Create an ontology of genomic region file formats in JSON format

[donaldcampbelljr]

We should also create an ontology of genomic region file formats in JSON format to be hosted on PEPhub:
narrowPeak + broadPeak vs bed 6+4 etc

Originally posted by @donaldcampbelljr in #91

[donaldcampbelljr]

Here is a first pass of what this could look like, just need to determine how to handle the nonstrict versions of the format (this schema only has ns_narrowpeak):

type: object
properties:
  chrom:
    type: string
    description: "Name of the chromosome (e.g., chr1, chrX)."
  chromStart:
    type: integer
    description: "Starting position of the feature (0-based)."
    minimum: 0
  chromEnd:
    type: integer
    description: "Ending position of the feature (0-based, exclusive)."
    minimum: 0
  spec_compliant_columns:
    type: integer
    description: "Number of columns compliant with the ucsc BED specification."
    minimum: 3
  non_spec_compliant_columns:
    type: integer
    description: "Number of additional, non-compliant BED columns."
    minimum: 0
  bed_format:
    type: string
    enum:
      - ucsc_bed
      - encode_narrowpeak
      - encode_broadpeak
      - encode_rna_elements
      - encode_gappedpeak
      - unknown_bed_format
  format_specific_details:
    type: object
    description: "Details specific to the detected BED format."
    oneOf:
      - $ref: '#/definitions/narrowpeak_details'
      - $ref: '#/definitions/broadpeak_details'
      - $ref: '#/definitions/gappedpeak_details'
      - $ref: '#/definitions/rna_elements_details'
      - $ref: '#/definitions/ucsc_bed_details'
      - type: object
        properties: {}

definitions:
  narrowpeak_details:
    type: object
    properties:
      name:
        type: string
        description: "Name of the BED line."
      score:
        type: integer
        description: "Score between 0 and 1000."
        minimum: 0
        maximum: 1000
      strand:
        type: string
        enum: [".", "+", "-"]
        description: "Strand. Either '.', '+', or '-'."
      signalValue:
        type: number
        description: "Measurement of overall enrichment."
      pValue:
        type: number
        description: "Measurement of statistical significance (-log10)."
      qValue:
        type: number
        description: "Measurement of statistical significance using FDR (-log10)."
      peak:
        type: integer
        description: "Point-source called for this peak; 0-based offset."
    required:
      - name
      - score
      - strand
      - signalValue
      - pValue
      - qValue
      - peak

  broadpeak_details:
    type: object
    properties:
      name:
        type: string
        description: "Name of the BED line."
      score:
        type: integer
        description: "Score between 0 and 1000."
        minimum: 0
        maximum: 1000
      strand:
        type: string
        enum: [".", "+", "-"]
        description: "Strand. Either '.', '+', or '-'."
      signalValue:
        type: number
        description: "Measurement of overall enrichment."
      pValue:
        type: number
        description: "Measurement of statistical significance (-log10)."
      qValue:
        type: number
        description: "Measurement of statistical significance using FDR (-log10)."
    required:
      - name
      - score
      - strand
      - signalValue
      - pValue
      - qValue

  gappedpeak_details:
    type: object
    properties:
      name:
        type: string
        description: "Name of the BED line."
      score:
        type: integer
        description: "Score between 0 and 1000."
        minimum: 0
        maximum: 1000
      strand:
        type: string
        enum: [".", "+", "-"]
        description: "Strand. Either '.', '+', or '-'."
      thickStart:
        type: integer
        description: "Starting position at which the feature is drawn thickly."
      thickEnd:
        type: integer
        description: "Ending position at which the feature is drawn thickly."
      itemRgb:
        type: string
        description: "RGB value of the form R,G,B."
      blockCount:
        type: integer
        description: "Number of blocks (exons)."
      blockSizes:
        type: string
        description: "Comma-separated list of block sizes."
      blockStarts:
        type: string
        description: "Comma-separated list of block starts relative to chromStart."
      signalValue:
        type: number
        description: "Measurement of overall enrichment."
      pValue:
        type: number
        description: "Measurement of statistical significance (-log10)."
      qValue:
        type: number
        description: "Measurement of statistical significance using FDR (-log10)."
    required:
      - name
      - score
      - strand
      - thickStart
      - thickEnd
      - itemRgb
      - blockCount
      - blockSizes
      - blockStarts
      - signalValue
      - pValue
      - qValue

  rna_elements_details:
    type: object
    properties:
      name:
        type: string
        description: "Name of the BED line."
      score:
        type: integer
        description: "Score between 0 and 1000."
        minimum: 0
        maximum: 1000
      strand:
        type: string
        enum: [".", "+", "-"]
        description: "Strand. Either '.', '+', or '-'."
      level:
        type: number
        description: "Expression level, e.g. RPKM or FPKM."
      signif:
        type: number
        description: "Statistical significance, e.g. IDR."
      score2:
        type: integer
        description: "Additional measurement/count, e.g. number of reads."
    required:
      - name
      - score
      - strand
      - level
      - signif
      - score2

  ucsc_bed_details:
    type: object
    properties:
      name:
        type: string
        description: "Name of the BED line."
      score:
        type: integer
        description: "Score between 0 and 1000."
        minimum: 0
        maximum: 1000
      strand:
        type: string
        enum: [".", "+", "-"]
        description: "Strand. Either '.', '+', or '-'."
      thickStart:
        type: integer
        description: "Starting position at which the feature is drawn thickly."
      thickEnd:
        type: integer
        description: "Ending position at which the feature is drawn thickly."
      itemRgb:
        type: string
        description: "RGB value of the form R,G,B."
      blockCount:
        type: integer
        description: "Number of blocks (exons)."
      blockSizes:
        type: string
        description: "Comma-separated list of block sizes."
      blockStarts:
        type: string
        description: "Comma-separated list of block starts relative to chromStart."

required:
  - chrom
  - chromStart
  - chromEnd
  - spec_compliant_columns
  - non_spec_compliant_columns
  - bed_format
  - format_specific_details

Edit: Updated to remove ns_narrowpeak for now.