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STRtr-kit evidence schema #287
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a254d61
first draft of STRtr-kit evidence schema
hdashnow a469ec6
create page
vincerubinetti 79dd18d
simple conditional schema prop support
vincerubinetti a0a0b9d
simplify form state with context
vincerubinetti 1c8c9f5
add calc eval capability
vincerubinetti d85a3ea
add summary
vincerubinetti 243a31c
add pr submission capability
vincerubinetti ec99db5
first attempt at adding all categories
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| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "STRtr-kit-evidence.schema", | ||
| "title": "STRtr-kit Evidence", | ||
| "description": "Evidence to support pathogenicity of tandem repeat loci in human disease. Each entry describes evidence from a single publication or similar source. There will typically be multiple entries per locus, each describing evidence from different sources.", | ||
| "citation_format": "In free text strings: 'Some text [@doi:12345; @pmid:12345]'. In regular lists: ['doi:12345', 'pmid:12345']", | ||
| "type": "object", | ||
| "properties": { | ||
| "id": { | ||
| "section": "Evidence", | ||
| "title": "Locus", | ||
| "description": "Unique identifier for the locus within STRchive in the form [disease_id]_[gene]. Additional characters may be added to the end of the ID to make it unique within STRchive, e.g. HFG_HOXA13-I, HFG_HOXA13-II.", | ||
| "placeholder": "[disease_id]_[gene]", | ||
| "examples": ["CANVAS_RFC1", "HFG_HOXA13-I", "HFG_HOXA13-II"], | ||
| "type": ["string"], | ||
| "pattern": "^[\\S]+_[\\S]+$" | ||
| }, | ||
|
|
||
| "citation": { | ||
| "section": "Evidence", | ||
| "title": "Citation", | ||
| "description": "Citation for the source of the evidence", | ||
| "examples": ["pmid:29507423"], | ||
| "type": ["string"], | ||
| "pattern": "^(?:doi|pmc|pmid|arxiv|isbn|url|mondo|omim|genereviews|malacard|orphanet|stripy|gnomad):.+$" | ||
| }, | ||
|
|
||
| "genetic_evidence": { | ||
| "section": "Evidence", | ||
| "title": "Genetic Evidence", | ||
| "description": "One or more pieces of genetic evidence provided in the source", | ||
| "type": "array", | ||
| "uniqueItems": true, | ||
| "items": { | ||
| "title": "", | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { | ||
| "title": "Type", | ||
| "description": "The type(s) of genetic evidence provided in the source", | ||
| "type": ["string", "null"], | ||
| "enum": [ | ||
| "probands", | ||
| "allele_effect", | ||
| "method", | ||
| "segregation", | ||
| "case_control" | ||
| ], | ||
| "enum_descriptions": { | ||
| "probands": "Unrelated Probands", | ||
| "allele_effect": "Relationship between allele size and/or motif sequence and phenotype e.g. age of onset and/or severity", | ||
| "method": "Method of predicting Pathogenicity", | ||
| "segregation": "Linkage Region for disease", | ||
| "case_control": "Case-control study" | ||
| } | ||
| }, | ||
| "notes": { | ||
| "title": "Notes", | ||
| "description": "Additional notes about the genetic evidence provided in the source including point upgrades/downgrades", | ||
| "examples": [ | ||
| "Segregation analysis in 3 affected families with LOD score of 3.5" | ||
| ], | ||
| "type": ["string", "null"], | ||
| "multiline": true | ||
| } | ||
| }, | ||
| "required": ["type"], | ||
| "allOf": [ | ||
| { | ||
| "if": { "properties": { "type": { "const": "probands" } } }, | ||
| "then": { | ||
| "properties": { | ||
| "probands": { | ||
| "title": "Probands", | ||
| "description": "Number of probands with the pathogenic expansion reported in the source", | ||
| "type": ["integer"], | ||
| "minimum": 0 | ||
| }, | ||
| "points": { | ||
| "title": "Points", | ||
| "description": "Points assigned to this locus based on the genetic evidence provided in the source, according to the STRtr-kit scoring system.", | ||
| "type": ["number"], | ||
| "minimum": 0, | ||
| "maximum": 6, | ||
| "default": 0.5, | ||
| "calc": "min(6, {probands} * 0.5)", | ||
| "scoring_range": "0–1.5 points per proband", | ||
| "upgrades": "+0.5 for inheritance/de novo evidence, +0.5 for functional evidence" | ||
| } | ||
| }, | ||
| "required": ["probands", "points"] | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| "experimental_evidence": { | ||
| "section": "Evidence", | ||
| "title": "Experimental Evidence", | ||
| "description": "Experimental evidence supporting pathogenicity of the tandem repeat locus. Maximum overall score for all experimental evidence is 6.0 points.", | ||
| "type": "array", | ||
| "uniqueItems": true, | ||
