diff --git a/project/excel/smoc_schema.xlsx b/project/excel/modo_schema.xlsx similarity index 73% rename from project/excel/smoc_schema.xlsx rename to project/excel/modo_schema.xlsx index b6f61b4..991f718 100644 Binary files a/project/excel/smoc_schema.xlsx and b/project/excel/modo_schema.xlsx differ diff --git a/project/graphql/smoc_schema.graphql b/project/graphql/modo_schema.graphql similarity index 100% rename from project/graphql/smoc_schema.graphql rename to project/graphql/modo_schema.graphql diff --git a/project/jsonld/smoc_schema.context.jsonld b/project/jsonld/modo_schema.context.jsonld similarity index 91% rename from project/jsonld/smoc_schema.context.jsonld rename to project/jsonld/modo_schema.context.jsonld index e883a52..4f9279f 100644 --- a/project/jsonld/smoc_schema.context.jsonld +++ b/project/jsonld/modo_schema.context.jsonld @@ -1,8 +1,8 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-01-17T12:05:19", - "source": "smoc_schema.yaml" + "generation_date": "2024-02-21T16:55:55", + "source": "modo_schema.yaml" }, "@context": { "EDAM": "http://edamontology.org/", @@ -19,11 +19,11 @@ "bioschemas": "https://bioschemas.org/", "example": "https://example.org/", "linkml": "https://w3id.org/linkml/", + "modo": "https://w3id.org/sdsc-ordes/modo-schema/", "schema": "http://schema.org/", "skos": "http://www.w3.org/2004/02/skos/core#", - "smoc": "https://w3id.org/sdsc-ordes/smoc-schema/", "sphn": "https://biomedit.ch/rdf/sphn-schema/sphn#", - "@vocab": "https://w3id.org/sdsc-ordes/smoc-schema/", + "@vocab": "https://w3id.org/sdsc-ordes/modo-schema/", "creation_date": { "@type": "xsd:dateTime" }, diff --git a/project/jsonld/smoc_schema.jsonld b/project/jsonld/modo_schema.jsonld similarity index 80% rename from project/jsonld/smoc_schema.jsonld rename to project/jsonld/modo_schema.jsonld index 258c09a..22e776a 100644 --- a/project/jsonld/smoc_schema.jsonld +++ b/project/jsonld/modo_schema.jsonld @@ -1,19 +1,19 @@ { - "name": "smoc-schema", + "name": "modo-schema", "description": "Metadata schema for the SMOC Multi-Omics Digital Object", - "title": "smoc-schema", + "title": "modo-schema", "see_also": [ - "https://sdsc-ordes.github.io/smoc-schema" + "https://sdsc-ordes.github.io/modo-schema" ], - "id": "https://w3id.org/sdsc-ordes/smoc-schema", + "id": "https://w3id.org/sdsc-ordes/modo-schema", "imports": [ "linkml:types" ], "license": "MIT", "prefixes": [ { - "prefix_prefix": "smoc", - "prefix_reference": "https://w3id.org/sdsc-ordes/smoc-schema/" + "prefix_prefix": "modo", + "prefix_reference": "https://w3id.org/sdsc-ordes/modo-schema/" }, { "prefix_prefix": "linkml", @@ -56,7 +56,7 @@ "prefix_reference": "https://biomedit.ch/rdf/sphn-schema/sphn#" } ], - "default_prefix": "smoc", + "default_prefix": "modo", "default_range": "string", "types": [ { @@ -371,8 +371,8 @@ "enums": [ { "name": "Sex", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Sex", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/Sex", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "permissible_values": [ { "text": "Male", @@ -386,8 +386,8 @@ }, { "name": "OmicsType", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/OmicsType", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/OmicsType", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "permissible_values": [ { "text": "GENOMICS", @@ -413,8 +413,8 @@ }, { "name": "DataFormat", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/DataFormat", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/DataFormat", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "permissible_values": [ { "text": "CRAM", @@ -442,9 +442,9 @@ "slots": [ { "name": "id", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/id", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/id", "description": "A unique identifier for a thing", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "mappings": [ "http://schema.org/identifier" ], @@ -460,9 +460,9 @@ }, { "name": "name", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/name", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/name", "description": "A human-readable name for a thing", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "mappings": [ "http://schema.org/name" ], @@ -476,9 +476,9 @@ }, { "name": "description", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/description", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/description", "description": "A human-readable description for a thing", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "mappings": [ "http://schema.org/description" ], @@ -492,9 +492,9 @@ }, { "name": "has_part", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_part", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_part", "description": "Indicates an item that is part of this item.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "mappings": [ "http://schema.org/hasPart" ], @@ -505,10 +505,10 @@ }, { "name": "creation_date", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/creation_date", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/creation_date", "description": "The date on which something was created.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/creation_date", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/creation_date", "owner": "MODO", "domain_of": [ "MODO" @@ -519,10 +519,10 @@ }, { "name": "last_update_date", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/last_update_date", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/last_update_date", "description": "The date on which the thing was last modified.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/last_update_date", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/last_update_date", "owner": "MODO", "domain_of": [ "MODO" @@ -533,10 +533,10 @@ }, { "name": "omics_type", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/omics_type", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/omics_type", "description": "The type of omics considered.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/omics_type", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/omics_type", "multivalued": true, "owner": "Assay", "domain_of": [ @@ -548,11 +548,11 @@ }, { "name": "has_assay", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_assay", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_assay", "description": "An assay that was performed as part of a given thing.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "has_part", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_assay", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_assay", "multivalued": true, "owner": "MODO", "domain_of": [ @@ -563,11 +563,11 @@ }, { "name": "has_sample", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_sample", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_sample", "description": "Biological sample included or described by a given thing.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "has_part", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_sample", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_sample", "multivalued": true, "owner": "DataEntity", "domain_of": [ @@ -579,11 +579,11 @@ }, { "name": "has_data", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_data", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_data", "description": "Data entity included in a given collection.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "has_part", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_data", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_data", "multivalued": true, "owner": "Assay", "domain_of": [ @@ -594,11 +594,11 @@ }, { "name": "has_sequence", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_sequence", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_sequence", "description": "Denotes that a sequence belongs to a collection (e.g. a reference genome).", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "has_part", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_sequence", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_sequence", "multivalued": true, "owner": "ReferenceGenome", "domain_of": [ @@ -609,11 +609,11 @@ }, { "name": "has_reference", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_reference", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_reference", "description": "Specifies the reference coordinate system used by an omics dataset.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "has_part", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/has_reference", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/has_reference", "multivalued": true, "owner": "DataEntity", "domain_of": [ @@ -624,10 +624,10 @@ }, { "name": "data_format", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/data_format", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/data_format", "description": "Data/file format associated with a data entity.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/data_format", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/data_format", "owner": "DataEntity", "domain_of": [ "DataEntity" @@ -638,10 +638,10 @@ }, { "name": "taxon_id", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/taxon_id", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/taxon_id", "description": "The taxid number describing the taxonomic range of a sample.