0m in \u001b[0;36mload_schema\u001b[1;34m(self, schema, base_schema)\u001b[0m\n\u001b[0;32m 246\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfull_schema_nx\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mmerge_schema_networkx\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbase_schema_nx\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mschema_nx\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 247\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidator\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mSchemaValidator\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mschema\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfull_schema_nx\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbase_schema\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidator_options\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 248\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidator\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidate_full_schema\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 249\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 250\u001b[0m \u001b[1;31m# split the schema networkx into individual ones\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\validator.py\u001b[0m in \u001b[0;36mvalidate_full_schema\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m 357\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidate_class_schema\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 358\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidate_class_label\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m\"@id\"\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 359\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidate_validation_field\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 360\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0mrecord\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'@type'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;34m\"rdf:Property\"\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 361\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidate_property_schema\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\validator.py\u001b[0m in \u001b[0;36mvalidate_validation_field\u001b[1;34m(self, record)\u001b[0m\n\u001b[0;32m 302\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mmatched\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 303\u001b[0m \u001b[1;31m# raise ValueError(f'field \"{_property}\" in \"{VALIDATION_FIELD}\" is not defined in this class or any of its parent classes')\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 304\u001b[1;33m self.report_validation_error(\n\u001b[0m\u001b[0;32m 305\u001b[0m \u001b[1;34mf'field \"{_property}\" in \"{VALIDATION_FIELD}\" is not defined in this class or any of its parent classes'\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 306\u001b[0m \u001b[0merror_type\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"invalid_validation_schema\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfield\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0m_property\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mrecord_id\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0m_id\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m~\\Anaconda3\\envs\\outbreak\\lib\\site-packages\\biothings_schema\\validator.py\u001b[0m in \u001b[0;36mreport_validation_error\u001b[1;34m(self, err_msg, **kwargs)\u001b[0m\n\u001b[0;32m 127\u001b[0m \u001b[0merr\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mSchemaValidationWarning\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0merr_msg\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'warning'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;32mFalse\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32melse\u001b[0m \u001b[0mSchemaValidationError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0merr_msg\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 128\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0merr\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwarning\u001b[0m \u001b[1;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mraise_on_validation_error\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 129\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0merr\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 130\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 131\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mvalidation_errors\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0merr\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;31mSchemaValidationError\u001b[0m: field \"codeRepository\" in \"$validation\" is not defined in this class or any of its parent classes" + ] } ], "source": [ @@ -593,6 +608,30 @@ "run_update(script_path,True)" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "## Validate a generated json\n", + "script_\n", + "inputfile = os.path.join(script_path,'drafts','gbhBioSample.json')\n", + "with open(inputfile,'rb') as infile:\n", + " definedterm = json.load(infile)\n", + "\n", + "#print(definedterm)\n", + "sc = Schema(definedterm)\n", + "sc.validation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": null, diff --git a/specification_meta_generator.ipynb b/specification_meta_generator.ipynb index 611e993..6a558d5 100644 --- a/specification_meta_generator.ipynb +++ b/specification_meta_generator.ipynb @@ -589,7 +589,17 @@ "id": "196f2190", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "## Validate a schema\n", + "from biothings_schema import Schema\n", + "inputfile = os.path.join(script_path,'drafts','gbhBioSample.json')\n", + "with open(inputfile,'rb') as infile:\n", + " definedterm = json.load(infile)\n", + "\n", + "#print(definedterm)\n", + "sc = Schema(definedterm)\n", + "sc.validation" + ] }, { "cell_type": "markdown",