From 50752033f87b711b7b8657c96fc14e4b1aac0657 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Thu, 16 Jan 2025 11:57:31 -0500
Subject: [PATCH] fix!: use correct representation of `Coding` object in
`mappings`
* `system` MUST use `iriReference`, not a free-text label
* `code` MUST use syntax defined by the `system`
* `id` will use record `concept_id`
---
.github/workflows/checks.yaml | 2 +-
.../source/normalizing_data/normalization.rst | 48 ++-
src/gene/query.py | 18 +-
src/gene/schemas.py | 118 ++++----
tests/unit/test_query.py | 275 +++++++++++-------
tests/unit/test_schemas.py | 9 +-
6 files changed, 300 insertions(+), 170 deletions(-)
diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml
index ba000a7..3922bf1 100644
--- a/.github/workflows/checks.yaml
+++ b/.github/workflows/checks.yaml
@@ -2,7 +2,7 @@ name: Tests
on: [push, pull_request]
jobs:
test:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
strategy:
matrix:
db_url: ["http://localhost:8000", "postgres://postgres:postgres@localhost:5432/gene_normalizer_test"]
diff --git a/docs/source/normalizing_data/normalization.rst b/docs/source/normalizing_data/normalization.rst
index 84d245a..13aa83f 100644
--- a/docs/source/normalizing_data/normalization.rst
+++ b/docs/source/normalizing_data/normalization.rst
@@ -77,12 +77,13 @@ Normalized records are structured as `Genes <https://github.com/ga4gh/vrs/tree/2
{
"coding": {
"code": "HGNC:1097",
- "system": "https://www.genenames.org",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
+ "id": "ncbigene:673",
"code": "673",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
@@ -90,76 +91,97 @@ Normalized records are structured as `Genes <https://github.com/ga4gh/vrs/tree/2
},
{
"coding": {
+ "id": "ensembl:ENSG00000157764",
"code": "ENSG00000157764",
- "system": "https://www.ensembl.org",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "iuphar:1943",
"code": "1943",
- "system": "https://www.guidetopharmacology.org",
+ "system": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "119066", "system": "orphanet"},
+ "coding": {
+ "id": "orphanet:119066",
+ "code": "119066",
+ "system": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=",
+ },
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "cosmic:BRAF",
"code": "BRAF",
- "system": "https://cancer.sanger.ac.uk/cosmic",
+ "system": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=",
},
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "pubmed:2284096",
"code": "2284096",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "ucsc:uc003vwc.5",
"code": "uc003vwc.5",
- "system": "https://genome.ucsc.edu",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "164757", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:164757",
+ "code": "164757",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "refseq:NM_004333",
"code": "NM_004333",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "uniprot:P15056",
"code": "P15056",
- "system": "https://www.uniprot.org",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "ena.embl:M95712",
"code": "M95712",
- "system": "https://www.ebi.ac.uk/ena/",
+ "system": "https://www.ebi.ac.uk/ena/browser/view/",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "OTTHUMG00000157457", "system": "vega"},
+ "coding": {
+ "id": "vega:OTTHUMG00000157457",
+ "code": "OTTHUMG00000157457",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
+ },
"relation": "relatedMatch",
},
{
"coding": {
+ "id": "pubmed:1565476",
"code": "1565476",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
diff --git a/src/gene/query.py b/src/gene/query.py
index 238b8e1..570fc41 100644
--- a/src/gene/query.py
+++ b/src/gene/query.py
@@ -21,7 +21,6 @@
from gene.database import AbstractDatabase, DatabaseReadException
from gene.schemas import (
NAMESPACE_TO_SYSTEM_URI,
- SYSTEM_URI_TO_NAMESPACE,
BaseGene,
BaseNormalizationService,
Gene,
@@ -348,7 +347,7 @@ def _add_merged_meta(self, response: NormalizeService) -> NormalizeService:
sources = []
for m in gene.mappings or []:
- ns = SYSTEM_URI_TO_NAMESPACE.get(m.coding.system)
+ ns = m.coding.id.split(":")[0]
if ns in PREFIX_LOOKUP:
sources.append(PREFIX_LOOKUP[ns])
@@ -406,8 +405,7 @@ def _create_concept_mapping(
) -> ConceptMapping:
"""Create concept mapping for identifier
- ``system`` will use source homepage or namespace prefix, in that order of \
- preference, if available.
+ ``system`` will use system prefix URL or system homepage
:param concept_id: A lowercase concept identifier represented as a curie
:param relation: SKOS mapping relationship, default is relatedMatch
@@ -415,7 +413,7 @@ def _create_concept_mapping(
``NamespacePrefix``
:return: Concept mapping for identifier
"""
- source = concept_id.split(":")[0]
+ source, source_code = concept_id.split(":")
try:
source = NamespacePrefix(source)
@@ -423,10 +421,16 @@ def _create_concept_mapping(
err_msg = f"Namespace prefix not supported: {source}"
raise ValueError(err_msg) from e
- system = NAMESPACE_TO_SYSTEM_URI.get(source, source)
+ if source == NamespacePrefix.HGNC:
+ source_code = concept_id.upper()
return ConceptMapping(
- coding=Coding(code=code(concept_id), system=system), relation=relation
+ coding=Coding(
+ id=concept_id,
+ code=code(source_code),
+ system=NAMESPACE_TO_SYSTEM_URI[source],
+ ),
+ relation=relation,
)
gene_obj = MappableConcept(
diff --git a/src/gene/schemas.py b/src/gene/schemas.py
index 9275dac..dfc6adf 100644
--- a/src/gene/schemas.py
+++ b/src/gene/schemas.py
@@ -169,7 +169,6 @@ class NamespacePrefix(Enum):
HORDE = "hordedb"
MEROPS = "merops"
IUPHAR = "iuphar"
- KZNF = "knzfgc"
MAMIT = "mamittrnadb"
CD = "hcdmdb"
LNCRNADB = "lncrnadb"
@@ -178,31 +177,35 @@ class NamespacePrefix(Enum):
RFAM = "rfam"
-# Source to URI. Will use source homepage
+# Source to URI. Will use system URI prefix or system homepage
NAMESPACE_TO_SYSTEM_URI: dict[NamespacePrefix, str] = {
- NamespacePrefix.HGNC: "https://www.genenames.org",
- NamespacePrefix.ENSEMBL: "https://www.ensembl.org",
+ NamespacePrefix.HGNC: "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
+ NamespacePrefix.ENSEMBL: "https://www.ensembl.org/id/",
NamespacePrefix.NCBI: "https://www.ncbi.nlm.nih.gov/gene/",
NamespacePrefix.ENTREZ: "https://www.ncbi.nlm.nih.gov/gene/",
- NamespacePrefix.VEGA: "https://www.sanger.ac.uk/tool/vega-genome-browser/",
- NamespacePrefix.UCSC: "https://genome.ucsc.edu",
- NamespacePrefix.ENA: "https://www.ebi.ac.uk/ena/",
- NamespacePrefix.REFSEQ: "https://www.ncbi.nlm.nih.gov/refseq/",
- NamespacePrefix.CCDS: "https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi",
- NamespacePrefix.UNIPROT: "https://www.uniprot.org",
- NamespacePrefix.PUBMED: "https://pubmed.ncbi.nlm.nih.gov",
- NamespacePrefix.COSMIC: "https://cancer.sanger.ac.uk/cosmic/",
- NamespacePrefix.OMIM: "https://www.omim.org",
- NamespacePrefix.SNORNABASE: "https://www-snorna.biotoul.fr",
- NamespacePrefix.PSEUDOGENE: "http://pseudogene.org",
- NamespacePrefix.MEROPS: "https://www.ebi.ac.uk/merops/",
- NamespacePrefix.IUPHAR: "https://www.guidetopharmacology.org",
- NamespacePrefix.RFAM: "https://rfam.org",
-}
-
-# URI to source
-SYSTEM_URI_TO_NAMESPACE = {
- system_uri: ns.value for ns, system_uri in NAMESPACE_TO_SYSTEM_URI.items()
+ NamespacePrefix.VEGA: "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
+ NamespacePrefix.UCSC: "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
+ NamespacePrefix.ENA: "https://www.ebi.ac.uk/ena/browser/view/",
+ NamespacePrefix.REFSEQ: "https://www.ncbi.nlm.nih.gov/nuccore/",
+ NamespacePrefix.CCDS: "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=",
+ NamespacePrefix.UNIPROT: "http://purl.uniprot.org/uniprot/",
+ NamespacePrefix.PUBMED: "https://pubmed.ncbi.nlm.nih.gov/",
+ NamespacePrefix.COSMIC: "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=",
+ NamespacePrefix.OMIM: "https://www.omim.org/MIM:",
+ NamespacePrefix.MIRBASE: "https://mirbase.org/hairpin/",
+ NamespacePrefix.HOMEODB: "http://homeodb.zoo.ox.ac.uk",
+ NamespacePrefix.SNORNABASE: "http://www-snorna.biotoul.fr/plus.php?id=",
+ NamespacePrefix.ORPHANET: "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=",
+ NamespacePrefix.PSEUDOGENE: "http://tables.pseudogene.org/",
+ NamespacePrefix.HORDE: "http://genome.weizmann.ac.il/horde/card/index/symbol:",
+ NamespacePrefix.MEROPS: "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=",
+ NamespacePrefix.IUPHAR: "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
+ NamespacePrefix.MAMIT: "http://mamit-trna.u-strasbg.fr/mutations.asp?idAA=",
+ NamespacePrefix.CD: "http://www.hcdm.org/index.php?option=com_molecule&cdnumber=",
+ NamespacePrefix.IMGT: "https://www.imgt.org/genedb/GENElect?species=Homo+sapiens&query=2+",
+ NamespacePrefix.IMGT_GENE_DB: "https://www.imgt.org/genedb/GENElect?species=Homo+sapiens&query=2+",
+ NamespacePrefix.LNCRNADB: "https://rnacentral.org/rna/",
+ NamespacePrefix.RFAM: "https://rfam.org/family/",
}
@@ -347,96 +350,113 @@ class NormalizeService(BaseNormalizationService):
"mappings": [
{
"coding": {
- "code": "hgnc:1097",
- "system": "https://www.genenames.org",
+ "id": "hgnc:1097",
+ "code": "HGNC:1097",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ncbigene:673",
+ "id": "ncbigene:673",
+ "code": "673",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ensembl:ENSG00000157764",
- "system": "https://www.ensembl.org",
+ "id": "ensembl:ENSG00000157764",
+ "code": "ENSG00000157764",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "iuphar:1943",
- "system": "https://www.guidetopharmacology.org",
+ "id": "iuphar:1943",
+ "code": "1943",
+ "system": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "orphanet:119066", "system": "orphanet"},
+ "coding": {
+ "id": "orphanet:119066",
+ "code": "119066",
+ "system": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "cosmic:BRAF",
- "system": "https://cancer.sanger.ac.uk/cosmic",
+ "id": "cosmic:BRAF",
+ "code": "BRAF",
+ "system": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:2284096",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:2284096",
+ "code": "2284096",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ucsc:uc003vwc.5",
- "system": "https://genome.ucsc.edu",
+ "id": "ucsc:uc003vwc.5",
+ "code": "uc003vwc.5",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "omim:164757",
- "system": "https://www.omim.org",
+ "id": "omim:164757",
+ "code": "164757",
+ "system": "https://www.omim.org/MIM:",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "refseq:NM_004333",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "id": "refseq:NM_004333",
+ "code": "NM_004333",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "uniprot:P15056",
- "system": "https://www.uniprot.org",
+ "id": "uniprot:P15056",
+ "code": "P15056",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ena.embl:M95712",
- "system": "https://www.ebi.ac.uk/ena/",
+ "id": "ena.embl:M95712",
+ "code": "M95712",
+ "system": "https://www.ebi.ac.uk/ena/browser/view/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "vega:OTTHUMG00000157457",
- "system": "vega",
+ "id": "vega:OTTHUMG00000157457",
+ "code": "OTTHUMG00000157457",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1565476",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1565476",
+ "code": "1565476",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
index 5414365..a7250e3 100644
--- a/tests/unit/test_query.py
+++ b/tests/unit/test_query.py
@@ -39,75 +39,89 @@ def normalized_ache():
"mappings": [
{
"coding": {
- "code": "hgnc:108",
- "system": "https://www.genenames.org",
+ "id": "hgnc:108",
+ "code": "HGNC:108",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ensembl:ENSG00000087085",
- "system": "https://www.ensembl.org",
+ "id": "ensembl:ENSG00000087085",
+ "code": "ENSG00000087085",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ncbigene:43",
+ "id": "ncbigene:43",
+ "code": "43",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "vega:OTTHUMG00000157033",
- "system": "https://www.sanger.ac.uk/tool/vega-genome-browser/",
+ "id": "vega:OTTHUMG00000157033",
+ "code": "OTTHUMG00000157033",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ucsc:uc003uxi.4",
- "system": "https://genome.ucsc.edu",
+ "id": "ucsc:uc003uxi.4",
+ "code": "uc003uxi.4",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "uniprot:P22303",
- "system": "https://www.uniprot.org",
+ "id": "uniprot:P22303",
+ "code": "P22303",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1380483",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1380483",
+ "code": "1380483",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "omim:100740", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:100740",
+ "code": "100740",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "merops:S09.979",
- "system": "https://www.ebi.ac.uk/merops/",
+ "id": "merops:S09.979",
+ "code": "S09.979",
+ "system": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "iuphar:2465",
- "system": "https://www.guidetopharmacology.org",
+ "id": "iuphar:2465",
+ "code": "2465",
+ "system": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "refseq:NM_015831",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "id": "refseq:NM_015831",
+ "code": "NM_015831",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
@@ -171,93 +185,113 @@ def normalized_braf():
"mappings": [
{
"coding": {
- "code": "hgnc:1097",
- "system": "https://www.genenames.org",
+ "id": "hgnc:1097",
+ "code": "HGNC:1097",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ncbigene:673",
+ "id": "ncbigene:673",
+ "code": "673",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ensembl:ENSG00000157764",
- "system": "https://www.ensembl.org",
+ "id": "ensembl:ENSG00000157764",
+ "code": "ENSG00000157764",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "iuphar:1943",
- "system": "https://www.guidetopharmacology.org",
+ "id": "iuphar:1943",
+ "code": "1943",
+ "system": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "orphanet:119066", "system": "orphanet"},
+ "coding": {
+ "id": "orphanet:119066",
+ "code": "119066",
+ "system": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "cosmic:BRAF",
- "system": "https://cancer.sanger.ac.uk/cosmic/",
+ "id": "cosmic:BRAF",
+ "code": "BRAF",
+ "system": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:2284096",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:2284096",
+ "code": "2284096",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ucsc:uc003vwc.5",
- "system": "https://genome.ucsc.edu",
+ "id": "ucsc:uc003vwc.5",
+ "code": "uc003vwc.5",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "omim:164757", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:164757",
+ "code": "164757",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "refseq:NM_004333",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "id": "refseq:NM_004333",
+ "code": "NM_004333",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "uniprot:P15056",
- "system": "https://www.uniprot.org",
+ "id": "uniprot:P15056",
+ "code": "P15056",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ena.embl:M95712",
- "system": "https://www.ebi.ac.uk/ena/",
+ "id": "ena.embl:M95712",
+ "code": "M95712",
+ "system": "https://www.ebi.ac.uk/ena/browser/view/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "vega:OTTHUMG00000157457",
- "system": "https://www.sanger.ac.uk/tool/vega-genome-browser/",
+ "id": "vega:OTTHUMG00000157457",
+ "code": "OTTHUMG00000157457",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1565476",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1565476",
+ "code": "1565476",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
@@ -323,93 +357,113 @@ def normalized_abl1():
"mappings": [
{
"coding": {
- "code": "hgnc:76",
- "system": "https://www.genenames.org",
+ "id": "hgnc:76",
+ "code": "HGNC:76",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ensembl:ENSG00000097007",
- "system": "https://www.ensembl.org",
+ "id": "ensembl:ENSG00000097007",
+ "code": "ENSG00000097007",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ncbigene:25",
+ "id": "ncbigene:25",
+ "code": "25",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "vega:OTTHUMG00000020813",
- "system": "https://www.sanger.ac.uk/tool/vega-genome-browser/",
+ "id": "vega:OTTHUMG00000020813",
+ "code": "OTTHUMG00000020813",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ucsc:uc004bzv.4",
- "system": "https://genome.ucsc.edu",
+ "id": "ucsc:uc004bzv.4",
+ "code": "uc004bzv.4",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "uniprot:P00519",
- "system": "https://www.uniprot.org",
+ "id": "uniprot:P00519",
+ "code": "P00519",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1857987",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1857987",
+ "code": "1857987",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:12626632",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:12626632",
+ "code": "12626632",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "cosmic:ABL1",
- "system": "https://cancer.sanger.ac.uk/cosmic/",
+ "id": "cosmic:ABL1",
+ "code": "ABL1",
+ "system": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "omim:189980", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:189980",
+ "code": "189980",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
- "coding": {"code": "orphanet:117691", "system": "orphanet"},
+ "coding": {
+ "id": "orphanet:117691",
+ "code": "117691",
+ "system": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "iuphar:1923",
