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Controlled vocabulary for pcr_target_locus

The current description and examples for key `pcr_target_locus` do
not match. Furthermore there is some ambiguity about the term "locus".
See #175.

Introduce controlled vocabulary and clarify description and example.
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bussec committed Feb 15, 2019
1 parent 3b0a49b commit 2cc8e2413a8f3792b414b02d036cf402600b106c
Showing with 14 additions and 6 deletions.
  1. +1 −1 AIRR_Minimal_Standard_Data_Elements.tsv
  2. +11 −3 specs/airr-schema.yaml
  3. +2 −2 specs/miairr.yaml
@@ -53,7 +53,7 @@ MiAIRR data set / subset MiAIRR field designation Data type Content format MiAIR
3 / process (nucl. acid) Library generation method string {"controlled_vocabulary": ["PCR", "RT(RHP)+PCR", "RT(oligo-dT)+PCR", "RT(oligo-dT)+TS+PCR", "RT(oligo-dT)+TS(UMI)+PCR", "RT(specific)+PCR", "RT(specific)+TS+PCR", "RT(specific)+TS(UMI)+PCR", "RT(specific+UMI)+PCR", "RT(specific+UMI)+TS+PCR", "RT(specific)+TS", "other"]} Generic type of library generation RT(oligo-dT)+PCR library_generation_method
3 / process (nucl. acid) Library generation protocol string Free text Description of processes applied to substrate to obtain a library that is ready for sequencing cDNA was generated using library_generation_protocol
3 / process (nucl. acid) Protocol IDs string Free text When using a library generation protocol from a commercial provider, provide the protocol version number v2.1 (2016-09-15) library_generation_kit_version
3 / process (nucl. acid [pcr]) Target locus for PCR string Free text Designation of the target locus according to standard gene nomencleature Constant region vs. V region amplification pcr_target_locus
3 / process (nucl. acid [pcr]) Target locus for PCR string {"controlled_vocabulary": ["IGH", "IGI", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG"]} Designation of the target locus according to IMGT nomencleature IGK pcr_target_locus
3 / process (nucl. acid [pcr]) Forward PCR primer target location string Free text Position of the most distal nucleotide templated by the forward primer or primer mix IGHV, +23 forward_pcr_primer_target_location
3 / process (nucl. acid [pcr]) Reverse PCR primer target location string Free text Position of the most proximal nucleotide templated by the reverse primer or primer mix IGHG, +57 reverse_pcr_primer_target_location
3 / process (nucl. acid) Complete sequences string {"controlled_vocabulary": ["partial", "complete", "complete+untemplated"]} To be considered `complete`, the procedure used for library construction MUST generate sequences that 1) include the first V segment codon that encodes the mature polypeptide chain (i.e. after the leader sequence) and 2) include the last complete codon of the J segment (i.e. 1 bp before the J->C splice site) and 3) provide sequence information for all positions between 1) and 2). To be considered `complete & untemplated`, the sections of the sequences defined in points 1) to 3) of the previous sentence MUST be untemplated, i.e. MUST NOT overlap with the primers used in library preparation. partial complete_sequences
@@ -262,8 +262,16 @@ PCRTarget:
type: object
properties:
pcr_target_locus:
type: string
description: Designation of the target locus according to standard gene nomencleature
enum:
- IGH
- IGI
- IGK
- IGL
- TRA
- TRB
- TRD
- TRG
description: Designation of the target locus according to IMGT nomencleature
x-miairr: true
forward_pcr_primer_target_location:
type: string
@@ -627,7 +635,7 @@ Rearrangement:
description: True if the aligned sequence contains a stop codon.
locus:
type: string
description: Gene locus (chain type). For example, IGH, IGK, IGL, TRA, TRB, TRD, or TRG.
description: Gene locus (chain type). For example, IGH, IGI, IGK, IGL, TRA, TRB, TRD, or TRG.
v_call:
type: string
description: V gene with allele. For example, IGHV4-59*01.
@@ -326,8 +326,8 @@ pcr_target_locus:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Target locus for PCR
format: free text
example: Constant region vs. V region amplification
format: {"controlled_vocabulary": ["IGH", "IGI", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG"]}
example: IGK
forward_pcr_primer_target_location:
miairr_set: 3
miairr_subset: process (nucleic acid)

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