Adding Databases object

examples/configurations/database-sources/prod-nexus-sources.yml

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+Model:
+  name: RdfModel
+  origin: store
+  source: BlueBrainNexus
+  context:
+    iri: "https://bbp.neuroshapes.org"
+    bucket: "neurosciencegraph/datamodels"
+Store:
+  name: BlueBrainNexus
+  endpoint: https://bbp.epfl.ch/nexus/v1
+  searchendpoints:
+    sparql:
+      endpoint: "https://bluebrain.github.io/nexus/vocabulary/defaultSparqlIndex"
+    elastic:
+      endpoint: "https://bbp.epfl.ch/neurosciencegraph/data/views/aggreg-es/dataset"
+      mapping: "https://bbp.epfl.ch/neurosciencegraph/data/views/es/dataset"
+      default_str_keyword_field: "keyword"
+  vocabulary:
+    metadata:
+      iri: "https://bluebrain.github.io/nexus/contexts/metadata.json"
+      local_iri: "https://bluebrainnexus.io/contexts/metadata.json"
+    namespace: "https://bluebrain.github.io/nexus/vocabulary/"
+    deprecated_property: "https://bluebrain.github.io/nexus/vocabulary/deprecated"
+    project_property: "https://bluebrain.github.io/nexus/vocabulary/project"
+  max_connection: 50
+  versioned_id_template: "{x.id}?rev={x._store_metadata._rev}"
+  file_resource_mapping: https://raw.githubusercontent.com/BlueBrain/nexus-forge/master/examples/configurations/nexus-store/file-to-resource-mapping.hjson
+
+Resolvers:
+  ontology:
+    - resolver: OntologyResolver
+      origin: store
+      source: BlueBrainNexus
+      targets:
+        - identifier: terms
+          bucket: neurosciencegraph/datamodels
+      searchendpoints:
+        sparql:
+          endpoint: "https://bluebrain.github.io/nexus/vocabulary/defaultSparqlIndex"
+      result_resource_mapping: https://raw.githubusercontent.com/BlueBrain/nexus-forge/master/examples/configurations/nexus-resolver/term-to-resource-mapping.hjson
+  agent:
+    - resolver: AgentResolver
+      origin: store
+      source: BlueBrainNexus
+      targets:
+        - identifier: agents
+          bucket: bbp/agents
+      searchendpoints:
+        sparql:
+          endpoint: "https://bluebrain.github.io/nexus/vocabulary/defaultSparqlIndex"
+      result_resource_mapping: https://raw.githubusercontent.com/BlueBrain/nexus-forge/master/examples/configurations/nexus-resolver/agent-to-resource-mapping.hjson
+
+Formatters:
+  identifier: https://bbp.epfl.ch/neurosciencegraph/data/{}/{}
+  identifier_neuroelectro: http://neuroelectro.org/api/1/{}/{}
+  identifier_neurolex: http://neurolex.org/wiki/{}
+
+Databases:
+  UniProt:
+    origin: store
+    source: SPARQLStore
+    searchendpoints:
+      sparql:
+        endpoint: "https://sparql.uniprot.org/sparql"
+    model: 
+      name: RdfModel 
+      origin: directory
+      source: /Users/cgonzale/Documents/code/nexus-forge/examples/database-sources/UniProt
+      context:
+        iri: /Users/cgonzale/Documents/code/nexus-forge/examples/database-sources/UniProt/jsonld_context.json
+  NeuroElectro:
+    origin: store
+    source: BlueBrainNexus
+    bucket: bbp/neuroelectro
+    model:
+      name: RdfModel
+      origin: directory
+      source: /Users/cgonzale/Documents/code/nexus-forge/examples/database-sources/NeuroElectro
+      context:
+        iri: /Users/cgonzale/Documents/code/nexus-forge/examples/models/neuroshapes_context.json 
+  NeuroMorpho:
+    origin: web_service
+    source: http://neuromorpho.org/api/neuron
+    health: http://neuromorpho.org/api/health
+    files_download:
+      endpoint: https://neuromorpho.org/dableFiles
+      Accept: "*/*"
+    max_connection: 50
+    content_type: application/json;charset=UTF-8
+    accept: "*/*"
+    model:
+      name: RdfModel
+      origin: directory
+      source: /Users/cgonzale/Documents/code/nexus-forge/examples/database-sources/Neuromorpho
+      context:
+        iri: /Users/cgonzale/Documents/code/nexus-forge/examples/database-sources/Neuromorpho/jsonld_context.json

examples/database-sources/DemoDB/mappings/DictionaryMappings/Example.hjson

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+{
+  id: forge.format('identifier', "examples", x.id.split('/')[-1])
+  type: [
+    Entity
+    ]
+  name: x.name
+  label: x.label
+  subject: forge.resolve(x.subject, scope='ontology') if forge.resolve(x.subject, scope='ontology') is not None else {"label": x.subject}
+}

examples/database-sources/MouseLight/mappings/DictionaryMapping/NeuronMorphology.hjson

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+{
+    type: [
+        Dataset
+        NeuronMorphology
+    ]
+    id: forge.format("identifier", "neuronmorphologies/mouselight", x.neurons[0]["idString"])
+    brainLocation:
+    {
+        type: BrainLocation
+        brainRegion:
+        {
+            id: f"http://api.brain-map.org/api/v2/data/Structure/{x.neurons[0]['soma']['allenId']}"
+            label: x.neurons[0]["allenLabel"]
+        }
+        coordinatesInBrainAtlas:
+        {
+            valueX: x.neurons[0]["soma"]["x"]
+            valueY: x.neurons[0]["soma"]["y"]
+            valueZ: x.neurons[0]["soma"]["z"]
+        }
+    }
+    contribution:
+    {
+        type: Contribution
+        agent:
+        {
+            type: Organization
+            id: https://www.grid.ac/institutes/grid.443970.d
+            label: "Janelia Research Campus"
+        }
+    }
+    distribution: forge.attach(f"./mouselight/{x.neurons[0]['idString']}.swc", content_type="application/swc")
+    identifier: x.neurons[0]["idString"]
+    name: x.neurons[0]["idString"]
+    generation:
+    {
+        type: Generation
+        activity:
+        {
+            type: "nsg:NeuronMorphologyReconstruction"
+            hadProtocol:{
+
+            }
+        }
+    }
+    subject:
+    {
+        type: Subject
+        species: {
+            id: http://purl.obolibrary.org/obo/NCBITaxon_10090
+            label: Mus musculus
+        }
+        strain: {
+            label: x.neurons[0]["sample"]["strain"]
+        }
+    }
+    license:
+    {
+        type: License
+        id: https://mouselight.janelia.org
+    }
+    objectOfStudy:
+    {
+        type: ObjectOfStudy
+        id: http://bbp.epfl.ch/neurosciencegraph/taxonomies/objectsofstudy/singlecells
+        label: Single Cell
+    }
+    dateCreated: x.neurons[0]["sample"]["date"]
+    version: x.neurons[0]["annotationSpace"]["version"]
+    description: x.neurons[0]["annotationSpace"]["description"]
+    virus: x.neurons[0]["label"]["virus"]
+    fluorophore: x.neurons[0]["label"]["fluorophore"]
+}

examples/database-sources/MouseLight/metadata.json

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+{
+  "description": "The MouseLight project generates datasets of whole mouse brains imaged at submicron resolution that allows reconstructions of complete axonal arbors of individual neurons across the entire mouse brain. ",
+  "url": "https://www.janelia.org/project-team/mouselight/neuronbrowser",
+  "license" : {
+    "id": "https://creativecommons.org/licenses/by-nc/4.0",
+    "label": "CC BY-NC 4.0"
+  }
+}