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/taxon_id", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/taxon_id", "multivalued": true, "owner": "ReferenceGenome", "domain_of": [ @@ -653,10 +653,10 @@ }, { "name": "collector", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/collector", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/collector", "description": "The organization responsible for collecting a given sample.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/collector", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/collector", "multivalued": true, "owner": "Sample", "domain_of": [ @@ -667,7 +667,7 @@ }, { "name": "data_path", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/data_path", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/data_path", "description": "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path.", "examples": [ { @@ -683,8 +683,8 @@ "@type": "Example" } ], - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/data_path", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/data_path", "owner": "ReferenceGenome", "domain_of": [ "DataEntity", @@ -696,10 +696,10 @@ }, { "name": "sequence_md5", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/sequence_md5", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/sequence_md5", "description": "The pre-computed hash uniquely representing a biological sequence. Calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/sequence_md5", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/sequence_md5", "owner": "ReferenceSequence", "domain_of": [ "ReferenceSequence" @@ -710,10 +710,10 @@ }, { "name": "source_uri", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/source_uri", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/source_uri", "description": "The URI from which a resource or dataset was obtained or derived.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/source_uri", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/source_uri", "owner": "ReferenceSequence", "domain_of": [ "MODO", @@ -725,10 +725,10 @@ }, { "name": "version", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/version", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/version", "description": "A string specifying the release or version of a software or resource.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/version", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/version", "owner": "ReferenceSequence", "domain_of": [ "ReferenceGenome", @@ -739,10 +739,10 @@ }, { "name": "cell_type", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/cell_type", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/cell_type", "description": "The cell type name.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/cell_type", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/cell_type", "owner": "Sample", "domain_of": [ "Sample" @@ -752,10 +752,10 @@ }, { "name": "source_material", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/source_material", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/source_material", "description": "The biological source from which the sample was isolated (tissue, organ, ...).", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/source_material", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/source_material", "owner": "Sample", "domain_of": [ "Sample" @@ -765,10 +765,10 @@ }, { "name": "sex", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/sex", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/sex", "description": "The biological sex of a sample.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/sex", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/sex", "owner": "Sample", "domain_of": [ "Sample" @@ -778,8 +778,8 @@ }, { "name": "mODOCollection__entries", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", - "slot_uri": "https://w3id.org/sdsc-ordes/smoc-schema/entries", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", + "slot_uri": "https://w3id.org/sdsc-ordes/modo-schema/entries", "multivalued": true, "alias": "entries", "owner": "MODOCollection", @@ -794,9 +794,9 @@ "classes": [ { "name": "NamedThing", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/NamedThing", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/NamedThing", "description": "A generic grouping for any identifiable entity", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "mappings": [ "schema:Thing" ], @@ -811,9 +811,9 @@ }, { "name": "MODO", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/MODO", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/MODO", "description": "Represents the Multi-Omics Digital Object. It encapsulates omics and other datasets and their metadata.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "NamedThing", "slots": [ "id", @@ -825,14 +825,14 @@ "source_uri" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/MODO", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/MODO", "@type": "ClassDefinition" }, { "name": "Assay", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Assay", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/Assay", "description": "A coordinated set of actions designed to generate data from samples.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "see_also": [ "NCIT:C42790", "sphn:Assay" @@ -847,14 +847,14 @@ "omics_type" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Assay", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/Assay", "@type": "ClassDefinition" }, { "name": "Sample", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Sample", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/Sample", "description": "A biological sample used in assays. Examples include a whole organism, tissue or cell line.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "see_also": [ "bioschemas:Sample" ], @@ -870,14 +870,14 @@ "collector" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Sample", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/Sample", "@type": "ClassDefinition" }, { "name": "DataEntity", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/DataEntity", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/DataEntity", "description": "An entity containing data.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "NamedThing", "slots": [ "id", @@ -889,14 +889,14 @@ "has_reference" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/DataEntity", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/DataEntity", "@type": "ClassDefinition" }, { "name": "ReferenceGenome", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/ReferenceGenome", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/ReferenceGenome", "description": "Reference assembly of a given genome, consisting of a collection of congiguous sequences (contigs).", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "see_also": [ "GENO:0000914" ], @@ -912,14 +912,14 @@ "version" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/ReferenceGenome", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/ReferenceGenome", "@type": "ClassDefinition" }, { "name": "ReferenceSequence", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/ReferenceSequence", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/ReferenceSequence", "description": "A contiguous sequence of DNA part of a reference coordinate system (genome assembly).", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "see_also": [ "GENO:0000017" ], @@ -933,14 +933,14 @@ "version" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/ReferenceSequence", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/ReferenceSequence", "@type": "ClassDefinition" }, { "name": "AlignmentSet", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/AlignmentSet", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/AlignmentSet", "description": "A data entity consisting of genomic intervals aligned to a reference.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "DataEntity", "slots": [ "id", @@ -952,14 +952,14 @@ "has_reference" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/AlignmentSet", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/AlignmentSet", "@type": "ClassDefinition" }, { "name": "VariantSet", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/VariantSet", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/VariantSet", "description": "A data entity consisting of genomic variants relative to a reference.