Add description about layering of species information

airr-community · Nov 8, 2019 · 7e2b4af · 7e2b4af
1 parent 8e4edc5
commit 7e2b4af
Show file tree

Hide file tree

Showing 3 changed files with 30 additions and 6 deletions.
diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/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

diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/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

diff --git a/specs/airr-schema.yaml b/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