Playing around with GFF spec
- 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
- Seq - A biological sequence
- gff attribute
- gff column
- gff coordinate - A positive 1-based integer coordinate indicating start or end
- 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
- ➞gff version
- has attributes
- has metadata
- ➞genome build
- ➞sequence region
- 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).
- 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