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Add description about layering of species information

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bussec authored and schristley committed Nov 8, 2019
1 parent 8e4edc5 commit 7e2b4af29a0eaf2f660928d932953428f504d568
Showing with 30 additions and 6 deletions.
  1. +10 −2 lang/R/inst/extdata/airr-schema.yaml
  2. +10 −2 lang/python/airr/specs/airr-schema.yaml
  3. +10 −2 specs/airr-schema.yaml
@@ -687,7 +687,11 @@ CellProcessing:
name: Cell subset phenotype
cell_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the analyzed cells originate. Important e.g., for chimeric animal models.
description: >
Binomial designation of the species from which the analyzed cells originate. Typically, this value
should be identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are
valid experimental setups in which the two might differ, e.g. chimeric animal models. If set, this
key will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
@@ -1425,7 +1429,11 @@ Rearrangement:
description: Gene locus (chain type). For example, IGH, IGI, IGK, IGL, TRA, TRB, TRD, or TRG.
locus_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the locus originates. Important e.g., for transgenic animal models.
description: >
Binomial designation of the species from which the locus originates. Typically, this value should be
identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are valid
experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key
will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
@@ -687,7 +687,11 @@ CellProcessing:
name: Cell subset phenotype
cell_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the analyzed cells originate. Important e.g., for chimeric animal models.
description: >
Binomial designation of the species from which the analyzed cells originate. Typically, this value
should be identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are
valid experimental setups in which the two might differ, e.g. chimeric animal models. If set, this
key will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
@@ -1425,7 +1429,11 @@ Rearrangement:
description: Gene locus (chain type). For example, IGH, IGI, IGK, IGL, TRA, TRB, TRD, or TRG.
locus_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the locus originates. Important e.g., for transgenic animal models.
description: >
Binomial designation of the species from which the locus originates. Typically, this value should be
identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are valid
experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key
will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
@@ -687,7 +687,11 @@ CellProcessing:
name: Cell subset phenotype
cell_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the analyzed cells originate. Important e.g., for chimeric animal models.
description: >
Binomial designation of the species from which the analyzed cells originate. Typically, this value
should be identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are
valid experimental setups in which the two might differ, e.g. chimeric animal models. If set, this
key will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
@@ -1425,7 +1429,11 @@ Rearrangement:
description: Gene locus (chain type). For example, IGH, IGI, IGK, IGL, TRA, TRB, TRD, or TRG.
locus_species:
$ref: '#/Ontology'
description: Binomial designation of the species from which the locus originates. Important e.g., for transgenic animal models.
description: >
Binomial designation of the species from which the locus originates. Typically, this value should be
identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are valid
experimental setups in which the two might differ, e.g. transgenic animal models. If set, this key
will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens

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