Adjusting and adding examples for every specification

Beacon/examples/Amplab_jsonld.json

@@ -0,0 +1,62 @@
+{
+    "@context": "http://schema.org",
+    "@type": "Beacon",
+    "identifier": "amplab",
+    "name": "AMPLab - 1000 Genomes Project",
+    "supportedReference": "hg38",
+    "url": "https://amplab.cs.berkeley.edu/",
+    "version": "v0.1",
+    "dataset": [
+        {
+            "@type": "Dataset",
+            "identifier": "EGAD00001000227",
+            "name": "UK10K NEURO ABERDEEN",
+            "description": "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.",
+            "url": "https://www.ebi.ac.uk/ega/dacs/EGAC00001000205",
+            "provider": [
+                {
+                    "@type": "Organization",
+                    "name": "EMBL-EBI",
+                    "contactPoint": {
+                        "email": "",
+                        "name": ""
+                    },
+                    "description": "",
+                    "url": "http://www.ebi.ac.uk/",
+                    "address": "",
+                    "logo": "https://example.com/logo.png"
+                },
+                {
+                    "@type": "Organization",
+                    "name": "CRG",
+                    "contactPoint": {
+                        "email": "",
+                        "name": ""
+                    },
+                    "description": "",
+                    "url": "https://ega.crg.eu",
+                    "address": "",
+                    "logo": ""
+                }
+            ]
+        }
+    ],
+    "provider": {
+        "@type": "Organization",
+        "memberOf": [
+            {
+                "@type": "Organization",
+                "name": "Beacon network",
+                "url": "https://beacon-network.org"
+            },
+            {
+                "@type": "Organization",
+                "name": "Global Alliance for Genomics and Health",
+                "url": "https://www.ga4gh.org/"
+            }
+        ],
+        "name": "Beacon Network",
+        "url": "https://beacon-network.org",
+        "email": "[email protected]"
+    }
+}

Beacon/examples/EGA_beacon_jsonld.json

@@ -0,0 +1,36 @@
+{
+  "@context": "http://bioschemas.org",
+  "@type": "Beacon",
+  "identifier": "ega",
+  "name:": "European Genome-Phenome Archive",
+  "url": "https://ega.crg.eu/beacon_web/",
+  "provider": [
+    {
+      "@type": "Organization",
+      "name": "EMBL-EBI",
+      "contactPoint":{"email":"","name":""},
+      "description":"",
+      "url":"http://www.ebi.ac.uk/",
+      "address":"",
+      "logo":"https://example.com/logo.png"
+    },
+    {
+      "@type": "Organization",
+      "name": "CRG",
+      "contactPoint":{"email":"","name":""},
+      "description":"",
+      "url":"https://ega.crg.eu",
+      "address":"",
+      "logo":""
+    }
+  ],
+  "dataset": [
+    {
+      "@type": "Dataset",
+      "identifier": "EGAD00001000227",
+      ...
+    },
+    ...
+  ],
+  "supportedReference": "HG19"  
+}

PhysicalEntity/examples/BioChemEntity-min+rec.jsonld → BioChemEntity/examples/BioChemEntity-min+rec_jsonld.json

@@ -44,4 +44,4 @@
 		"name": "Homo sapiens",
 		"url": "http://purl.bioontology.org/ontology/NCBITAXON/9606"
 	}
-}
+}

PhysicalEntity/examples/BioChemEntity-min.jsonld → BioChemEntity/examples/BioChemEntity-min_jsonld.json

@@ -27,4 +27,4 @@
 		"name": "Homo sapiens",
 		"url": "http://purl.bioontology.org/ontology/NCBITAXON/9606"
 	}
-}
+}

PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld → BioChemEntity/examples/BioChemEntityAlt-min+rec_jsonld.json

@@ -31,4 +31,4 @@
 		},
 		"sameAs": "http://www.uniprot.org/disease/DI-0375"
 	}
-}
+}

DataCatalog/examples/BioSamples.json → DataCatalog/examples/BioSamples_jsonld.json

@@ -8,4 +8,4 @@
         "@type": "Organization",
         "name": "EMBL-EBI"
     }
-}
+}