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "DataEntity", "slots": [ "id", @@ -971,14 +971,14 @@ "has_reference" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/VariantSet", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/VariantSet", "@type": "ClassDefinition" }, { "name": "Array", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Array", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/Array", "description": "Data entity consisting of an N-dimensional array.", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "is_a": "DataEntity", "slots": [ "id", @@ -990,14 +990,14 @@ "has_reference" ], "slot_usage": {}, - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/Array", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/Array", "@type": "ClassDefinition" }, { "name": "MODOCollection", - "definition_uri": "https://w3id.org/sdsc-ordes/smoc-schema/MODOCollection", + "definition_uri": "https://w3id.org/sdsc-ordes/modo-schema/MODOCollection", "description": "A holder for Multi-Omics Digital Objects", - "from_schema": "https://w3id.org/sdsc-ordes/smoc-schema", + "from_schema": "https://w3id.org/sdsc-ordes/modo-schema", "slots": [ "mODOCollection__entries" ], @@ -1011,22 +1011,22 @@ "@type": "SlotDefinition" } ], - "class_uri": "https://w3id.org/sdsc-ordes/smoc-schema/MODOCollection", + "class_uri": "https://w3id.org/sdsc-ordes/modo-schema/MODOCollection", "tree_root": true, "@type": "ClassDefinition" } ], "metamodel_version": "1.7.0", - "source_file": "smoc_schema.yaml", - "source_file_date": "2024-01-17T12:04:23", + "source_file": "modo_schema.yaml", + "source_file_date": "2024-02-21T16:46:11", "source_file_size": 7674, - "generation_date": "2024-01-17T12:05:20", + "generation_date": "2024-02-21T16:55:56", "@type": "SchemaDefinition", "@context": [ - "project/jsonld/smoc_schema.context.jsonld", + "project/jsonld/modo_schema.context.jsonld", "https://w3id.org/linkml/types.context.jsonld", { - "@base": "https://w3id.org/sdsc-ordes/smoc-schema/" + "@base": "https://w3id.org/sdsc-ordes/modo-schema/" } ] } diff --git a/project/jsonschema/smoc_schema.schema.json b/project/jsonschema/modo_schema.schema.json similarity index 99% rename from project/jsonschema/smoc_schema.schema.json rename to project/jsonschema/modo_schema.schema.json index 87ae9a7..1ce5b4f 100644 --- a/project/jsonschema/smoc_schema.schema.json +++ b/project/jsonschema/modo_schema.schema.json @@ -528,7 +528,7 @@ "type": "object" } }, - "$id": "https://w3id.org/sdsc-ordes/smoc-schema", + "$id": "https://w3id.org/sdsc-ordes/modo-schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, "description": "A holder for Multi-Omics Digital Objects", @@ -541,7 +541,7 @@ "type": "object" } }, - "title": "smoc-schema", + "title": "modo-schema", "type": "object", "version": null } \ No newline at end of file diff --git a/project/owl/smoc_schema.owl.ttl b/project/owl/modo_schema.owl.ttl similarity index 57% rename from project/owl/smoc_schema.owl.ttl rename to project/owl/modo_schema.owl.ttl index 4173424..c059eda 100644 --- a/project/owl/smoc_schema.owl.ttl +++ b/project/owl/modo_schema.owl.ttl @@ -4,408 +4,408 @@ @prefix bioschemas: . @prefix dcterms: . @prefix linkml: . +@prefix modo: . @prefix owl: . @prefix rdf: . @prefix rdfs: . @prefix schema1: . @prefix skos: . -@prefix smoc: . @prefix sphn: . @prefix xsd: . -smoc:AlignmentSet a owl:Class, +modo:AlignmentSet a owl:Class, linkml:ClassDefinition ; rdfs:label "AlignmentSet" ; - rdfs:subClassOf smoc:DataEntity ; + rdfs:subClassOf modo:DataEntity ; skos:definition "A data entity consisting of genomic intervals aligned to a reference." ; - skos:inScheme . + skos:inScheme . -smoc:Array a owl:Class, +modo:Array a owl:Class, linkml:ClassDefinition ; rdfs:label "Array" ; - rdfs:subClassOf smoc:DataEntity ; + rdfs:subClassOf modo:DataEntity ; skos:definition "Data entity consisting of an N-dimensional array." ; - skos:inScheme . + skos:inScheme . -smoc:MODOCollection a owl:Class, +modo:MODOCollection a owl:Class, linkml:ClassDefinition ; rdfs:label "MODOCollection" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:entries ], + owl:onProperty modo:entries ], [ a owl:Restriction ; - owl:allValuesFrom smoc:MODO ; - owl:onProperty smoc:entries ] ; + owl:allValuesFrom modo:MODO ; + owl:onProperty modo:entries ] ; skos:definition "A holder for Multi-Omics Digital Objects" ; - skos:inScheme . + skos:inScheme . -smoc:VariantSet a owl:Class, +modo:VariantSet a owl:Class, linkml:ClassDefinition ; rdfs:label "VariantSet" ; - rdfs:subClassOf smoc:DataEntity ; + rdfs:subClassOf modo:DataEntity ; skos:definition "A data entity consisting of genomic variants relative to a reference." ; - skos:inScheme . + skos:inScheme . -smoc:MODO a owl:Class, +modo:MODO a owl:Class, linkml:ClassDefinition ; rdfs:label "MODO" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:has_assay ], + owl:minCardinality 1 ; + owl:onProperty modo:last_update_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:source_uri ], + owl:onProperty modo:source_uri ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty modo:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:creation_date ], + owl:onProperty modo:creation_date ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uri ; - owl:onProperty smoc:source_uri ], + owl:minCardinality 0 ; + owl:onProperty modo:has_assay ], [ a owl:Restriction ; owl:allValuesFrom linkml:Datetime ; - owl:onProperty smoc:creation_date ], + owl:onProperty modo:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:last_update_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:has_assay ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:source_uri ], + owl:onProperty modo:has_assay ], [ a owl:Restriction ; owl:allValuesFrom linkml:Datetime ; - owl:onProperty smoc:last_update_date ], + owl:onProperty modo:last_update_date ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:creation_date ], + owl:allValuesFrom linkml:Uri ; + owl:onProperty modo:source_uri ], [ a owl:Restriction ; - owl:allValuesFrom smoc:Assay ; - owl:onProperty smoc:has_assay ], + owl:minCardinality 0 ; + owl:onProperty modo:source_uri ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:last_update_date ], - smoc:NamedThing ; + owl:maxCardinality 1 ; + owl:onProperty modo:last_update_date ], + [ a owl:Restriction ; + owl:allValuesFrom modo:Assay ; + owl:onProperty modo:has_assay ], + modo:NamedThing ; skos:definition "Represents the Multi-Omics Digital Object. It encapsulates omics and other datasets and their metadata." ; - skos:inScheme . + skos:inScheme . EDAM:format_1929 a owl:Class, - smoc:DataFormat ; + modo:DataFormat ; rdfs:label "FASTA" ; - rdfs:subClassOf smoc:DataFormat . + rdfs:subClassOf modo:DataFormat . EDAM:format_1930 a owl:Class, - smoc:DataFormat ; + modo:DataFormat ; rdfs:label "FASTQ" ; - rdfs:subClassOf smoc:DataFormat . + rdfs:subClassOf modo:DataFormat . EDAM:format_3462 a owl:Class, - smoc:DataFormat ; + modo:DataFormat ; rdfs:label "CRAM" ; - rdfs:subClassOf smoc:DataFormat . + rdfs:subClassOf modo:DataFormat . EDAM:format_3915 a owl:Class, - smoc:DataFormat ; + modo:DataFormat ; rdfs:label "Zarr" ; - rdfs:subClassOf smoc:DataFormat . + rdfs:subClassOf modo:DataFormat . NCIT:C153189 a owl:Class, - smoc:OmicsType ; + modo:OmicsType ; rdfs:label "TRANSCRIPTOMICS" ; - rdfs:subClassOf smoc:OmicsType . + rdfs:subClassOf modo:OmicsType . NCIT:C20085 a owl:Class, - smoc:OmicsType ; + modo:OmicsType ; rdfs:label "PROTEOMICS" ; - rdfs:subClassOf smoc:OmicsType . + rdfs:subClassOf modo:OmicsType . NCIT:C49019 a owl:Class, - smoc:OmicsType ; + modo:OmicsType ; rdfs:label "METABOLOMICS" ; - rdfs:subClassOf smoc:OmicsType . + rdfs:subClassOf modo:OmicsType . NCIT:C84343 a owl:Class, - smoc:OmicsType ; + modo:OmicsType ; rdfs:label "GENOMICS" ; - rdfs:subClassOf smoc:OmicsType . + rdfs:subClassOf modo:OmicsType . -smoc:Assay a owl:Class, +modo:Assay a owl:Class, linkml:ClassDefinition ; rdfs:label "Assay" ; rdfs:seeAlso NCIT:C42790, sphn:Assay ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:has_sample ], + owl:allValuesFrom modo:DataEntity ; + owl:onProperty modo:has_data ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:has_data ], + owl:allValuesFrom modo:Sample ; + owl:onProperty modo:has_sample ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:has_data ], - [ a owl:Restriction ; - owl:allValuesFrom smoc:DataEntity ; - owl:onProperty smoc:has_data ], + owl:onProperty modo:has_sample ], [ a owl:Restriction ; - owl:allValuesFrom smoc:OmicsType ; - owl:onProperty smoc:omics_type ], + owl:allValuesFrom modo:OmicsType ; + owl:onProperty modo:omics_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:omics_type ], + owl:maxCardinality 1 ; + owl:onProperty modo:has_data ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:has_sample ], + owl:onProperty modo:has_data ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty modo:omics_type ], [ a owl:Restriction ; - owl:allValuesFrom smoc:Sample ; - owl:onProperty smoc:has_sample ], - smoc:NamedThing ; + owl:maxCardinality 1 ; + owl:onProperty modo:has_sample ], + modo:NamedThing ; skos:definition "A coordinated set of actions designed to generate data from samples." ; - skos:inScheme . + skos:inScheme . -smoc:ReferenceGenome a owl:Class, +modo:ReferenceGenome a owl:Class, linkml:ClassDefinition ; rdfs:label "ReferenceGenome" ; rdfs:seeAlso GENO:0000914 ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty smoc:taxon_id ], + owl:maxCardinality 1 ; + owl:onProperty modo:source_uri ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty modo:source_uri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:source_uri ], + owl:onProperty modo:version ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:version ], + owl:onProperty modo:has_sequence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:taxon_id ], + owl:onProperty modo:version ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uri ; - owl:onProperty smoc:source_uri ], + owl:minCardinality 0 ; + owl:onProperty modo:taxon_id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty smoc:data_path ], + owl:onProperty modo:data_path ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:has_sequence ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty modo:taxon_id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty modo:data_path ], [ a owl:Restriction ; - owl:allValuesFrom smoc:ReferenceSequence ; - owl:onProperty smoc:has_sequence ], + owl:allValuesFrom linkml:String ; + owl:onProperty modo:version ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:has_sequence ], + owl:onProperty modo:has_sequence ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:version ], + owl:allValuesFrom linkml:Uri ; + owl:onProperty modo:source_uri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:data_path ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty smoc:version ], + owl:onProperty modo:data_path ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:source_uri ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:data_path ], - smoc:NamedThing ; + owl:allValuesFrom modo:ReferenceSequence ; + owl:onProperty modo:has_sequence ], + modo:NamedThing ; skos:definition "Reference assembly of a given genome, consisting of a collection of congiguous sequences (contigs)." ; - skos:inScheme . + skos:inScheme . -smoc:ReferenceSequence a owl:Class, +modo:ReferenceSequence a owl:Class, linkml:ClassDefinition ; rdfs:label "ReferenceSequence" ; rdfs:seeAlso GENO:0000017 ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:sequence_md5 ], + owl:onProperty modo:sequence_md5 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:version ], + owl:minCardinality 0 ; + owl:onProperty modo:version ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[a-f0-9]{32}$" ] ) ] ) ] ; - owl:onProperty smoc:sequence_md5 ], + owl:onProperty modo:sequence_md5 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty smoc:version ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:sequence_md5 ], + owl:maxCardinality 1 ; + owl:onProperty modo:source_uri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:source_uri ], + owl:onProperty modo:sequence_md5 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uri ; - owl:onProperty smoc:source_uri ], + owl:onProperty modo:source_uri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:version ], + owl:onProperty modo:source_uri ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty modo:version ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:source_uri ], - smoc:NamedThing ; + owl:onProperty modo:version ], + modo:NamedThing ; skos:definition "A contiguous sequence of DNA part of a reference coordinate system (genome assembly)." ; - skos:inScheme . + skos:inScheme . - a owl:Class, - smoc:Sex ; + a owl:Class, + modo:Sex ; rdfs:label "Female" ; - rdfs:subClassOf smoc:Sex . + rdfs:subClassOf modo:Sex . - a owl:Class, - smoc:Sex ; + a owl:Class, + modo:Sex ; rdfs:label "Male" ; - rdfs:subClassOf smoc:Sex . + rdfs:subClassOf modo:Sex . -smoc:collector a owl:ObjectProperty, +modo:collector a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "collector" ; rdfs:range linkml:String ; skos:definition "The organization responsible for collecting a given sample." ; - skos:inScheme . + skos:inScheme . -smoc:entries a owl:ObjectProperty, +modo:entries a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "entries" ; - skos:inScheme . + skos:inScheme . -smoc:omics_type a owl:ObjectProperty, +modo:omics_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "omics_type" ; - rdfs:range smoc:OmicsType ; + rdfs:range modo:OmicsType ; skos:definition "The type of omics considered." ; - skos:inScheme . + skos:inScheme . -smoc:Sample a owl:Class, +modo:Sample a owl:Class, linkml:ClassDefinition ; rdfs:label "Sample" ; rdfs:seeAlso bioschemas:Sample ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:cell_type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty smoc:collector ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:collector ], + owl:onProperty modo:cell_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:source_material ], + owl:minCardinality 0 ; + owl:onProperty modo:collector ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:source_material ], + owl:onProperty modo:source_material ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty smoc:source_material ], + owl:onProperty modo:source_material ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:taxon_id ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty modo:taxon_id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:sex ], + owl:onProperty modo:taxon_id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty smoc:taxon_id ], + owl:allValuesFrom modo:Sex ; + owl:onProperty modo:sex ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:cell_type ], + owl:allValuesFrom linkml:String ; + owl:onProperty modo:cell_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:sex ], + owl:onProperty modo:sex ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty modo:sex ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty smoc:cell_type ], + owl:onProperty modo:collector ], [ a owl:Restriction ; - owl:allValuesFrom smoc:Sex ; - owl:onProperty smoc:sex ], - smoc:NamedThing ; + owl:maxCardinality 1 ; + owl:onProperty modo:source_material ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty modo:cell_type ], + modo:NamedThing ; skos:definition "A biological sample used in assays. Examples include a whole organism, tissue or cell line." ; - skos:inScheme . + skos:inScheme . -smoc:cell_type a owl:ObjectProperty, +modo:cell_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "cell_type" ; rdfs:range linkml:String ; skos:definition "The cell type name." ; - skos:inScheme . + skos:inScheme . -smoc:creation_date a owl:ObjectProperty, +modo:creation_date a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "creation_date" ; rdfs:range linkml:Datetime ; skos:definition "The date on which something was created." ; - skos:inScheme . + skos:inScheme . -smoc:data_format a owl:ObjectProperty, +modo:data_format a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "data_format" ; - rdfs:range smoc:DataFormat ; + rdfs:range modo:DataFormat ; skos:definition "Data/file format associated with a data entity." ; - skos:inScheme . + skos:inScheme . -smoc:description a owl:ObjectProperty, +modo:description a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "description" ; skos:definition "A human-readable description for a thing" ; - skos:inScheme . + skos:inScheme . -smoc:has_assay a owl:ObjectProperty, +modo:has_assay a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_assay" ; - rdfs:range smoc:Assay ; - rdfs:subPropertyOf smoc:has_part ; + rdfs:range modo:Assay ; + rdfs:subPropertyOf modo:has_part ; skos:definition "An assay that was performed as part of a given thing." ; - skos:inScheme . + skos:inScheme . -smoc:has_data a owl:ObjectProperty, +modo:has_data a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_data" ; - rdfs:range smoc:DataEntity ; - rdfs:subPropertyOf smoc:has_part ; + rdfs:range modo:DataEntity ; + rdfs:subPropertyOf modo:has_part ; skos:definition "Data entity included in a given collection." ; - skos:inScheme . + skos:inScheme . -smoc:has_reference a owl:ObjectProperty, +modo:has_reference a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_reference" ; - rdfs:range smoc:ReferenceGenome ; - rdfs:subPropertyOf smoc:has_part ; + rdfs:range modo:ReferenceGenome ; + rdfs:subPropertyOf modo:has_part ; skos:definition "Specifies the reference coordinate system used by an omics dataset." ; - skos:inScheme . + skos:inScheme . -smoc:has_sequence a owl:ObjectProperty, +modo:has_sequence a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_sequence" ; - rdfs:range smoc:ReferenceSequence ; - rdfs:subPropertyOf smoc:has_part ; + rdfs:range modo:ReferenceSequence ; + rdfs:subPropertyOf modo:has_part ; skos:definition "Denotes that a sequence belongs to a collection (e.g. a reference genome)." ; - skos:inScheme . + skos:inScheme . -smoc:id a owl:ObjectProperty, +modo:id a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "id" ; rdfs:range linkml:Uriorcurie ; skos:definition "A unique identifier for a thing" ; - skos:inScheme . + skos:inScheme . -smoc:last_update_date a owl:ObjectProperty, +modo:last_update_date a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "last_update_date" ; rdfs:range linkml:Datetime ; skos:definition "The date on which the thing was last modified." ; - skos:inScheme . + skos:inScheme . -smoc:name a owl:ObjectProperty, +modo:name a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "name" ; skos:definition "A human-readable name for a thing" ; - skos:inScheme . + skos:inScheme . -smoc:sequence_md5 a owl:ObjectProperty, +modo:sequence_md5 a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "sequence_md5" ; rdfs:range [ a rdfs:Datatype ; @@ -413,148 +413,148 @@ smoc:sequence_md5 a owl:ObjectProperty, owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[a-f0-9]{32}$" ] ) ] ) ] ; skos:definition "The pre-computed hash uniquely representing a biological sequence. Calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)." ; - skos:inScheme . + skos:inScheme . -smoc:sex a owl:ObjectProperty, +modo:sex a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "sex" ; - rdfs:range smoc:Sex ; + rdfs:range modo:Sex ; skos:definition "The biological sex of a sample." ; - skos:inScheme . + skos:inScheme . -smoc:source_material a owl:ObjectProperty, +modo:source_material a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "source_material" ; rdfs:range linkml:String ; skos:definition "The biological source from which the sample was isolated (tissue, organ, ...)." ; - skos:inScheme . + skos:inScheme . -smoc:taxon_id a owl:ObjectProperty, +modo:taxon_id a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "taxon_id" ; rdfs:range linkml:Integer ; skos:definition "The taxid number describing the taxonomic range of a sample." ; - skos:inScheme . + skos:inScheme . -smoc:DataEntity a owl:Class, +modo:DataEntity a owl:Class, linkml:ClassDefinition ; rdfs:label "DataEntity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty modo:data_path ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:data_path ], + owl:onProperty modo:has_sample ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:has_reference ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:data_path ], + owl:onProperty modo:has_sample ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:has_sample ], + owl:maxCardinality 1 ; + owl:onProperty modo:data_path ], [ a owl:Restriction ; - owl:allValuesFrom smoc:DataFormat ; - owl:onProperty smoc:data_format ], + owl:allValuesFrom modo:DataFormat ; + owl:onProperty modo:data_format ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty smoc:has_sample ], + owl:minCardinality 1 ; + owl:onProperty modo:data_path ], [ a owl:Restriction ; - owl:allValuesFrom smoc:Sample ; - owl:onProperty smoc:has_sample ], + owl:allValuesFrom modo:Sample ; + owl:onProperty modo:has_sample ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:data_format ], + owl:onProperty modo:has_reference ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty smoc:data_format ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty smoc:data_path ], + owl:allValuesFrom modo:ReferenceGenome ; + owl:onProperty modo:has_reference ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:has_reference ], + owl:onProperty modo:data_format ], [ a owl:Restriction ; - owl:allValuesFrom smoc:ReferenceGenome ; - owl:onProperty smoc:has_reference ], - smoc:NamedThing ; + owl:minCardinality 0 ; + owl:onProperty modo:has_reference ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty modo:data_format ], + modo:NamedThing ; skos:definition "An entity containing data." ; - skos:inScheme . + skos:inScheme . -smoc:has_part a owl:ObjectProperty, +modo:has_part a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_part" ; skos:definition "Indicates an item that is part of this item." ; - skos:inScheme . + skos:inScheme . -smoc:NamedThing a owl:Class, +modo:NamedThing a owl:Class, linkml:ClassDefinition ; rdfs:label "NamedThing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty smoc:id ], + owl:allValuesFrom linkml:String ; + owl:onProperty modo:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:description ], + owl:onProperty modo:id ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty smoc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty smoc:description ], + owl:onProperty modo:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty smoc:name ], + owl:onProperty modo:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty smoc:description ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty modo:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty smoc:name ], + owl:onProperty modo:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:name ], + owl:onProperty modo:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty smoc:id ] ; + owl:onProperty modo:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty modo:name ] ; skos:definition "A generic grouping for any identifiable entity" ; skos:exactMatch schema1:Thing ; - skos:inScheme . + skos:inScheme . -smoc:Sex a owl:Class, +modo:Sex a owl:Class, linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - . + owl:unionOf ( ) ; + linkml:permissible_values , + . -smoc:data_path a owl:ObjectProperty, +modo:data_path a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "data_path" ; rdfs:range linkml:String ; skos:definition "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; - skos:inScheme . + skos:inScheme . -smoc:has_sample a owl:ObjectProperty, +modo:has_sample a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_sample" ; - rdfs:range smoc:Sample ; - rdfs:subPropertyOf smoc:has_part ; + rdfs:range modo:Sample ; + rdfs:subPropertyOf modo:has_part ; skos:definition "Biological sample included or described by a given thing." ; - skos:inScheme . + skos:inScheme . -smoc:version a owl:ObjectProperty, +modo:version a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "version" ; rdfs:range linkml:String ; skos:definition "A string specifying the release or version of a software or resource." ; - skos:inScheme . + skos:inScheme . -smoc:source_uri a owl:ObjectProperty, +modo:source_uri a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "source_uri" ; rdfs:range linkml:Uri ; skos:definition "The URI from which a resource or dataset was obtained or derived." ; - skos:inScheme . + skos:inScheme . -smoc:DataFormat a owl:Class, +modo:DataFormat a owl:Class, linkml:EnumDefinition ; owl:unionOf ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; linkml:permissible_values EDAM:format_1929, @@ -562,7 +562,7 @@ smoc:DataFormat a owl:Class, EDAM:format_3462, EDAM:format_3915 . -smoc:OmicsType a owl:Class, +modo:OmicsType a owl:Class, linkml:EnumDefinition ; owl:unionOf ( NCIT:C84343 NCIT:C153189 NCIT:C49019 NCIT:C20085 ) ; linkml:permissible_values NCIT:C153189, @@ -570,10 +570,10 @@ smoc:OmicsType a owl:Class, NCIT:C49019, NCIT:C84343 . - a owl:Ontology ; - rdfs:label "smoc-schema" ; + a owl:Ontology ; + rdfs:label "modo-schema" ; dcterms:license "MIT" ; - dcterms:title "smoc-schema" ; - rdfs:seeAlso ; + dcterms:title "modo-schema" ; + rdfs:seeAlso ; skos:definition "Metadata schema for the SMOC Multi-Omics Digital Object" . diff --git a/project/prefixmap/smoc_schema.yaml b/project/prefixmap/modo_schema.yaml similarity index 90% rename from project/prefixmap/smoc_schema.yaml rename to project/prefixmap/modo_schema.yaml index 0dabef3..a477893 100644 --- a/project/prefixmap/smoc_schema.yaml +++ b/project/prefixmap/modo_schema.yaml @@ -7,8 +7,8 @@ "bioschemas": "https://bioschemas.org/", "example": "https://example.org/", "linkml": "https://w3id.org/linkml/", + "modo": "https://w3id.org/sdsc-ordes/modo-schema/", "schema": "http://schema.org/", - "smoc": "https://w3id.org/sdsc-ordes/smoc-schema/", "sphn": "https://biomedit.ch/rdf/sphn-schema/sphn#", "NamedThing": { "@id": "schema:Thing" diff --git a/project/protobuf/smoc_schema.proto b/project/protobuf/modo_schema.proto similarity index 100% rename from project/protobuf/smoc_schema.proto rename to project/protobuf/modo_schema.proto diff --git a/project/shacl/smoc_schema.shacl.ttl b/project/shacl/modo_schema.shacl.ttl similarity index 82% rename from project/shacl/smoc_schema.shacl.ttl rename to project/shacl/modo_schema.shacl.ttl index f160b1a..f257186 100644 --- a/project/shacl/smoc_schema.shacl.ttl +++ b/project/shacl/modo_schema.shacl.ttl @@ -1,9 +1,9 @@ @prefix EDAM: . @prefix NCIT: . +@prefix modo: . @prefix rdf: . @prefix schema1: . @prefix sh: . -@prefix smoc: . @prefix xsd: . schema1:Thing a sh:NodeShape ; @@ -15,85 +15,75 @@ schema1:Thing a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path schema1:name ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 2 ; - sh:path schema1:description ] ; + sh:path schema1:description ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path schema1:identifier ] ; sh:targetClass schema1:Thing . -smoc:AlignmentSet a sh:NodeShape ; +modo:AlignmentSet a sh:NodeShape ; sh:closed true ; sh:description "A data entity consisting of genomic intervals aligned to a reference." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], + sh:order 6 ; + sh:path schema1:description ], + [ sh:class modo:Sample ; + sh:description "Biological sample included or described by a given thing." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path modo:has_sample ], [ sh:description "Data/file format associated with a data entity." ; sh:in ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path smoc:data_format ], - [ sh:class smoc:Sample ; - sh:description "Biological sample included or described by a given thing." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path smoc:has_sample ], - [ sh:class smoc:ReferenceGenome ; - sh:description "Specifies the reference coordinate system used by an omics dataset." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path smoc:has_reference ], + sh:path modo:data_format ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path smoc:data_path ], + sh:path modo:data_path ], + [ sh:class modo:ReferenceGenome ; + sh:description "Specifies the reference coordinate system used by an omics dataset." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path modo:has_reference ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ] ; - sh:targetClass smoc:AlignmentSet . + sh:path schema1:name ] ; + sh:targetClass modo:AlignmentSet . -smoc:Array a sh:NodeShape ; +modo:Array a sh:NodeShape ; sh:closed true ; sh:description "Data entity consisting of an N-dimensional array." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class smoc:ReferenceGenome ; - sh:description "Specifies the reference coordinate system used by an omics dataset." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path smoc:has_reference ], - [ sh:description "Data/file format associated with a data entity." ; - sh:in ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path smoc:data_format ], + sh:order 0 ; + sh:path modo:data_path ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path schema1:identifier ], - [ sh:class smoc:Sample ; - sh:description "Biological sample included or described by a given thing." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path smoc:has_sample ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; @@ -104,76 +94,91 @@ smoc:Array a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; + [ sh:class modo:Sample ; + sh:description "Biological sample included or described by a given thing." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path modo:has_sample ], + [ sh:description "Data/file format associated with a data entity." ; + sh:in ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path smoc:data_path ] ; - sh:targetClass smoc:Array . + sh:order 1 ; + sh:path modo:data_format ], + [ sh:class modo:ReferenceGenome ; + sh:description "Specifies the reference coordinate system used by an omics dataset." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path modo:has_reference ] ; + sh:targetClass modo:Array . -smoc:MODOCollection a sh:NodeShape ; +modo:MODOCollection a sh:NodeShape ; sh:closed true ; sh:description "A holder for Multi-Omics Digital Objects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class smoc:MODO ; + sh:property [ sh:class modo:MODO ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path smoc:entries ] ; - sh:targetClass smoc:MODOCollection . + sh:path modo:entries ] ; + sh:targetClass modo:MODOCollection . -smoc:VariantSet a sh:NodeShape ; +modo:VariantSet a sh:NodeShape ; sh:closed true ; sh:description "A data entity consisting of genomic variants relative to a reference." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class smoc:Sample ; - sh:description "Biological sample included or described by a given thing." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path smoc:has_sample ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path smoc:data_path ], - [ sh:class smoc:ReferenceGenome ; - sh:description "Specifies the reference coordinate system used by an omics dataset." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path smoc:has_reference ], + sh:path modo:data_path ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], [ sh:description "Data/file format associated with a data entity." ; sh:in ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path smoc:data_format ] ; - sh:targetClass smoc:VariantSet . + sh:path modo:data_format ], + [ sh:class modo:Sample ; + sh:description "Biological sample included or described by a given thing." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path modo:has_sample ], + [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema1:name ], + [ sh:class modo:ReferenceGenome ; + sh:description "Specifies the reference coordinate system used by an omics dataset." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path modo:has_reference ] ; + sh:targetClass modo:VariantSet . -smoc:Assay a sh:NodeShape ; +modo:Assay a sh:NodeShape ; sh:closed true ; sh:description "A coordinated set of actions designed to generate data from samples." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class smoc:DataEntity ; - sh:description "Data entity included in a given collection." ; + sh:property [ sh:class modo:Sample ; + sh:description "Biological sample included or described by a given thing." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path smoc:has_data ], + sh:order 0 ; + sh:path modo:has_sample ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path schema1:name ], [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -184,233 +189,228 @@ smoc:Assay a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path schema1:name ], + [ sh:class modo:DataEntity ; + sh:description "Data entity included in a given collection." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path modo:has_data ], [ sh:description "The type of omics considered." ; sh:in ( NCIT:C84343 NCIT:C153189 NCIT:C49019 NCIT:C20085 ) ; sh:minCount 1 ; sh:order 2 ; - sh:path smoc:omics_type ], - [ sh:class smoc:Sample ; - sh:description "Biological sample included or described by a given thing." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path smoc:has_sample ] ; - sh:targetClass smoc:Assay . + sh:path modo:omics_type ] ; + sh:targetClass modo:Assay . -smoc:DataEntity a sh:NodeShape ; +modo:DataEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity containing data." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable description for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:property [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], [ sh:description "Data/file format associated with a data entity." ; sh:in ( EDAM:format_3462 EDAM:format_1930 EDAM:format_3915 EDAM:format_1929 ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path smoc:data_format ], + sh:path modo:data_format ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema1:description ], [ sh:datatype xsd:string ; sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path smoc:data_path ], - [ sh:class smoc:ReferenceGenome ; + sh:path modo:data_path ], + [ sh:class modo:ReferenceGenome ; sh:description "Specifies the reference coordinate system used by an omics dataset." ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path smoc:has_reference ], - [ sh:class smoc:Sample ; + sh:path modo:has_reference ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema1:name ], + [ sh:class modo:Sample ; sh:description "Biological sample included or described by a given thing." ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path smoc:has_sample ], - [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ] ; - sh:targetClass smoc:DataEntity . + sh:path modo:has_sample ] ; + sh:targetClass modo:DataEntity . -smoc:MODO a sh:NodeShape ; +modo:MODO a sh:NodeShape ; sh:closed true ; sh:description "Represents the Multi-Omics Digital Object. It encapsulates omics and other datasets and their metadata." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a thing" ; + sh:property [ sh:datatype xsd:dateTime ; + sh:description "The date on which the thing was last modified." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], + sh:order 2 ; + sh:path modo:last_update_date ], + [ sh:datatype xsd:anyURI ; + sh:description "The URI from which a resource or dataset was obtained or derived." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path modo:source_uri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema1:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path schema1:description ], - [ sh:datatype xsd:dateTime ; - sh:description "The date on which something was created." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path smoc:creation_date ], - [ sh:datatype xsd:dateTime ; - sh:description "The date on which the thing was last modified." ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path smoc:last_update_date ], - [ sh:class smoc:Assay ; + sh:order 4 ; + sh:path schema1:identifier ], + [ sh:class modo:Assay ; sh:description "An assay that was performed as part of a given thing." ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path smoc:has_assay ], - [ sh:datatype xsd:anyURI ; - sh:description "The URI from which a resource or dataset was obtained or derived." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path smoc:source_uri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:path modo:has_assay ], + [ sh:datatype xsd:dateTime ; + sh:description "The date on which something was created." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ] ; - sh:targetClass smoc:MODO . + sh:minCount 1 ; + sh:order 0 ; + sh:path modo:creation_date ] ; + sh:targetClass modo:MODO . -smoc:ReferenceSequence a sh:NodeShape ; +modo:ReferenceSequence a sh:NodeShape ; sh:closed true ; sh:description "A contiguous sequence of DNA part of a reference coordinate system (genome assembly)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "The URI from which a resource or dataset was obtained or derived." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path smoc:source_uri ], - [ sh:description "A unique identifier for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The pre-computed hash uniquely representing a biological sequence. Calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path schema1:identifier ], + sh:order 0 ; + sh:path modo:sequence_md5 ; + sh:pattern "^[a-f0-9]{32}$" ], [ sh:datatype xsd:string ; sh:description "A string specifying the release or version of a software or resource." ; sh:maxCount 1 ; sh:order 2 ; - sh:path smoc:version ], + sh:path modo:version ], + [ sh:datatype xsd:anyURI ; + sh:description "The URI from which a resource or dataset was obtained or derived." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path modo:source_uri ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "The pre-computed hash uniquely representing a biological sequence. Calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)." ; + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path smoc:sequence_md5 ; - sh:pattern "^[a-f0-9]{32}$" ], + sh:minCount 1 ; + sh:order 3 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path schema1:name ] ; - sh:targetClass smoc:ReferenceSequence . + sh:targetClass modo:ReferenceSequence . -smoc:ReferenceGenome a sh:NodeShape ; +modo:ReferenceGenome a sh:NodeShape ; sh:closed true ; sh:description "Reference assembly of a given genome, consisting of a collection of congiguous sequences (contigs)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a thing" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A string specifying the release or version of a software or resource." ; sh:maxCount 1 ; sh:order 4 ; - sh:path smoc:version ], + sh:path modo:version ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path schema1:description ], - [ sh:class smoc:ReferenceSequence ; - sh:description "Denotes that a sequence belongs to a collection (e.g. a reference genome)." ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path smoc:has_sequence ], [ sh:datatype xsd:string ; sh:description "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path smoc:data_path ], - [ sh:datatype xsd:integer ; - sh:description "The taxid number describing the taxonomic range of a sample." ; - sh:order 2 ; - sh:path smoc:taxon_id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; + sh:path modo:data_path ], + [ sh:description "A unique identifier for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:name ], + sh:minCount 1 ; + sh:order 5 ; + sh:path schema1:identifier ], [ sh:datatype xsd:anyURI ; sh:description "The URI from which a resource or dataset was obtained or derived." ; sh:maxCount 1 ; sh:order 3 ; - sh:path smoc:source_uri ] ; - sh:targetClass smoc:ReferenceGenome . + sh:path modo:source_uri ], + [ sh:class modo:ReferenceSequence ; + sh:description "Denotes that a sequence belongs to a collection (e.g. a reference genome)." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path modo:has_sequence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema1:name ], + [ sh:datatype xsd:integer ; + sh:description "The taxid number describing the taxonomic range of a sample." ; + sh:order 2 ; + sh:path modo:taxon_id ] ; + sh:targetClass modo:ReferenceGenome . -smoc:Sample a sh:NodeShape ; +modo:Sample a sh:NodeShape ; sh:closed true ; sh:description "A biological sample used in assays. Examples include a whole organism, tissue or cell line." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A unique identifier for a thing" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path schema1:identifier ], + [ sh:datatype xsd:string ; sh:description "The cell type name." ; sh:maxCount 1 ; sh:order 0 ; - sh:path smoc:cell_type ], + sh:path modo:cell_type ], [ sh:datatype xsd:string ; sh:description "The organization responsible for collecting a given sample." ; sh:order 4 ; - sh:path smoc:collector ], + sh:path modo:collector ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path schema1:description ], [ sh:datatype xsd:string ; - sh:description "The biological source from which the sample was isolated (tissue, organ, ...)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path smoc:source_material ], - [ sh:description "A unique identifier for a thing" ; + sh:description "A human-readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path schema1:identifier ], + sh:order 6 ; + sh:path schema1:name ], [ sh:description "The biological sex of a sample." ; sh:in ( "Male" "Female" ) ; sh:maxCount 1 ; sh:order 2 ; - sh:path smoc:sex ], + sh:path modo:sex ], + [ sh:datatype xsd:string ; + sh:description "The biological source from which the sample was isolated (tissue, organ, ...)." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path modo:source_material ], [ sh:datatype xsd:integer ; sh:description "The taxid number describing the taxonomic range of a sample." ; sh:order 3 ; - sh:path smoc:taxon_id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:name ] ; - sh:targetClass smoc:Sample . + sh:path modo:taxon_id ] ; + sh:targetClass modo:Sample . diff --git a/project/shex/smoc_schema.shex b/project/shex/modo_schema.shex similarity index 98% rename from project/shex/smoc_schema.shex rename to project/shex/modo_schema.shex index 093731c..40eb0fd 100644 --- a/project/shex/smoc_schema.shex +++ b/project/shex/modo_schema.shex @@ -1,4 +1,4 @@ -BASE +BASE PREFIX rdf: PREFIX xsd: PREFIX linkml: diff --git a/project/sqlschema/smoc_schema.sql b/project/sqlschema/modo_schema.sql similarity index 100% rename from project/sqlschema/smoc_schema.sql rename to project/sqlschema/modo_schema.sql diff --git a/src/modo_schema/datamodel/smoc_schema.py b/src/modo_schema/datamodel/modo_schema.py similarity index 77% rename from src/modo_schema/datamodel/smoc_schema.py rename to src/modo_schema/datamodel/modo_schema.py index 66b817b..0e29ae3 100644 --- a/src/modo_schema/datamodel/smoc_schema.py +++ b/src/modo_schema/datamodel/modo_schema.py @@ -1,8 +1,8 @@ -# Auto generated from smoc_schema.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-01-17T12:05:25 -# Schema: smoc-schema +# Auto generated from modo_schema.yaml by pythongen.py version: 0.0.1 +# Generation date: 2024-02-21T16:56:00 +# Schema: modo-schema # -# id: https://w3id.org/sdsc-ordes/smoc-schema +# id: https://w3id.org/sdsc-ordes/modo-schema # description: Metadata schema for the SMOC Multi-Omics Digital Object # license: MIT @@ -39,10 +39,10 @@ BIOSCHEMAS = CurieNamespace('bioschemas', 'https://bioschemas.org/') EXAMPLE = CurieNamespace('example', 'https://example.org/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') +MODO = CurieNamespace('modo', 'https://w3id.org/sdsc-ordes/modo-schema/') SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SMOC = CurieNamespace('smoc', 'https://w3id.org/sdsc-ordes/smoc-schema/') SPHN = CurieNamespace('sphn', 'https://biomedit.ch/rdf/sphn-schema/sphn#') -DEFAULT_ = SMOC +DEFAULT_ = MODO # Types @@ -98,7 +98,7 @@ class NamedThing(YAMLRoot): class_class_uri: ClassVar[URIRef] = SCHEMA["Thing"] class_class_curie: ClassVar[str] = "schema:Thing" class_name: ClassVar[str] = "NamedThing" - class_model_uri: ClassVar[URIRef] = SMOC.NamedThing + class_model_uri: ClassVar[URIRef] = MODO.NamedThing id: Union[str, NamedThingId] = None name: Optional[str] = None @@ -126,10 +126,10 @@ class MODO(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["MODO"] - class_class_curie: ClassVar[str] = "smoc:MODO" + class_class_uri: ClassVar[URIRef] = MODO["MODO"] + class_class_curie: ClassVar[str] = "modo:MODO" class_name: ClassVar[str] = "MODO" - class_model_uri: ClassVar[URIRef] = SMOC.MODO + class_model_uri: ClassVar[URIRef] = MODO.MODO id: Union[str, MODOId] = None creation_date: Union[str, XSDDateTime] = None @@ -170,10 +170,10 @@ class Assay(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["Assay"] - class_class_curie: ClassVar[str] = "smoc:Assay" + class_class_uri: ClassVar[URIRef] = MODO["Assay"] + class_class_curie: ClassVar[str] = "modo:Assay" class_name: ClassVar[str] = "Assay" - class_model_uri: ClassVar[URIRef] = SMOC.Assay + class_model_uri: ClassVar[URIRef] = MODO.Assay id: Union[str, AssayId] = None omics_type: Union[Union[str, "OmicsType"], List[Union[str, "OmicsType"]]] = None @@ -210,10 +210,10 @@ class Sample(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["Sample"] - class_class_curie: ClassVar[str] = "smoc:Sample" + class_class_uri: ClassVar[URIRef] = MODO["Sample"] + class_class_curie: ClassVar[str] = "modo:Sample" class_name: ClassVar[str] = "Sample" - class_model_uri: ClassVar[URIRef] = SMOC.Sample + class_model_uri: ClassVar[URIRef] = MODO.Sample id: Union[str, SampleId] = None cell_type: Optional[str] = None @@ -255,10 +255,10 @@ class DataEntity(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["DataEntity"] - class_class_curie: ClassVar[str] = "smoc:DataEntity" + class_class_uri: ClassVar[URIRef] = MODO["DataEntity"] + class_class_curie: ClassVar[str] = "modo:DataEntity" class_name: ClassVar[str] = "DataEntity" - class_model_uri: ClassVar[URIRef] = SMOC.DataEntity + class_model_uri: ClassVar[URIRef] = MODO.DataEntity id: Union[str, DataEntityId] = None data_path: str = None @@ -300,10 +300,10 @@ class ReferenceGenome(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["ReferenceGenome"] - class_class_curie: ClassVar[str] = "smoc:ReferenceGenome" + class_class_uri: ClassVar[URIRef] = MODO["ReferenceGenome"] + class_class_curie: ClassVar[str] = "modo:ReferenceGenome" class_name: ClassVar[str] = "ReferenceGenome" - class_model_uri: ClassVar[URIRef] = SMOC.ReferenceGenome + class_model_uri: ClassVar[URIRef] = MODO.ReferenceGenome id: Union[str, ReferenceGenomeId] = None data_path: str = None @@ -347,10 +347,10 @@ class ReferenceSequence(NamedThing): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["ReferenceSequence"] - class_class_curie: ClassVar[str] = "smoc:ReferenceSequence" + class_class_uri: ClassVar[URIRef] = MODO["ReferenceSequence"] + class_class_curie: ClassVar[str] = "modo:ReferenceSequence" class_name: ClassVar[str] = "ReferenceSequence" - class_model_uri: ClassVar[URIRef] = SMOC.ReferenceSequence + class_model_uri: ClassVar[URIRef] = MODO.ReferenceSequence id: Union[str, ReferenceSequenceId] = None sequence_md5: Optional[str] = None @@ -382,10 +382,10 @@ class AlignmentSet(DataEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["AlignmentSet"] - class_class_curie: ClassVar[str] = "smoc:AlignmentSet" + class_class_uri: ClassVar[URIRef] = MODO["AlignmentSet"] + class_class_curie: ClassVar[str] = "modo:AlignmentSet" class_name: ClassVar[str] = "AlignmentSet" - class_model_uri: ClassVar[URIRef] = SMOC.AlignmentSet + class_model_uri: ClassVar[URIRef] = MODO.AlignmentSet id: Union[str, AlignmentSetId] = None data_path: str = None @@ -407,10 +407,10 @@ class VariantSet(DataEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["VariantSet"] - class_class_curie: ClassVar[str] = "smoc:VariantSet" + class_class_uri: ClassVar[URIRef] = MODO["VariantSet"] + class_class_curie: ClassVar[str] = "modo:VariantSet" class_name: ClassVar[str] = "VariantSet" - class_model_uri: ClassVar[URIRef] = SMOC.VariantSet + class_model_uri: ClassVar[URIRef] = MODO.VariantSet id: Union[str, VariantSetId] = None data_path: str = None @@ -432,10 +432,10 @@ class Array(DataEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["Array"] - class_class_curie: ClassVar[str] = "smoc:Array" + class_class_uri: ClassVar[URIRef] = MODO["Array"] + class_class_curie: ClassVar[str] = "modo:Array" class_name: ClassVar[str] = "Array" - class_model_uri: ClassVar[URIRef] = SMOC.Array + class_model_uri: ClassVar[URIRef] = MODO.Array id: Union[str, ArrayId] = None data_path: str = None @@ -457,10 +457,10 @@ class MODOCollection(YAMLRoot): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = SMOC["MODOCollection"] - class_class_curie: ClassVar[str] = "smoc:MODOCollection" + class_class_uri: ClassVar[URIRef] = MODO["MODOCollection"] + class_class_curie: ClassVar[str] = "modo:MODOCollection" class_name: ClassVar[str] = "MODOCollection" - class_model_uri: ClassVar[URIRef] = SMOC.MODOCollection + class_model_uri: ClassVar[URIRef] = MODO.MODOCollection entries: Optional[Union[Dict[Union[str, MODOId], Union[dict, MODO]], List[Union[dict, MODO]]]] = empty_dict() @@ -535,71 +535,71 @@ class slots: pass slots.id = Slot(uri=SCHEMA.identifier, name="id", curie=SCHEMA.curie('identifier'), - model_uri=SMOC.id, domain=None, range=URIRef) + model_uri=MODO.id, domain=None, range=URIRef) slots.name = Slot(uri=SCHEMA.name, name="name", curie=SCHEMA.curie('name'), - model_uri=SMOC.name, domain=None, range=Optional[str]) + model_uri=MODO.name, domain=None, range=Optional[str]) slots.description = Slot(uri=SCHEMA.description, name="description", curie=SCHEMA.curie('description'), - model_uri=SMOC.description, domain=None, range=Optional[str]) + model_uri=MODO.description, domain=None, range=Optional[str]) slots.has_part = Slot(uri=SCHEMA.hasPart, name="has_part", curie=SCHEMA.curie('hasPart'), - model_uri=SMOC.has_part, domain=None, range=Optional[Union[str, List[str]]]) + model_uri=MODO.has_part, domain=None, range=Optional[Union[str, List[str]]]) -slots.creation_date = Slot(uri=SMOC.creation_date, name="creation_date", curie=SMOC.curie('creation_date'), - model_uri=SMOC.creation_date, domain=None, range=Union[str, XSDDateTime]) +slots.creation_date = Slot(uri=MODO.creation_date, name="creation_date", curie=MODO.curie('creation_date'), + model_uri=MODO.creation_date, domain=None, range=Union[str, XSDDateTime]) -slots.last_update_date = Slot(uri=SMOC.last_update_date, name="last_update_date", curie=SMOC.curie('last_update_date'), - model_uri=SMOC.last_update_date, domain=None, range=Union[str, XSDDateTime]) +slots.last_update_date = Slot(uri=MODO.last_update_date, name="last_update_date", curie=MODO.curie('last_update_date'), + model_uri=MODO.last_update_date, domain=None, range=Union[str, XSDDateTime]) -slots.omics_type = Slot(uri=SMOC.omics_type, name="omics_type", curie=SMOC.curie('omics_type'), - model_uri=SMOC.omics_type, domain=None, range=Union[Union[str, "OmicsType"], List[Union[str, "OmicsType"]]]) +slots.omics_type = Slot(uri=MODO.omics_type, name="omics_type", curie=MODO.curie('omics_type'), + model_uri=MODO.omics_type, domain=None, range=Union[Union[str, "OmicsType"], List[Union[str, "OmicsType"]]]) -slots.has_assay = Slot(uri=SMOC.has_assay, name="has_assay", curie=SMOC.curie('has_assay'), - model_uri=SMOC.has_assay, domain=None, range=Optional[Union[Union[str, AssayId], List[Union[str, AssayId]]]]) +slots.has_assay = Slot(uri=MODO.has_assay, name="has_assay", curie=MODO.curie('has_assay'), + model_uri=MODO.has_assay, domain=None, range=Optional[Union[Union[str, AssayId], List[Union[str, AssayId]]]]) -slots.has_sample = Slot(uri=SMOC.has_sample, name="has_sample", curie=SMOC.curie('has_sample'), - model_uri=SMOC.has_sample, domain=None, range=Optional[Union[Union[str, SampleId], List[Union[str, SampleId]]]]) +slots.has_sample = Slot(uri=MODO.has_sample, name="has_sample", curie=MODO.curie('has_sample'), + model_uri=MODO.has_sample, domain=None, range=Optional[Union[Union[str, SampleId], List[Union[str, SampleId]]]]) -slots.has_data = Slot(uri=SMOC.has_data, name="has_data", curie=SMOC.curie('has_data'), - model_uri=SMOC.has_data, domain=None, range=Optional[Union[Union[str, DataEntityId], List[Union[str, DataEntityId]]]]) +slots.has_data = Slot(uri=MODO.has_data, name="has_data", curie=MODO.curie('has_data'), + model_uri=MODO.has_data, domain=None, range=Optional[Union[Union[str, DataEntityId], List[Union[str, DataEntityId]]]]) -slots.has_sequence = Slot(uri=SMOC.has_sequence, name="has_sequence", curie=SMOC.curie('has_sequence'), - model_uri=SMOC.has_sequence, domain=None, range=Optional[Union[Union[str, ReferenceSequenceId], List[Union[str, ReferenceSequenceId]]]]) +slots.has_sequence = Slot(uri=MODO.has_sequence, name="has_sequence", curie=MODO.curie('has_sequence'), + model_uri=MODO.has_sequence, domain=None, range=Optional[Union[Union[str, ReferenceSequenceId], List[Union[str, ReferenceSequenceId]]]]) -slots.has_reference = Slot(uri=SMOC.has_reference, name="has_reference", curie=SMOC.curie('has_reference'), - model_uri=SMOC.has_reference, domain=None, range=Optional[Union[Union[str, ReferenceGenomeId], List[Union[str, ReferenceGenomeId]]]]) +slots.has_reference = Slot(uri=MODO.has_reference, name="has_reference", curie=MODO.curie('has_reference'), + model_uri=MODO.has_reference, domain=None, range=Optional[Union[Union[str, ReferenceGenomeId], List[Union[str, ReferenceGenomeId]]]]) -slots.data_format = Slot(uri=SMOC.data_format, name="data_format", curie=SMOC.curie('data_format'), - model_uri=SMOC.data_format, domain=None, range=Union[str, "DataFormat"]) +slots.data_format = Slot(uri=MODO.data_format, name="data_format", curie=MODO.curie('data_format'), + model_uri=MODO.data_format, domain=None, range=Union[str, "DataFormat"]) -slots.taxon_id = Slot(uri=SMOC.taxon_id, name="taxon_id", curie=SMOC.curie('taxon_id'), - model_uri=SMOC.taxon_id, domain=None, range=Optional[Union[int, List[int]]]) +slots.taxon_id = Slot(uri=MODO.taxon_id, name="taxon_id", curie=MODO.curie('taxon_id'), + model_uri=MODO.taxon_id, domain=None, range=Optional[Union[int, List[int]]]) -slots.collector = Slot(uri=SMOC.collector, name="collector", curie=SMOC.curie('collector'), - model_uri=SMOC.collector, domain=None, range=Optional[Union[str, List[str]]]) +slots.collector = Slot(uri=MODO.collector, name="collector", curie=MODO.curie('collector'), + model_uri=MODO.collector, domain=None, range=Optional[Union[str, List[str]]]) -slots.data_path = Slot(uri=SMOC.data_path, name="data_path", curie=SMOC.curie('data_path'), - model_uri=SMOC.data_path, domain=None, range=str) +slots.data_path = Slot(uri=MODO.data_path, name="data_path", curie=MODO.curie('data_path'), + model_uri=MODO.data_path, domain=None, range=str) -slots.sequence_md5 = Slot(uri=SMOC.sequence_md5, name="sequence_md5", curie=SMOC.curie('sequence_md5'), - model_uri=SMOC.sequence_md5, domain=None, range=Optional[str], +slots.sequence_md5 = Slot(uri=MODO.sequence_md5, name="sequence_md5", curie=MODO.curie('sequence_md5'), + model_uri=MODO.sequence_md5, domain=None, range=Optional[str], pattern=re.compile(r'^[a-f0-9]{32}$')) -slots.source_uri = Slot(uri=SMOC.source_uri, name="source_uri", curie=SMOC.curie('source_uri'), - model_uri=SMOC.source_uri, domain=None, range=Optional[Union[str, URI]]) +slots.source_uri = Slot(uri=MODO.source_uri, name="source_uri", curie=MODO.curie('source_uri'), + model_uri=MODO.source_uri, domain=None, range=Optional[Union[str, URI]]) -slots.version = Slot(uri=SMOC.version, name="version", curie=SMOC.curie('version'), - model_uri=SMOC.version, domain=None, range=Optional[str]) +slots.version = Slot(uri=MODO.version, name="version", curie=MODO.curie('version'), + model_uri=MODO.version, domain=None, range=Optional[str]) -slots.cell_type = Slot(uri=SMOC.cell_type, name="cell_type", curie=SMOC.curie('cell_type'), - model_uri=SMOC.cell_type, domain=None, range=Optional[str]) +slots.cell_type = Slot(uri=MODO.cell_type, name="cell_type", curie=MODO.curie('cell_type'), + model_uri=MODO.cell_type, domain=None, range=Optional[str]) -slots.source_material = Slot(uri=SMOC.source_material, name="source_material", curie=SMOC.curie('source_material'), - model_uri=SMOC.source_material, domain=None, range=Optional[str]) +slots.source_material = Slot(uri=MODO.source_material, name="source_material", curie=MODO.curie('source_material'), + model_uri=MODO.source_material, domain=None, range=Optional[str]) -slots.sex = Slot(uri=SMOC.sex, name="sex", curie=SMOC.curie('sex'), - model_uri=SMOC.sex, domain=None, range=Optional[Union[str, "Sex"]]) +slots.sex = Slot(uri=MODO.sex, name="sex", curie=MODO.curie('sex'), + model_uri=MODO.sex, domain=None, range=Optional[Union[str, "Sex"]]) -slots.mODOCollection__entries = Slot(uri=SMOC.entries, name="mODOCollection__entries", curie=SMOC.curie('entries'), - model_uri=SMOC.mODOCollection__entries, domain=None, range=Optional[Union[Dict[Union[str, MODOId], Union[dict, MODO]], List[Union[dict, MODO]]]]) \ No newline at end of file +slots.mODOCollection__entries = Slot(uri=MODO.entries, name="mODOCollection__entries", curie=MODO.curie('entries'), + model_uri=MODO.mODOCollection__entries, domain=None, range=Optional[Union[Dict[Union[str, MODOId], Union[dict, MODO]], List[Union[dict, MODO]]]]) \ No newline at end of file diff --git a/src/modo_schema/schema/smoc_schema.yaml b/src/modo_schema/schema/modo_schema.yaml similarity index 100% rename from src/modo_schema/schema/smoc_schema.yaml rename to src/modo_schema/schema/modo_schema.yaml