| "category_max": 6.0, | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { | ||
| "title": "Type", | ||
| "description": "The type of experimental evidence provided in the source", | ||
| "type": ["string", "null"], | ||
| "enum": [ | ||
| "biochemical_function", | ||
| "protein_interaction", | ||
| "regulatory_impact", | ||
| "functional_alteration_patient_cells", | ||
| "functional_alteration_non_patient_cells", | ||
| "model_non_human", | ||
| "model_cell_culture", | ||
| "rescue_human_control", | ||
| "rescue_non_human_model", | ||
| "rescue_cell_culture", | ||
| "rescue_patient_cells" | ||
| ], | ||
| "enum_descriptions": { | ||
| "biochemical_function": "Biochemical function of the gene or repeat", | ||
| "protein_interaction": "Protein–protein interaction evidence", | ||
| "regulatory_impact": "Impact on regulation such as splicing, expression, or epigenetics", | ||
| "functional_alteration_patient_cells": "Functional alteration observed in patient-derived cells", | ||
| "functional_alteration_non_patient_cells": "Functional alteration observed in non-patient cells", | ||
| "model_non_human": "Evidence from non-human model organisms", | ||
| "model_cell_culture": "Evidence from cultured cell models", | ||
| "rescue_human_control": "Rescue experiments in healthy human cells", | ||
| "rescue_non_human_model": "Rescue experiments in non-human model organisms", | ||
| "rescue_cell_culture": "Rescue experiments in cultured cells", | ||
| "rescue_patient_cells": "Rescue experiments in patient-derived cells" | ||
| } | ||
| }, | ||
|
|
||
| "notes": { | ||
| "title": "Notes", | ||
| "description": "Additional notes about the experimental evidence including point upgrades/downgrades", | ||
| "type": ["string", "null"], | ||
| "multiline": true | ||
| }, | ||
|
|
||
| "points": { | ||
| "title": "Points", | ||
| "description": "Points assigned based on the experimental evidence provided in the source", | ||
| "type": ["number"], | ||
| "minimum": 0 | ||
| } | ||
| }, | ||
| "required": ["type", "points"], | ||
| "allOf": [ | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { | ||
| "enum": [ | ||
| "biochemical_function", | ||
| "protein_interaction", | ||
| "regulatory_impact" | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 0.5, | ||
| "maximum": 2.0, | ||
| "scoring_range": "0–2", | ||
| "upgrades": "Multiple forms of evidence" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { "const": "functional_alteration_patient_cells" } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 1.0, | ||
| "maximum": 2.0, | ||
| "scoring_range": "0–2", | ||
| "upgrades": "Multiple patient cells studied" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { "const": "functional_alteration_non_patient_cells" } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 0.5, | ||
| "maximum": 1.0, | ||
| "scoring_range": "0–1", | ||
| "upgrades": "Multiple control cell types" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { "const": "model_non_human" } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 2.0, | ||
| "maximum": 4.0, | ||
| "scoring_range": "0–4", | ||
| "upgrades": "Multiple model organisms" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { "const": "model_cell_culture" } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 1.0, | ||
| "maximum": 2.0, | ||
| "scoring_range": "0–2", | ||
| "upgrades": "Multiple cell types cultured" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { | ||
| "enum": [ | ||
| "rescue_human_control", | ||
| "rescue_non_human_model" | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 2.0, | ||
| "maximum": 4.0, | ||
| "scoring_range": "0–4", | ||
| "upgrades": "Multiple rescue systems" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "if": { | ||
| "properties": { | ||
| "type": { | ||
| "enum": [ | ||
| "rescue_cell_culture", | ||
| "rescue_patient_cells" | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
| "then": { | ||
| "properties": { | ||
| "points": { | ||
| "default": 1.0, | ||
| "maximum": 2.0, | ||
| "scoring_range": "0–2", | ||
| "upgrades": "Multiple rescue approaches" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
|
|
||
| "required": ["id", "citation"] | ||
| } | ||
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@vincerubinetti I'm a little confused about this structure. Should this have a title? Is this just an unnamed grouping object?
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In this case, this would be the title of each piece of evidence, which I guess I figured didn't warrant a name. But if you put one, here's where/how it appears ("test title"):