ChromoSchema schema

Schema for representing Chromosomes and Chromosomal Regions.

Objects created using this schema can be directly worked with in YAML/Python, Additionally they can be translated to OWL

Classes

• ChromosomePart - A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)
• ChromosomePartCollection
• Genome - Represents a sequenced genome, one per species.
• GenomeBuild - Represents a specific build of a sequenced genome
• OrganismTaxon - Represents a species, e.g. Homo sapiens

Mixins

Slots

• band_descriptor - A string representing a chromosome band, e.g. p31.1. This is local to the chromosome, so the chromosome is not included in the descriptor
• broad_synonyms
• build - A descriptor for the genome and build number. E.g hg38
  • Genome➞build - the current genome build for this genome
• cell_location - which organelle the chromosome is associated with. For eukaryotes this is mitochondrion or nucleus. For prokaryotes the distinction does not make sense
• children - Direct parts of this chromosome. zero to many.
• ➞genomes
• ➞has
• ➞name
• ➞taxons
• chromosome_name - E.g. chr1, chrM. Some species like C elegans may use roman numerals
• common_name - E.g. human, mouse
• download_url
• end - Start location of the chromosomal part. Note we also include this for whole chromosomes - end will be rightmost point
• exact_mappings - For a whole chromosome, this may be an assembled sequence in a database such as genbank or ensembl
• exact_synonyms
• id - A unique identifier
  • ChromosomePart➞id
  • GenomeBuild➞id - E.g. mm10
  • Genome➞id - E.g. mm, hg
• name - Unique human-readable label for the entity
  • Genome➞name - E.g. Homo sapiens
• parent - Direct chromosomal part which this is a part of. The partonomy forms a tree so this is always zero or one. Different species have different rules but typically the partonomy will be something like 1p31.1 -> 1p31 -> 1p3 -> 1p -> 1
• previous_builds - List of previous non-current builds
• sex_chromosome_type - Only populated for sex chromosomes. Indicates the chromosome type. This is X or Y in mammals, W or Z in avians
• somal_type - indicates whether this is a sex-chromosome or not
• start - Start location of the chromosomal part. Note we also include this for whole chromosomes - start will be zero
• strand
• taxon - The taxon to which the chromosome part belongs. Always NCBITaxon.
• type

Enums

• AutosomeVsSexChromosome - sex or autosome
• ChromatinType
• EntityType - SO or GO type
• LocationType - where in the cell
• SexChromosomeType - what type of sex chromosome

Subsets

Types

Built in

• Bool
• Decimal
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• BandDescriptor (String) - e.g. p, p1, p1.1, ...
• ChromosomeNameType (String) - E.g. chr1
• LabelType (String) - A string that provides a human-readable name for an entity
• StrandType (Integer) - 0, 1, or -1
• TaxonIdentifier (String)
• Boolean (Bool) - A binary (true or false) value
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• Datetime (XSDDateTime) - The combination of a date and time
• Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• Ncname (NCName) - Prefix part of CURIE
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE