Slot: physical_linkage

In case an experimental setup is used that physically links nucleic acids derived from distinct Rearrangements before library preparation, this field describes the mode of that linkage. All hetero_* terms indicate that in case of paired-read sequencing, the two reads should be expected to map to distinct IG/TR loci. *_head-head refers to techniques that link the 5' ends of transcripts in a single-cell context. *_tail-head refers to techniques that link the 3' end of one transcript to the 5' end of another one in a single-cell context. This term does not provide any information whether a continuous reading-frame between the two is generated. *_prelinked refers to constructs in which the linkage was already present on the DNA level (e.g. scFv).

URI: https://github.com/vdjserver/vdjserver-airr-schema/physical_linkage

Applicable Classes

Name	Description	Modifies Slot
NucleicAcidProcessing	Default NucleicAcidProcessing description	no
SampleProcessing	Default SampleProcessing description	no

Properties

Type and Range

Property	Value
Range	PhysicalLinkageEnum
Domain Of	NucleicAcidProcessing, SampleProcessing

Cardinality and Requirements

Property	Value

Identifier and Mapping Information

Annotations

property	value
nullable	False

Schema Source

• from schema: https://github.com/vdjserver/vdjserver-airr-schema

Mappings

Mapping Type	Mapped Value
self	https://github.com/vdjserver/vdjserver-airr-schema/physical_linkage
native	https://github.com/vdjserver/vdjserver-airr-schema/physical_linkage

LinkML Source

name: physical_linkage
annotations:
  nullable:
    tag: nullable
    value: false
description: In case an experimental setup is used that physically links nucleic acids
  derived from distinct `Rearrangements` before library preparation, this field describes
  the mode of that linkage. All `hetero_*` terms indicate that in case of paired-read
  sequencing, the two reads should be expected to map to distinct IG/TR loci. `*_head-head`
  refers to techniques that link the 5' ends of transcripts in a single-cell context.
  `*_tail-head` refers to techniques that link the 3' end of one transcript to the
  5' end of another one in a single-cell context. This term does not provide any information
  whether a continuous reading-frame between the two is generated. `*_prelinked` refers
  to constructs in which the linkage was already present on the DNA level (e.g. scFv).
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
rank: 1000
domain_of:
- NucleicAcidProcessing
- SampleProcessing
range: PhysicalLinkageEnum