Skip to main content

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

 

Synonyms

  

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

Name

  

Note

  

Alignments

 

alignment- and aligned sequence-specific scores, gaps, frameshifts, directions, note, provenance metadata

Sequence variation

 

variants, canonical variant, scores, position

Frame

  

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.