Class: TrackGeometry

Overall geometric properties of the sequence features in the genomic annotation file if considered as an one-dimensional genome browser track, in line with the track type delineations from Gundersen et. al, 2011. While conceptually based on visual characteristics, these properties are also useful to e.g. select relevant annotation files for non-visual analyses.

URI: https://w3id.org/fga-wg/schema/bundle/TrackGeometry

 classDiagram
    class TrackGeometry
    click TrackGeometry href "../TrackGeometry/"
      TrackGeometry : edge_weight_type





        TrackGeometry --> "0..1" DataTypes : edge_weight_type
        click DataTypes href "../DataTypes/"



      TrackGeometry : edges_are_directed

      TrackGeometry : edges_denote_parents

      TrackGeometry : edges_have_weights

      TrackGeometry : elements_circular

      TrackGeometry : elements_overlapping

      TrackGeometry : has_edges

      TrackGeometry : has_gaps

      TrackGeometry : has_lengths

      TrackGeometry : has_names

      TrackGeometry : has_strands

      TrackGeometry : has_values

      TrackGeometry : lengths_constant

      TrackGeometry : value_type





        TrackGeometry --> "0..1" DataTypes : value_type
        click DataTypes href "../DataTypes/"

Example

Example JSON

{
  "elements_circular": false,
  "elements_overlapping": false,
  "has_edges": false,
  "has_gaps": true,
  "has_lengths": true,
  "has_names": true,
  "has_strands": false,
  "has_values": true,
  "lengths_constant": false,
  "value_type": "multiple"
}

Slots

Name	Cardinality and Range	Description	Inheritance
has_gaps	1 Boolean	Whether there are gaps between the sequence features (there exists at least one gap between two features on the same sequence).	direct
has_lengths	1 Boolean	Whether the sequence features have lengths (at least one feature spans more than 1 base pair).	direct
has_strands	1 Boolean	Whether the sequence features are stranded (at least one feature has strand information).	direct
has_values	1 Boolean	Whether the sequence features have associated values (at least one feature has an associated value).	direct
has_edges	1 Boolean	Whether the sequence features are linked across positions (at least one edge between features exists).	direct
has_names	1 Boolean	Whether the sequence features are named (at least one feature has a name).	direct
elements_overlapping	1 Boolean	Whether the sequence features are overlapping (at least one base pair is simultaneously covered by two sequence features).	direct
elements_circular	1 Boolean	Whether the sequence features have circular coordinates (at least one feature that cross a sequence border).	direct
lengths_constant	0..1 Boolean	Whether the sequence lengths are constant (all sequence features have the same length, excluding features at the very end of a sequence).	direct
value_type	0..1 DataTypes	The type of values associated with the sequence features, if any.	direct
edges_have_weights	0..1 Boolean	Whether the edges linking sequence features are weighted (at least one edge between sequence features has an associated weight).	direct
edge_weight_type	0..1 DataTypes	The type of values associated with the edges.	direct
edges_are_directed	0..1 Boolean	Whether the edges linking sequence features are directed (at least one edge between sequence features is defined with a direction).	direct
edges_denote_parents	0..1 Boolean	Whether the edges linking sequence features denote a parent-child relationship (all edges between sequence features denote parent-child relationships such as genes to exons, i.e. where the child is fully covered by the parent).	direct

Usages

used by	used in	type	used
GenomicAnnotationFile	track_geometry	range	TrackGeometry

Rules

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'has_lengths': {'equals_number': True}}	{'lengths_constant': {'required': True}}

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'has_values': {'equals_number': True}}	{'value_type': {'required': True}}

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'has_edges': {'equals_number': True}}

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	{'edges_have_weights': {'equals_number': True}}	{'edge_weight_type': {'required': True}}

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/fga-wg/schema/bundle

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/fga-wg/schema/bundle/TrackGeometry
native	https://w3id.org/fga-wg/schema/bundle/TrackGeometry

