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Table 5 The allowed content of a BioXSD FeatureRecord

From: Identifying elemental genomic track types and representing them uniformly

  Notes May further contain
BioXSD description of feature type   
Name 1  
Ontology concepts 1  
Textual note   
References to database entries, databases, ontology concepts, other feature types type of relationship with the referenced object2
More specific type of feature   name and/or concepts, synonyms, database entries
More generic class of feature types   name and/or concepts
BioXSD feature occurrence   
Position segments, points3, positions outside of the actual sequence or feature occurrence4, dense points* (function) and dense partition* or step function* 5 strand, certainty
Scores (values) double-precision signed floats (8 bytes), or any well-formatted strings* unit, index, type of score2, note, position, provenance metadata
Evidence   references to databases, tools, and citations; scores, verdict, reliability, provenance metadata
Alignments   alignment- and aligned sequence-specific scores, gaps, frameshifts, directions, note, provenance metadata
Sequence variation   variants, canonical variant, scores, position
CDS phase   
References to ontology concepts, database entries, other feature occurences (interconnections) type of relationship with the referenced object2; scores of the relationship (weights of edges)*
  1. 1 At least one of these two is mandatory.
  2. 2 By any ontology concept, referred to by a concept URI, identifier, or term; or by a custom term if no ontology concept is available.
  3. 3 Points are bases/residues or insertions between them.
  4. 4 For example if annotating the position of a regulatory element of a coding sequence, or relations between genes or protein domains.
  5. 5 Positions can form multi-segment subsequences, multi-point tuples, and can be combined within feature occurrences according to users' needs. The positions are always 1-based. The feature occurence may apply to the whole sequence (being a non-positioned sequence property).
  6. * Added in BioXSD version 1.1.