DataCatalog/examples/CATH_jsonld.json

@@ -0,0 +1,61 @@
+{
+  "@context": "http://schema.org",
+  "@type": "DataCatalog",
+  "name": "CATH - Protein Structure Classification",
+  "description": "CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor.",
+  "url": "http://cathdb.info/",
+  "dataset": [
+    {
+      "@type": "Dataset",
+      "name": "Collection",
+      "description": "CATH Domain Classification List (latest release) - protein structural domains classified into CATH hierarchy.",
+      "identifier": "https://identifiers.org/MIR:00100005",
+      "url": "ftp://orengoftp.biochem.ucl.ac.uk/cath/releases/latest-release/cath-classification-data/cath-domain-list.txt",
+      "keywords": [
+        "protein",
+        "domain"
+      ]
+    },
+    {
+      "@type": "Dataset",
+      "name": "Collection",
+      "description": "CATH Domain Boundaries List (latest release) - PDB residue start/stop boundaries for CATH protein structural domains.",
+      "identifier": "https://identifiers.org/MIR:00100005",
+      "url": "ftp://orengoftp.biochem.ucl.ac.uk/cath/releases/latest-release/cath-classification-data/cath-domain-boundaries.txt",
+      "keywords": [
+        "protein",
+        "domain"
+      ]
+    }
+  ],
+  "keywords": [
+    "registry",
+    "life science"
+  ],
+  "provider": [
+    {
+      "@type": "Person",
+      "name": "CATH support",
+      "email": "[email protected]"
+    }
+  ],
+  "identifier": "www.cathdb.info",
+  "alternateName": "CATH-Gene3D",
+  "license": "http://creativecommons.org/licenses/by/4.0/",
+  "publication": {
+    "@id": "http://www.identifiers.org/pubmed/27899584",
+    "@type": "PublicationEvent",
+    "name": "CATH: an expanded resource to predict protein function through structure and sequence.",
+    "sameAs": [
+      "https://www.ncbi.nlm.nih.gov/pubmed/27899584",
+      "http://europepmc.org/abstract/MED/27899584",
+      "http://purl.uniprot.org/citations/27899584"
+    ]
+  },
+  "sourceOrganization": {
+    "@type": "Organization",
+    "name": "University College London (UCL)",
+    "identifier": "www.ucl.ac.uk"
+  },
+  "image": "http://www.cathdb.info/static/images/cath-favicon.png"
+}

DataCatalog/examples/EGA_jsonld.json

@@ -0,0 +1,49 @@
+{
+    "@context": "http://schema.org",
+    "@type": "DataCatalog",
+    "name": "European Genome-phenome Archive",
+    "alternateName": "EGA",
+    "description": "The EGA provides a service for the permanent archiving and distribution of personally identifiable genetic and phenotypic data resulting from biomedical research projects. Data at EGA was collected from individuals whose consent agreements authorise data release only for specific research use to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project.",
+    "url": "https://ega-archive.org",
+    "publication": {
+        "@type": "PublicationEvent",
+        "name": "The European Genome-phenome Archive of human data consented for biomedical research.",
+        "url": "http://europepmc.org/abstract/MED/26111507"
+    },
+    "keywords": [
+        "European Genome-phenome Archive",
+        "Genomics",
+        "Genomics Research",
+        "CRG",
+        "Centre for Genomic Regulation",
+        "EGA",
+        "EBI",
+        "European Bioinformatic Institute",
+        "Research",
+        "Genomics Archives",
+        "European Research",
+        "Human",
+        "Controlled Access",
+        "Human Data",
+        "Natural Science"
+    ],
+    "sourceOrganization": [
+        {
+            "@type": "Organization",
+            "name": "The European Bioinformatics Institute (EMBL-EBI)",
+            "url": "http://www.ebi.ac.uk/"
+        },
+        {
+            "@type": "Organization",
+            "name": "Centre for Genomic Regulation (CRG) ",
+            "url": "http://www.crg.eu/"
+        }
+    ],
+    "provider": [
+        {
+            "@type": "Person",
+            "name": "Helpdesk Officer",
+            "email": "[email protected]"
+        }
+    ]
+}