Gff schema

Playing around with GFF spec

Classes

• GenomeFeature - A feature localized to an interval along a genome
• GenomeFeatureAttributeSet - Holds a collection of attributes that can be used by a feature
• GffDocument - Collection of GFF features and metadata
• Metadata - A piece of metadata for a GFF document
  • GenomeBuildValue - Used for genome-build pragmas
  • SequenceRegionValue - Used for sequence-region pragmas
• Seq - A biological sequence
• TargetLocation

Mixins

Slots

• ➞name
• ➞source
• ➞species
• gff attribute
  • Aliases
  • Dbxref
  • Derives from
  • Gap
  • ID
  • Is circular
  • Name
  • Note
  • Ontology term
  • Parent
  • Target
• gff column
  • gff coordinate - A positive 1-based integer coordinate indicating start or end
    • end - The end of the feature in positive 1-based integer coordinates
    • start - The start of the feature in positive 1-based integer coordinates
  • seqid - The ID of the landmark used to establish the coordinate system for the current feature.
  • source - The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.
  • type - A type from the sequence ontology slot_uri: rdf:type
• ➞features
• ➞gff version
• ➞sequences
• has attributes
• has metadata
  • ➞genome build
  • ➞sequence region
  • ➞species
  • ontology URI
    • ➞attribute ontology URI - This directive indicates that the GFF3 uses the ontology of attribute names located at the indicated URI or URL.
    • ➞feature ontology URI - This directive indicates that the GFF3 file uses the ontology of feature types located at the indicated URI or URL.
    • ➞source ontology URI - This directive indicates that the GFF3 uses the ontology of source names located at the indicated URI or URL.
• has sequence string
• phase - The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.
• score - The score of the feature, a floating point number. As in earlier versions of the format, the semantics of the score are ill-defined. It is strongly recommended that E-values be used for sequence similarity features, and that P-values be used for ab initio gene prediction features.
• strand - The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).

Types

Built in

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

Defined

• Boolean (Bool) - A binary (true or false) value
• ControlledTermType (Uriorcurie) - An IRI
• 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
• GapString (String)
• 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