diff --git a/bioschemastypesdrafts.json b/bioschemastypesdrafts.json index 83b779a..902a233 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": "12/14/2023, 09:09:05" + "@dateModified": "12/21/2023, 08:22:13" }, "@graph": [ { @@ -23,8 +23,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "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" + "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" ] }, { @@ -37,8 +37,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "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" + "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" ] }, { @@ -65,8 +65,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/BioChemEntity/0.8-DRAFT", - "https://github.com/BioSchemas/specifications/blob/master/BioChemEntity/jsonld/type/BioChemEntity_v0.8-DRAFT.jsonld" + "https://github.com/BioSchemas/specifications/blob/master/BioChemEntity/jsonld/type/BioChemEntity_v0.8-DRAFT.jsonld", + "https://bioschemas.org/types/BioChemEntity/0.8-DRAFT" ] }, { @@ -79,14 +79,14 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/Study/0.3-DRAFT", - "https://github.com/BioSchemas/specifications/blob/master/Study/jsonld/type/Study_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/blob/master/Study/jsonld/type/Study_v0.3-DRAFT.json", + "https://bioschemas.org/types/Study/0.3-DRAFT" ] }, { "@id": "bioschemastypesdrafts:LabProtocol", "@type": "rdfs:Class", - "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:comment": "An experimental lab protocol is a sequence of tasks and operations executed to perform experimental research in wet- or dry-labs. \n\nVersion: v0.4 \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:HowTo" @@ -96,8 +96,8 @@ ], "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/LabProtocol/0.4-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.4-DRAFT.jsonld" + "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/type/LabProtocol_v0.4-DRAFT.jsonld", + "https://bioschemas.org/types/LabProtocol/0.4-DRAFT" ] }, { @@ -110,8 +110,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "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" + "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" ] }, { @@ -124,8 +124,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/SequenceAnnotation/0.1-DRAFT-2019_06_21", - "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/type/SequenceAnnotation_v0.1-DRAFT-2019_06_21.json" + "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/type/SequenceAnnotation_v0.1-DRAFT-2019_06_21.json", + "https://bioschemas.org/types/SequenceAnnotation/0.1-DRAFT-2019_06_21" ] }, { @@ -138,8 +138,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/type/Taxon_v0.4-DRAFT.json", - "https://bioschemas.org/types/Taxon/0.4-DRAFT" + "https://bioschemas.org/types/Taxon/0.4-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/type/Taxon_v0.4-DRAFT.json" ] }, { @@ -166,8 +166,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/DNA/0.2-DRAFT-2019_06_20", - "https://github.com/BioSchemas/specifications/tree/master/DNA/jsonld/type/DNA_v0.2-DRAFT-2019_06_20.json" + "https://github.com/BioSchemas/specifications/tree/master/DNA/jsonld/type/DNA_v0.2-DRAFT-2019_06_20.json", + "https://bioschemas.org/types/DNA/0.2-DRAFT-2019_06_20" ] }, { @@ -180,8 +180,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/types/Enzyme/0.1-DRAFT-2019_06_20", - "https://github.com/BioSchemas/specifications/tree/master/Enzyme/jsonld/type/Enzyme_v0.1-DRAFT-2019_06_20.json" + "https://github.com/BioSchemas/specifications/tree/master/Enzyme/jsonld/type/Enzyme_v0.1-DRAFT-2019_06_20.json", + "https://bioschemas.org/types/Enzyme/0.1-DRAFT-2019_06_20" ] }, { @@ -208,8 +208,8 @@ }, "additional_type": "https://bioschemas.org/types#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/SequenceMatchingModel/jsonld/type/SequenceMatchingModel_v0.1-DRAFT-2019_06_21.json", - "https://bioschemas.org/types/SequenceMatchingModel/0.1-DRAFT-2019_06_21" + "https://bioschemas.org/types/SequenceMatchingModel/0.1-DRAFT-2019_06_21", + "https://github.com/BioSchemas/specifications/tree/master/SequenceMatchingModel/jsonld/type/SequenceMatchingModel_v0.1-DRAFT-2019_06_21.json" ] }, { @@ -217,8 +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://bioschemas.org/types/Protein/0.4-DRAFT", - "https://github.com/BioSchemas/specifications/blob/master/Protein/jsonld/type/Protein_v0.4-DRAFT.json" + "https://github.com/BioSchemas/specifications/blob/master/Protein/jsonld/type/Protein_v0.4-DRAFT.json", + "https://bioschemas.org/types/Protein/0.4-DRAFT" ], "rdfs:label": "Protein", "rdfs:subClassOf": { @@ -542,6 +542,35 @@ } ] }, + { + "@id": "bioschemastypesdrafts:bioSample", + "@type": "rdf:Property", + "rdfs:comment": "BioSample 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": "bioSample", + "schema:domainIncludes": { + "@id": "bioschemastypesdrafts:LabProtocol" + }, + "schema:rangeIncludes": [ + { + "@id": "schema:BioChemEntity" + }, + { + "@id": "bioschemastypes:BioSample" + }, + { + "@id": "schema:DefinedTerm" + }, + { + "@id": "schema:Taxon" + }, + { + "@id": "schema:Text" + }, + { + "@id": "schema:URL" + } + ] + }, { "@id": "bioschemastypesdrafts:labEquipment", "@type": "rdf:Property", @@ -605,7 +634,7 @@ { "@id": "bioschemastypesdrafts:protocolLimitation", "@type": "rdf:Property", - "rdfs:comment": "Situations where the Protocol would be unreliable or otherwise unsuccessful", + "rdfs:comment": "Situations where the Protocol would be unreliable or otherwise unsuccessful.", "rdfs:label": "protocolLimitation", "schema:domainIncludes": [ { @@ -621,6 +650,25 @@ } ] }, + { + "@id": "bioschemastypesdrafts:protocolOutcome", + "@type": "rdf:Property", + "rdfs:comment": "Actual outcome or result by a protocol execution. The shape of the expected outcome/result can be described using the property 'output'.", + "rdfs:label": "protocolOutcome", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:LabProtocol" + } + ], + "schema:rangeIncludes": [ + { + "@id": "schema:Text" + }, + { + "@id": "schema:CreativeWork" + } + ] + }, { "@id": "bioschemastypesdrafts:reagent", "@type": "rdf:Property", @@ -635,9 +683,15 @@ { "@id": "schema:BioChemEntity" }, + { + "@id": "schema:ChemicalSubstance" + }, { "@id": "schema:DefinedTerm" }, + { + "@id": "schema:MolecularEntity" + }, { "@id": "schema:Text" }, @@ -1140,46 +1194,6 @@ } ] }, - { - "@id": "bioschemastypesdrafts:valueReference", - "@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", - "schema:domainIncludes": [ - { - "@id": "bioschemastypesdrafts:Phenotype" - }, - { - "@id": "bioschemastypesdrafts:SequenceAnnotation" - } - ], - "schema:rangeIncludes": [ - { - "@id": "schema:DefinedTerm" - }, - { - "@id": "schema:Enumeration" - }, - { - "@id": "schema:PropertyValue" - }, - { - "@id": "schema:QualitativeValue" - }, - { - "@id": "schema:QuantitativeValue" - }, - { - "@id": "schema:StructuredValue" - }, - { - "@id": "schema:URL" - }, - { - "@id": "schema:Text" - } - ] - }, { "@id": "bioschemastypesdrafts:encodesBioChemEntity", "@type": "rdf:Property", @@ -1203,62 +1217,70 @@ ] }, { - "@id": "bioschemastypesdrafts:hasSequence", + "@id": "bioschemastypesdrafts:hasSequenceAnnotation", "@type": "rdf:Property", - "rdfs:comment": "Nucleotide or amino acid sequence.", - "rdfs:label": "hasSequence", + "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity.", + "rdfs:label": "hasSequenceAnnotation", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:RNA" + "@id": "bioschemastypesdrafts:BioChemEntity" + }, + { + "@id": "bioschemastypesdrafts:BioChemStructure" }, { "@id": "bioschemastypesdrafts:DNA" + }, + { + "@id": "bioschemastypesdrafts:Enzyme" } ], "schema:rangeIncludes": [ { - "@id": "schema:Text" + "@id": "schema:URL" + }, + { + "@id": "bioschemastypesdrafts:SequenceAnnotation" } ] }, { - "@id": "bioschemastypesdrafts:isMatchedBy", + "@id": "bioschemastypesdrafts:valueReference", "@type": "rdf:Property", - "rdfs:comment": "A model matching this BioChemEntity.", - "rdfs:label": "isMatchedBy", + "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:BioChemStructure" + "@id": "bioschemastypesdrafts:Phenotype" }, { - "@id": "bioschemastypesdrafts:Enzyme" + "@id": "bioschemastypesdrafts:SequenceAnnotation" } ], "schema:rangeIncludes": [ { - "@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:DefinedTerm" + }, { - "@id": "bioschemastypesdrafts:Study" + "@id": "schema:Enumeration" }, { - "@id": "bioschemastypesdrafts:Phenotype" + "@id": "schema:PropertyValue" }, { - "@id": "bioschemastypesdrafts:Sample" - } - ], - "schema:rangeIncludes": [ + "@id": "schema:QualitativeValue" + }, { - "@id": "schema:PropertyValue" + "@id": "schema:QuantitativeValue" + }, + { + "@id": "schema:StructuredValue" + }, + { + "@id": "schema:URL" + }, + { + "@id": "schema:Text" } ] }, @@ -1284,6 +1306,31 @@ } ] }, + { + "@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": "bioschemastypesdrafts:BioChemStructure" + } + ], + "schema:rangeIncludes": [ + { + "@id": "schema:PropertyValue" + }, + { + "@id": "schema:Text" + }, + { + "@id": "schema:URL" + } + ] + }, { "@id": "bioschemastypesdrafts:taxonRank", "@type": "rdf:Property", @@ -1310,55 +1357,43 @@ ] }, { - "@id": "bioschemastypesdrafts:hasSequenceAnnotation", + "@id": "bioschemastypesdrafts:hasSequence", "@type": "rdf:Property", - "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity.", - "rdfs:label": "hasSequenceAnnotation", + "rdfs:comment": "Nucleotide or amino acid sequence.", + "rdfs:label": "hasSequence", "schema:domainIncludes": [ { - "@id": "bioschemastypesdrafts:BioChemEntity" - }, - { - "@id": "bioschemastypesdrafts:BioChemStructure" + "@id": "bioschemastypesdrafts:RNA" }, { "@id": "bioschemastypesdrafts:DNA" - }, - { - "@id": "bioschemastypesdrafts:Enzyme" } ], "schema:rangeIncludes": [ { - "@id": "schema:URL" - }, - { - "@id": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "schema:Text" } ] }, { - "@id": "bioschemastypesdrafts:creationMethod", + "@id": "bioschemastypesdrafts:additionalProperty", "@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", + "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": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "bioschemastypesdrafts:Study" }, { - "@id": "bioschemastypesdrafts:BioChemStructure" + "@id": "bioschemastypesdrafts:Phenotype" + }, + { + "@id": "bioschemastypesdrafts:Sample" } ], "schema:rangeIncludes": [ { "@id": "schema:PropertyValue" - }, - { - "@id": "schema:Text" - }, - { - "@id": "schema:URL" } ] }, @@ -1381,6 +1416,25 @@ } ] }, + { + "@id": "bioschemastypesdrafts:isMatchedBy", + "@type": "rdf:Property", + "rdfs:comment": "A model matching this BioChemEntity.", + "rdfs:label": "isMatchedBy", + "schema:domainIncludes": [ + { + "@id": "bioschemastypesdrafts:BioChemStructure" + }, + { + "@id": "bioschemastypesdrafts:Enzyme" + } + ], + "schema:rangeIncludes": [ + { + "@id": "bioschemastypesdrafts:SequenceMatchingModel" + } + ] + }, { "@id": "dct:conformsTo", "@type": "rdf:Property",