From c4595ae173e10195e6a7157364a6edb5a7276283 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Thu, 13 Apr 2023 08:50:41 -0400 Subject: [PATCH] update efo codes to CURIEs --- docs/source/terms_and_model.rst | 2 +- schema/defs/vrs/CopyNumberChange.rst | 2 +- schema/vrs-source.yaml | 8 ++++---- schema/vrs.json | 18 +++++++++--------- schema/vrs.yaml | 24 ++++++++++++------------ validation/models.yaml | 8 ++++---- 6 files changed, 31 insertions(+), 31 deletions(-) diff --git a/docs/source/terms_and_model.rst b/docs/source/terms_and_model.rst index 896e439a..653142d8 100644 --- 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 index 70ae2c5a..64adb97a 100644 --- 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 index 8a478037..1841fdfa 100644 --- 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 index 7b3f79ea..e9c99691 100644 --- 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 index 472e073e..e84f369e 100644 --- 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 index a8973133..98695c55 100644 --- 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: