update efo codes to CURIEs

ga4gh · Apr 13, 2023 · c4595ae · c4595ae
1 parent f5f0feb
commit c4595ae
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Showing 6 changed files with 31 additions and 31 deletions.
diff --git a/docs/source/terms_and_model.rst b/docs/source/terms_and_model.rst
@@ -427,7 +427,7 @@ Low-level copy gain of BRCA1:
 .. parsed-literal::
 
     {
-      "copy_change": "EFO_0030071", # low-level gain
+      "copy_change": "efo:0030071", # low-level gain
       "subject": {
         "gene_id": "ncbigene:348",          # BRCA1 gene
         "type": "Gene"

diff --git a/schema/defs/vrs/CopyNumberChange.rst b/schema/defs/vrs/CopyNumberChange.rst
@@ -31,4 +31,4 @@ Some CopyNumberChange attributes are inherited from :ref:`Variation`.
    *  - copy_change
       - string
       - 1..1
-      - MUST be one of "EFO_0030069" (complete genomic loss), "EFO_0020073" (high-level loss),  "EFO_0030068" (low-level loss), "EFO_0030067" (loss), "EFO_0030064" (regional base ploidy),  "EFO_0030070" (gain), "EFO_0030071" (low-level gain), "EFO_0030072" (high-level gain).
+      - MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss),  "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy),  "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).
diff --git a/schema/vrs-source.yaml b/schema/vrs-source.yaml
@@ -240,11 +240,11 @@ definitions:
           A location for which the number of systemic copies is described.
       copy_change:
         type: string
-        enum: [ "EFO_0030069", "EFO_0020073", "EFO_0030068", "EFO_0030067", "EFO_0030064", "EFO_0030070", "EFO_0030071", "EFO_0030072" ]
+        enum: [ "efo:0030069", "efo:0020073", "efo:0030068", "efo:0030067", "efo:0030064", "efo:0030070", "efo:0030071", "efo:0030072" ]
         description: >-
-          MUST be one of "EFO_0030069" (complete genomic loss), "EFO_0020073" (high-level loss), 
-          "EFO_0030068" (low-level loss), "EFO_0030067" (loss), "EFO_0030064" (regional base ploidy), 
-          "EFO_0030070" (gain), "EFO_0030071" (low-level gain), "EFO_0030072" (high-level gain).
+          MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), 
+          "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), 
+          "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).
     required: [  "subject", "copy_change" ]
 
   Genotype:

diff --git a/schema/vrs.json b/schema/vrs.json
@@ -344,16 +344,16 @@
             "copy_change": {
                "type": "string",
                "enum": [
-                  "EFO_0030069",
-                  "EFO_0020073",
-                  "EFO_0030068",
-                  "EFO_0030067",
-                  "EFO_0030064",
-                  "EFO_0030070",
-                  "EFO_0030071",
-                  "EFO_0030072"
+                  "efo:0030069",
+                  "efo:0020073",
+                  "efo:0030068",
+                  "efo:0030067",
+                  "efo:0030064",
+                  "efo:0030070",
+                  "efo:0030071",
+                  "efo:0030072"
                ],
-               "description": "MUST be one of \"EFO_0030069\" (complete genomic loss), \"EFO_0020073\" (high-level loss),  \"EFO_0030068\" (low-level loss), \"EFO_0030067\" (loss), \"EFO_0030064\" (regional base ploidy),  \"EFO_0030070\" (gain), \"EFO_0030071\" (low-level gain), \"EFO_0030072\" (high-level gain)."
+               "description": "MUST be one of \"efo:0030069\" (complete genomic loss), \"efo:0020073\" (high-level loss),  \"efo:0030068\" (low-level loss), \"efo:0030067\" (loss), \"efo:0030064\" (regional base ploidy),  \"efo:0030070\" (gain), \"efo:0030071\" (low-level gain), \"efo:0030072\" (high-level gain)."
             }
          },
          "required": [

diff --git a/schema/vrs.yaml b/schema/vrs.yaml
@@ -207,18 +207,18 @@ definitions:
       copy_change:
         type: string
         enum:
-        - EFO_0030069
-        - EFO_0020073
-        - EFO_0030068
-        - EFO_0030067
-        - EFO_0030064
-        - EFO_0030070
-        - EFO_0030071
-        - EFO_0030072
-        description: MUST be one of "EFO_0030069" (complete genomic loss), "EFO_0020073"
-          (high-level loss),  "EFO_0030068" (low-level loss), "EFO_0030067" (loss),
-          "EFO_0030064" (regional base ploidy),  "EFO_0030070" (gain), "EFO_0030071"
-          (low-level gain), "EFO_0030072" (high-level gain).
+        - efo:0030069
+        - efo:0020073
+        - efo:0030068
+        - efo:0030067
+        - efo:0030064
+        - efo:0030070
+        - efo:0030071
+        - efo:0030072
+        description: MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073"
+          (high-level loss),  "efo:0030068" (low-level loss), "efo:0030067" (loss),
+          "efo:0030064" (regional base ploidy),  "efo:0030070" (gain), "efo:0030071"
+          (low-level gain), "efo:0030072" (high-level gain).
     required:
     - copy_change
     - subject

diff --git a/validation/models.yaml b/validation/models.yaml
@@ -382,7 +382,7 @@ CopyNumberCount:
 CopyNumberChange:
   - name: "Low-level copy gain of BRCA1"
     in:
-      copy_change: EFO_0030071
+      copy_change: efo:0030071
       subject:
         sequence_id: ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
         interval:
@@ -396,9 +396,9 @@ CopyNumberChange:
         type: SequenceLocation
       type: CopyNumberChange
     out:
-      ga4gh_digest: W6Mr7EOuc8_oP--jzFqZeAj-ZC7pK9F_
-      ga4gh_identify: ga4gh:CX.W6Mr7EOuc8_oP--jzFqZeAj-ZC7pK9F_
-      ga4gh_serialize: '{"copy_change":"EFO_0030071","subject":"oz3NEuhtbBep3yqu3wrhqfDKbLPK7vcE","type":"CopyNumberChange"}'
+      ga4gh_digest: zRqNmX-TVTU5FOFxfR4y0jwBysw7ztPn
+      ga4gh_identify: ga4gh:CX.zRqNmX-TVTU5FOFxfR4y0jwBysw7ztPn
+      ga4gh_serialize: '{"copy_change":"efo:0030071","subject":"oz3NEuhtbBep3yqu3wrhqfDKbLPK7vcE","type":"CopyNumberChange"}'
 Text:
   -
     in: