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Merge pull request #10 from RNABioInfo/schema-properties-small-typo
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Schema properties small typo
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@jfallmann
jfallmann authored May 20, 2023
2 parents a8ef923 + 28c34e2 commit 544385a
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Showing 4 changed files with 38 additions and 24 deletions.
2 changes: 1 addition & 1 deletion examples/small.json
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Expand Up @@ -33,7 +33,7 @@
"type": "mRNA",
"genomic_coordinates": "chr1:-:2866559-2867551",
"organism_name": "Escherichia coli K-12 MG1655",
"organisms_acc": "NC_000913",
"organism_acc": "NC_000913",
"local_sites":{
"dsrA":[[70,83],[19,32]]
}
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6 changes: 3 additions & 3 deletions impl/python/RIF/tests/multi_test.json
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Expand Up @@ -35,7 +35,7 @@
"dsrA": [[60,78],[45,55]],
"rpoS": [[10,40]]
},
"other": {
"info": {
"description": "RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations.",
"sequence": "MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE",
"note": "https://www.ebi.ac.uk/pdbe/entry/pdb/5I21"
Expand Down Expand Up @@ -73,7 +73,7 @@
"Hfq": [[200,230]],
"dsrA": [[587,607]]
},
"other": {
"info": {
"description": "RNA polymerase, sigma S (sigma 38) factor",
"sequence": "TGAGTCAGAATACGCTGAAAGTTCATGATTTAAATGAAGATGCGGAATTTGATGAGAACGGAGTTGAGGTTTTTGACGAAAAGGCCTTAGTAGAACAGGAACCCAGTGATAACGATTTGGCCGAAGAGGAACTGTTATCGCAGGGAGCCACACAGCGTGTGTTGGACGCGACTCAGCTTTACCTTGGTGAGATTGGTTATTCACCACTGTTAACGGCCGAAGAAGAAGTTTATTTTGCGCGTCGCGCACTGCGTGGAGATGTCGCCTCTCGCCGCCGGATGATCGAGAGTAACTTGCGTCTGGTGGTAAAAATTGCCCGCCGTTATGGCAATCGTGGTCTGGCGTTGCTGGACCTTATCGAAGAGGGCAACCTGGGGCTGATCCGCGCGGTAGAGAAGTTTGACCCGGAACGTGGTTTCCGCTTCTCAACATACGCAACCTGGTGGATTCGCCAGACGATTGAACGGGCGATTATGAACCAAACCCGTACTATTCGTTTGCCGATTCACATCGTAAAGGAGCTGAACGTTTACCTGCGAACCGCACGTGAGTTGTCCCATAAGCTGGACCATGAACCAAGTGCGGAAGAGATCGCAGAGCAACTGGATAAGCCAGTTGATGACGTCAGCCGTATGCTTCGTCTTAACGAGCGCATACCTCGGTAGACACCCCGCTGGGTGGTGATTCCGAAAAAGCGTTGCTGGACATCCTGGCCGATGAAAAAGAGAACGGTCCGGAAGATACCACGCAAGATGACGATATGAAGCAGAGCATCGTCAAATGGCTGTTCGAGCTGAACGCCAAACAGCGTGAAGTGCTGGCACGTCGATTCGGTTTGCTGGGGTACGAAGCGGCAACACTGGAAGATGTAGGTCGTGAAATTGGCCTCACCCGTGAACGTGTTCGCCAGATTCAGGTTGAAGGCCTGCGCCGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAAGCGCTGTTCCGCGAGTAA",
"structure": "(((((((((((.........)))).))))))).........(((((((..((((.((((((..(((((((((((.....))))))))))).......((..(((.(((((((((......((.....))...))))))))).)))..)).....(((((((((.((((((....((((((..((((((..(((((((.....))))..)))....))).)))..)))))).......))))))....((((((((((....(((((((..(((((((((((..((((.....))))))))))))))).....(((((((((.....)))..(((.((((((((...))))))))....)))...))))))...))))).)))))))))))).(((((((..((((((...)).))))...))))))))))))))))...((((((....))))))((((....(((((...............))))).....))))...))).))).))))........(((((.((((...((((((.((((((.((.(((((((........))))....))))).))))))......))))))..(((((((....)))))))..))))))))).(((((((((((....))))).)))))).((((....((((((....)).))))...))))...(((((((((((...(((.(((((.............))))).))).....))).)))......((((((..(((......((((((((((((.((((.....))))(((...((((.((((...((((((((((..((((((((((((..........)))))).)))))).)))))((((((......))))))(((........)))...))))).)))).))))..)))....)))))))).))))..((((((....)))))))))..))))))..))))))))))))......"
Expand Down Expand Up @@ -177,7 +177,7 @@
"sequence_type": "rna",
"genomic_coordinates": "NC_000913.3:+:932595-933089",
"organism_name": "Escherichia coli K-12 MG1655",
"organisms_acc": "NC_000913.3",
"organism_acc": "NC_000913.3",
"local_sites": {
"micF": [[100,107],[158,167]]
},
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2 changes: 1 addition & 1 deletion impl/python/RIF/tests/test.json
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Expand Up @@ -73,7 +73,7 @@
"Hfq": [[200,230]],
"dsrA": [[587,607]]
},
"other": {
"info": {
"description": "RNA polymerase, sigma S (sigma 38) factor",
"sequence": "TGAGTCAGAATACGCTGAAAGTTCATGATTTAAATGAAGATGCGGAATTTGATGAGAACGGAGTTGAGGTTTTTGACGAAAAGGCCTTAGTAGAACAGGAACCCAGTGATAACGATTTGGCCGAAGAGGAACTGTTATCGCAGGGAGCCACACAGCGTGTGTTGGACGCGACTCAGCTTTACCTTGGTGAGATTGGTTATTCACCACTGTTAACGGCCGAAGAAGAAGTTTATTTTGCGCGTCGCGCACTGCGTGGAGATGTCGCCTCTCGCCGCCGGATGATCGAGAGTAACTTGCGTCTGGTGGTAAAAATTGCCCGCCGTTATGGCAATCGTGGTCTGGCGTTGCTGGACCTTATCGAAGAGGGCAACCTGGGGCTGATCCGCGCGGTAGAGAAGTTTGACCCGGAACGTGGTTTCCGCTTCTCAACATACGCAACCTGGTGGATTCGCCAGACGATTGAACGGGCGATTATGAACCAAACCCGTACTATTCGTTTGCCGATTCACATCGTAAAGGAGCTGAACGTTTACCTGCGAACCGCACGTGAGTTGTCCCATAAGCTGGACCATGAACCAAGTGCGGAAGAGATCGCAGAGCAACTGGATAAGCCAGTTGATGACGTCAGCCGTATGCTTCGTCTTAACGAGCGCATACCTCGGTAGACACCCCGCTGGGTGGTGATTCCGAAAAAGCGTTGCTGGACATCCTGGCCGATGAAAAAGAGAACGGTCCGGAAGATACCACGCAAGATGACGATATGAAGCAGAGCATCGTCAAATGGCTGTTCGAGCTGAACGCCAAACAGCGTGAAGTGCTGGCACGTCGATTCGGTTTGCTGGGGTACGAAGCGGCAACACTGGAAGATGTAGGTCGTGAAATTGGCCTCACCCGTGAACGTGTTCGCCAGATTCAGGTTGAAGGCCTGCGCCGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAAGCGCTGTTCCGCGAGTAA",
"structure": "(((((((((((.........)))).))))))).........(((((((..((((.((((((..(((((((((((.....))))))))))).......((..(((.(((((((((......((.....))...))))))))).)))..)).....(((((((((.((((((....((((((..((((((..(((((((.....))))..)))....))).)))..)))))).......))))))....((((((((((....(((((((..(((((((((((..((((.....))))))))))))))).....(((((((((.....)))..(((.((((((((...))))))))....)))...))))))...))))).)))))))))))).(((((((..((((((...)).))))...))))))))))))))))...((((((....))))))((((....(((((...............))))).....))))...))).))).))))........(((((.((((...((((((.((((((.((.(((((((........))))....))))).))))))......))))))..(((((((....)))))))..))))))))).(((((((((((....))))).)))))).((((....((((((....)).))))...))))...(((((((((((...(((.(((((.............))))).))).....))).)))......((((((..(((......((((((((((((.((((.....))))(((...((((.((((...((((((((((..((((((((((((..........)))))).)))))).)))))((((((......))))))(((........)))...))))).)))).))))..)))....)))))))).))))..((((((....)))))))))..))))))..))))))))))))......"