examples/database-sources/NeuroElectro/jsonld_context.json

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+{
+    "@context": {
+      "@vocab": "http://example.org/vocab/",
+      "Activity": {
+        "@id": "prov:Activity"
+      },
+      "Agent": {
+        "@id": "prov:Agent"
+      },
+      "Class": {
+        "@id": "owl:Class"
+      },
+      "Entity": {
+        "@id": "prov:Entity"
+      },
+      "Association": {
+        "@id": "schema:Association"
+      },
+      "BrainRegion": {
+        "@id": "nsg:BrainRegion"
+      },
+      "Building": {
+        "@id": "http://schema.org/Building"
+      },
+      "Employee": {
+        "@id": "http://www.example.com/Employee"
+      },
+      "Organization": {
+        "@id": "schema:Organization"
+      },
+      "Person": {
+        "@id": "schema:Person"
+      },
+      "PostalAddress": {
+        "@id": "schema:PostalAddress"
+      },
+      "address": {
+        "@id": "schema:address"
+      },
+      "agent": {
+        "@id": "schema:agent"
+      },
+      "birthDate": {
+        "@id": "schema:birthDate",
+        "@type": "xsd:date"
+      },
+      "citation": {
+        "@id": "schema:citation"
+      },
+      "contractor": {
+        "@id": "schema:contractor"
+      },
+      "deathDate": {
+        "@id": "schema:deathDate",
+        "@type": "xsd:date"
+      },
+      "department": {
+        "@id": "schema:department"
+      },
+      "description": {
+        "@id": "schema:description"
+      },
+      "endedAtTime": {
+        "@id": "prov:endedAtTime"
+      },
+      "familyName": {
+        "@id": "schema:familyName"
+      },
+      "founder": {
+        "@id": "schema:founder"
+      },
+      "gender": {
+        "@id": "schema:gender"
+      },
+      "generated": {
+        "@id": "prov:generated"
+      },
+      "geo": {
+        "@id": "schema:geo"
+      },
+      "givenName": {
+        "@id": "schema:givenName"
+      },
+      "image": {
+        "@id": "http://schema.org/image",
+        "@type": "@id"
+      },
+      "isDefinedBy": {
+        "@id": "rdfs:isDefinedBy",
+        "@type": "@id"
+      },
+      "label": "rdfs:label",
+      "latitude": {
+        "@id": "schema:latitude",
+        "@type": "xsd:float"
+      },
+      "longitude": {
+        "@id": "schema:longitude"
+      },
+      "name": {
+        "@id": "schema:name"
+      },
+      "notation": "skos:notation",
+      "nsg": "https://neuroshapes.org/",
+      "owl": "http://www.w3.org/2002/07/owl#",
+      "postalCode": {
+        "@id": "schema:postalCode"
+      },
+      "prefLabel": "skos:prefLabel",
+      "prov": "http://www.w3.org/ns/prov#",
+      "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+      "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+      "schema": "http://schema.org/",
+      "skos": "http://www.w3.org/2004/02/skos/core#",
+      "startDate": {
+        "@id": "schema:startDate",
+        "@type": "xsd:date"
+      },
+      "startedAtTime": {
+        "@id": "prov:startedAtTime",
+        "@type": "xsd:dateTime"
+      },
+      "status": {
+        "@id": "schema:status"
+      },
+      "streetAddress": {
+        "@id": "schema:streetAddress"
+      },
+      "subClassOf": {
+        "@id": "rdfs:subClassOf",
+        "@type": "@id"
+      },
+      "supervisor": {
+        "@id": "schema:supervisor",
+        "@type": "@id"
+      },
+      "type": {
+        "@id": "rdf:type",
+        "@type": "@id"
+      },
+      "used": {
+        "@id": "prov:used"
+      },
+      "validated": {
+        "@id": "schema:validated"
+      },
+      "value": {
+        "@id": "schema:value"
+      },
+      "wasStartedBy": {
+        "@id": "prov:wasStartedBy",
+        "@type": "@id"
+      },
+      "xsd": "http://www.w3.org/2001/XMLSchema#",
+      "foaf": "http://xmlns.com/foaf/0.1/"
+    },
+    "@id": "http://context.example.org"
+  }