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Slot: seqcol_ordered_coord_system

Content-derived digest that uniquely identifies the ordered coordinate system of the genome assembly. (Coordinate systems with the same sequence names and lengths, but where the sequences are ordered differently, will have different ordered digests.). Usage is the ordered coordinate system digest can be used to uniquely generate a chromSizes file, useful in a number of analysis tools. Definition is the ordered coordinate system digest is defined as the level 1 digest of the name_length_pairs attribute of the sequence collection generated from the genome assembly.

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

Applicable Classes

Name Description Modifies Slot
GenomeAssembly Information about of the exact genome assembly used to generate the annotation file, defining the genomic coordinate system for the sequence features. no

Properties

Type and Range

Property Value
Range Curie
Domain Of GenomeAssembly

Cardinality and Requirements

Property Value
Required Yes

Examples

Value
ga4gh:SC.name_length_pairs.Yyz0Expaluj09xdDYg2Y6VOApvjg05Hf

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/seqcol_ordered_coord_system
native https://w3id.org/fga-wg/schema/bundle/seqcol_ordered_coord_system

LinkML Source

name: seqcol_ordered_coord_system
description: Content-derived digest that uniquely identifies the ordered coordinate
  system of the genome assembly. (Coordinate systems with the same sequence names
  and lengths, but where the sequences are ordered differently, will have different
  ordered digests.). Usage is the ordered coordinate system digest can be used to
  uniquely generate a chromSizes file, useful in a number of analysis tools. Definition
  is the ordered coordinate system digest is defined as the level 1 digest of the
  name_length_pairs attribute of the sequence collection generated from the genome
  assembly.
examples:
- value: ga4gh:SC.name_length_pairs.Yyz0Expaluj09xdDYg2Y6VOApvjg05Hf
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
domain_of:
- GenomeAssembly
range: curie
required: true