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Adding mock data JSONs

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mvaradi 2018-10-12 17:25:27 +01:00
parent ef52242835
commit 1abe739044
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202
data/funpdbe_schema.json Normal file
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{
"$schema": "http://json-schema.org/draft-06/schema#",
"$id": "https://github.com/funpdbe-consortium/funpdbe_schema/blob/master/funpdbe_schema.v0.0.1.json",
"title": "funpdbe_schema",
"type": "object",
"properties": {
"data_resource": {
"type": "string",
"description": "Name of the database or software"
},
"resource_version": {
"type": "string",
"description": "Version of the resource"
},
"software_version": {
"type": "string",
"description": "Version of the software used"
},
"resource_entry_url": {
"type": "string",
"description": "URL linking to the entry at the partner resource"
},
"release_date": {
"type": "string",
"description": "Release date of the annotation",
"pattern": "^[0-3]*[0-9]/[0-1]*[0-9]/[1-2][0-9]{3}$"
},
"pdb_id": {
"type": "string",
"description": "PDB identifier",
"pattern": "^[1-9][a-zA-Z0-9]{3}$"
},
"additional_entry_annotations": {
"type": "object",
"description": "Additional entry-level annotations"
},
"chains": {
"type": "array",
"items": {
"type": "object",
"properties": {
"chain_label": {
"type": "string",
"description": "PDB chain identifier"
},
"additional_chain_annotations": {
"type": "object",
"description": "Additional chain-level annotations"
},
"residues": {
"type": "array",
"items": {
"type": "object",
"properties": {
"pdb_res_label": {
"type": "string",
"description": "Residue index from the related PDB entry"
},
"aa_type": {
"type": "string",
"description": "Three-letter amino acid code",
"pattern": "^[A-Za-z0-9]+$"
},
"additional_residue_annotations": {
"type": "object",
"description": "Additional residue-level annotations"
},
"site_data": {
"type": "array",
"items": {
"type": "object",
"properties": {
"site_id_ref": {
"type": "integer",
"description": "Reference to site_id"
},
"raw_score": {
"type": "number",
"description": "Raw calculated score"
},
"confidence_score": {
"type": "number",
"description": "Confidence level of the annotation (0-1)",
"minimum": 0.0,
"maximum": 1.0
},
"confidence_classification": {
"type": "string",
"description": "Confidence classification of the residue",
"enum": [
"high",
"medium",
"low",
"null"
]
}
},
"required": [
"site_id_ref",
"raw_score",
"confidence_score",
"confidence_classification"
],
"additionalProperties": false
},
"minItems": 1,
"uniqueItems": true
}
},
"required": [
"pdb_res_label",
"aa_type",
"site_data"
],
"additionalProperties": false
},
"minItems": 1,
"uniqueItems": true
}
},
"required": [
"chain_label",
"residues"
],
"additionalProperties": false
},
"minItems": 1,
"uniqueItems": true
},
"sites": {
"type": "array",
"items": {
"type": "object",
"properties": {
"site_id": {
"type": "integer",
"description": "Site identifier"
},
"label": {
"type": "string",
"description": "Site label"
},
"source_database": {
"type": "string",
"description": "Name of the source database"
},
"source_accession": {
"type": "string",
"description": "Accession identifier"
},
"source_release_date": {
"type": "string",
"description": "Date of acquiring data from source",
"pattern": "^[0-3]*[0-9]/[0-1]*[0-9]/[1-2][0-9]{3}$"
},
"additional_site_annotations": {
"type": "object",
"description": "Additional site-level annotations"
}
},
"required": [
"site_id",
"label"
],
"additionalProperties": false
},
"minItems": 1,
"uniqueItems": true
},
"evidence_code_ontology": {
"type": "array",
"items": {
"type": "object",
"properties": {
"eco_term": {
"type": "string",
"description": "Evidence Code Ontology (ECO) term - http://www.evidenceontology.org/"
},
"eco_code": {
"type": "string",
"description": "Evidence Code Ontology (ECO) code - http://www.evidenceontology.org/",
"pattern": "^ECO_[0-9]{7}$"
}
},
"required": [
"eco_code"
],
"additionalProperties": false
},
"minItems": 1,
"uniqueItems": true
}
},
"required": [
"data_resource",
"pdb_id",
"chains",
"evidence_code_ontology",
"sites"
],
"additionalProperties": false
}

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data/test_data.json Normal file
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{
"data_resource": "ProKinO",
"resource_version": "2.0",
"software_version": "2.0",
"resource_entry_url": "http://vulcan.cs.uga.edu/prokino/",
"release_date": "10/02/2017",
"pdb_id": "2gs6",
"chains": [
{
"additional_chain_annotations": {},
"residues": [
{
"additional_residue_annotations": {},
"pdb_res_label": 811,
"aa_type": "HIS",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 811,
"confidence_classification": "high",
"raw_score": 1
}
]
},
{
"additional_residue_annotations": {},
"pdb_res_label": 812,
"aa_type": "ARG",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 812,
"confidence_classification": "high",
"raw_score": 1
}
]
},
{
"additional_residue_annotations": {},
"pdb_res_label": 813,
"aa_type": "ASP",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 813,
"confidence_classification": "high",
"raw_score": 1
}
]
}
],
"chain_label": "A"
}
],
"sites": [
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 811,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
},
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 812,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
},
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 813,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
}
],
"additional_entry_annotations": {},
"evidence_code_ontology": [
{
"eco_term": "computational combinatorial evidence",
"eco_code": "ECO_0000246"
}
]
}

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data/test_data_malformed.json Normal file
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