LinkML Source

Direct

name: TrackGeometry
description: Overall geometric properties of the sequence features in the genomic
  annotation file if considered as an one-dimensional genome browser track, in line
  with the track type delineations from Gundersen et. al, 2011. While conceptually
  based on visual characteristics, these properties are also useful to e.g. select
  relevant annotation files for non-visual analyses.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- has_gaps
- has_lengths
- has_strands
- has_values
- has_edges
- has_names
- elements_overlapping
- elements_circular
- lengths_constant
- value_type
- edges_have_weights
- edge_weight_type
- edges_are_directed
- edges_denote_parents
rules:
- preconditions:
    slot_conditions:
      has_lengths:
        name: has_lengths
        equals_number: true
  postconditions:
    slot_conditions:
      lengths_constant:
        name: lengths_constant
        required: true
- preconditions:
    slot_conditions:
      has_values:
        name: has_values
        equals_number: true
  postconditions:
    slot_conditions:
      value_type:
        name: value_type
        required: true
- preconditions:
    slot_conditions:
      has_edges:
        name: has_edges
        equals_number: true
  postconditions:
    all_of:
    - slot_conditions:
        edges_have_weights:
          name: edges_have_weights
          required: true
    - slot_conditions:
        edges_are_directed:
          name: edges_are_directed
          required: true
    - slot_conditions:
        edges_denote_parents:
          name: edges_denote_parents
          required: true
- preconditions:
    slot_conditions:
      edges_have_weights:
        name: edges_have_weights
        equals_number: true
  postconditions:
    slot_conditions:
      edge_weight_type:
        name: edge_weight_type
        required: true

Induced

name: TrackGeometry
description: Overall geometric properties of the sequence features in the genomic
  annotation file if considered as an one-dimensional genome browser track, in line
  with the track type delineations from Gundersen et. al, 2011. While conceptually
  based on visual characteristics, these properties are also useful to e.g. select
  relevant annotation files for non-visual analyses.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
  has_gaps:
    name: has_gaps
    description: Whether there are gaps between the sequence features (there exists
      at least one gap between two features on the same sequence).
    examples:
    - value: 'True'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  has_lengths:
    name: has_lengths
    description: Whether the sequence features have lengths (at least one feature
      spans more than 1 base pair).
    examples:
    - value: 'True'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  has_strands:
    name: has_strands
    description: Whether the sequence features are stranded (at least one feature
      has strand information).
    examples:
    - value: 'False'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  has_values:
    name: has_values
    description: Whether the sequence features have associated values (at least one
      feature has an associated value).
    examples:
    - value: 'True'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  has_edges:
    name: has_edges
    description: Whether the sequence features are linked across positions (at least
      one edge between features exists).
    examples:
    - value: 'False'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  has_names:
    name: has_names
    description: Whether the sequence features are named (at least one feature has
      a name).
    examples:
    - value: 'True'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  elements_overlapping:
    name: elements_overlapping
    description: Whether the sequence features are overlapping (at least one base
      pair is simultaneously covered by two sequence features).
    examples:
    - value: 'False'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  elements_circular:
    name: elements_circular
    description: Whether the sequence features have circular coordinates (at least
      one feature that cross a sequence border).
    examples:
    - value: 'False'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
    required: true
  lengths_constant:
    name: lengths_constant
    description: Whether the sequence lengths are constant (all sequence features
      have the same length, excluding features at the very end of a sequence).
    examples:
    - value: 'False'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
  value_type:
    name: value_type
    description: The type of values associated with the sequence features, if any.
    examples:
    - value: multiple
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: DataTypes
  edges_have_weights:
    name: edges_have_weights
    description: Whether the edges linking sequence features are weighted (at least
      one edge between sequence features has an associated weight).
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
  edge_weight_type:
    name: edge_weight_type
    description: The type of values associated with the edges.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: DataTypes
  edges_are_directed:
    name: edges_are_directed
    description: Whether the edges linking sequence features are directed (at least
      one edge between sequence features is defined with a direction).
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
  edges_denote_parents:
    name: edges_denote_parents
    description: Whether the edges linking sequence features denote a parent-child
      relationship (all edges between sequence features denote parent-child relationships
      such as genes to exons, i.e. where the child is fully covered by the parent).
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: TrackGeometry
    domain_of:
    - TrackGeometry
    range: boolean
rules:
- preconditions:
    slot_conditions:
      has_lengths:
        name: has_lengths
        equals_number: true
  postconditions:
    slot_conditions:
      lengths_constant:
        name: lengths_constant
        required: true
- preconditions:
    slot_conditions:
      has_values:
        name: has_values
        equals_number: true
  postconditions:
    slot_conditions:
      value_type:
        name: value_type
        required: true
- preconditions:
    slot_conditions:
      has_edges:
        name: has_edges
        equals_number: true
  postconditions:
    all_of:
    - slot_conditions:
        edges_have_weights:
          name: edges_have_weights
          required: true
    - slot_conditions:
        edges_are_directed:
          name: edges_are_directed
          required: true
    - slot_conditions:
        edges_denote_parents:
          name: edges_denote_parents
          required: true
- preconditions:
    slot_conditions:
      edges_have_weights:
        name: edges_have_weights
        equals_number: true
  postconditions:
    slot_conditions:
      edge_weight_type:
        name: edge_weight_type
        required: true