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52 changes: 33 additions & 19 deletions rna-interaction-schema_v1.json
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Expand Up @@ -10,23 +10,24 @@
"type": "object",
"properties": {
"ID": {
"type": "string",
"pattern": "^[0-9a-zA-z-_]*$",
"description": "The unique identifier for an interaction"
"description": "The unique identifier for an interaction",
"type": "string"
},
"version": {
"description": "The file version of RIF. Currently only RIFv1.0 allowed",
"type": "string",
"pattern": "^RIFv1.0$",
"description": "The file version of RIF. Currently only RIFv1.0 allowed"
"pattern": "^RIFv1.0$"
},
"class": {
"description": "The class of the described interaction",
"enum": ["RNA-RNA", "RNA-Protein", "RNA-RNA-Protein"]
},
"type": {
"description": "The type of interaction, i.e. molecular mechanism",
"type": "string"
},
"evidence": {
"description": "evidence that supports the interaction",
"description": "Evidence that supports the interaction",
"type": "array",
"minItems": 1,
"uniqueItems": true,
Expand All @@ -42,10 +43,11 @@
"type": "string"
},
"command": {
"description": "command for computational method",
"description": "Command of the computational method",
"type": "string"
},
"data": {
"description": "Data that supports the interaction",
"type": "object",
"additionalProperties": {
"oneOf": [
Expand All @@ -62,39 +64,47 @@
}
}
},
"additionalProperties": false,
"required": ["type", "method", "data"]
}
},
"partners": {
"description": "RNA/Proteins involved in the interaction",
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"description": "",
"description": "Description of the RNA/Protein",
"type": "string"
},
"symbol": {
"description": "",
"description": "Scientific naming of the RNA/protein",
"type": "string"
},
"type": {
"description": "",
"description": "Type of the of the RNA/Protein. Should match entry in sequence ontology",
"type": "string"
},
"sequence_type": {
"description": "",
"description": "Type of sequence which can be either DNA, RNA or Protein",
"enum": ["dna","rna","protein"]
},
"genomic_coordinates": {
"description": "",
"type": "string"
"description": "chromosome, strand and genomic coordinates of the RNA/Protein",
"type": "string",
"pattern": "[a-zA-Z0-9]+:[+-]:[0-9]+-[0-9]+"
},
"organism_name": {
"description": "",
"description": "Name of the organism",
"type": "string"
},
"organism_acc": {
"description": "Unique accession id of the organism",
"type": "string"
},
"local_sites": {
"description": "Interaction sites of the organism",
"type": "object",
"patternProperties": {
"^.*$": {
Expand All @@ -106,40 +116,44 @@
"items": {
"type": "number"
}

}
}
}
},
"info": {
"description": "Optional properties of the interaction partner",
"type": "object",
"properties": {
"description": {
"type": "string",
"description": ""
"description": "Details on the function of gene/transcript/protein",
"type": "string"
},
"sequence": {
"description": "Sequence of the gene/transcript/protein as specified in genomic coordinates",
"type": "string",
"pattern": "^([ATGC]*|[ARNDCQEGHILKMFPSTWYV]*)$"
},
"structure": {
"description": "Representation of the RNA secondary structure in dot-bracket notation",
"type": "string",
"pattern": "^[.()]*$"
},
"note": {
"type": "string"
}
}
},
"additionalProperties":true
},
"custom": {
"type": "object"
}
},
"additionalProperties": false,
"required": ["name", "type", "local_sites"]
}
}
},
"additionalProperties": false,
"required": ["ID", "version", "class", "type", "evidence","partners"]
"required": ["ID", "version", "class", "type", "evidence", "partners"]
}
}

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