- "system": "https://www.guidetopharmacology.org",
+ "id": "iuphar:1923",
+ "code": "1923",
+ "system": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ena.embl:M14752",
- "system": "https://www.ebi.ac.uk/ena/",
+ "id": "ena.embl:M14752",
+ "code": "M14752",
+ "system": "https://www.ebi.ac.uk/ena/browser/view/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "refseq:NM_007313",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "id": "refseq:NM_007313",
+ "code": "NM_007313",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
@@ -491,75 +545,89 @@ def normalized_p150():
"mappings": [
{
"coding": {
- "code": "hgnc:1910",
- "system": "https://www.genenames.org",
+ "id": "hgnc:1910",
+ "code": "HGNC:1910",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ensembl:ENSG00000167670",
- "system": "https://www.ensembl.org",
+ "id": "ensembl:ENSG00000167670",
+ "code": "ENSG00000167670",
+ "system": "https://www.ensembl.org/id/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ncbigene:10036",
+ "id": "ncbigene:10036",
+ "code": "10036",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "omim:601246", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:601246",
+ "code": "601246",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ccds:CCDS32875",
- "system": "https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi",
+ "id": "ccds:CCDS32875",
+ "code": "CCDS32875",
+ "system": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:7600578",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:7600578",
+ "code": "7600578",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "vega:OTTHUMG00000181922",
- "system": "https://www.sanger.ac.uk/tool/vega-genome-browser/",
+ "id": "vega:OTTHUMG00000181922",
+ "code": "OTTHUMG00000181922",
+ "system": "https://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "uniprot:Q13111",
- "system": "https://www.uniprot.org",
+ "id": "uniprot:Q13111",
+ "code": "Q13111",
+ "system": "http://purl.uniprot.org/uniprot/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "refseq:NM_005483",
- "system": "https://www.ncbi.nlm.nih.gov/refseq/",
+ "id": "refseq:NM_005483",
+ "code": "NM_005483",
+ "system": "https://www.ncbi.nlm.nih.gov/nuccore/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ena.embl:U20979",
- "system": "https://www.ebi.ac.uk/ena/",
+ "id": "ena.embl:U20979",
+ "code": "U20979",
+ "system": "https://www.ebi.ac.uk/ena/browser/view/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "ucsc:uc002mal.4",
- "system": "https://genome.ucsc.edu",
+ "id": "ucsc:uc002mal.4",
+ "code": "uc002mal.4",
+ "system": "http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&hgg_type=knownGene&hgg_gene=",
},
"relation": "relatedMatch",
},
@@ -638,7 +706,8 @@ def normalized_loc_653303():
"mappings": [
{
"coding": {
- "code": "ncbigene:653303",
+ "id": "ncbigene:653303",
+ "code": "653303",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "exactMatch",
@@ -923,33 +992,41 @@ def normalized_ifnr():
"mappings": [
{
"coding": {
- "code": "hgnc:5447",
- "system": "https://www.genenames.org",
+ "id": "hgnc:5447",
+ "code": "HGNC:5447",
+ "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
},
"relation": "exactMatch",
},
{
"coding": {
- "code": "ncbigene:3466",
+ "id": "ncbigene:3466",
+ "code": "3466",
"system": "https://www.ncbi.nlm.nih.gov/gene/",
},
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1906174",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1906174",
+ "code": "1906174",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
{
- "coding": {"code": "omim:147573", "system": "https://www.omim.org"},
+ "coding": {
+ "id": "omim:147573",
+ "code": "147573",
+ "system": "https://www.omim.org/MIM:",
+ },
"relation": "relatedMatch",
},
{
"coding": {
- "code": "pubmed:1193239",
- "system": "https://pubmed.ncbi.nlm.nih.gov",
+ "id": "pubmed:1193239",
+ "code": "1193239",
+ "system": "https://pubmed.ncbi.nlm.nih.gov/",
},
"relation": "relatedMatch",
},
diff --git a/tests/unit/test_schemas.py b/tests/unit/test_schemas.py
index 7dbc2a5..f367112 100644
--- a/tests/unit/test_schemas.py
+++ b/tests/unit/test_schemas.py
@@ -4,7 +4,7 @@
import pytest
from ga4gh.vrs.models import SequenceLocation, SequenceReference
-from gene.schemas import Gene
+from gene.schemas import NAMESPACE_TO_SYSTEM_URI, Gene, NamespacePrefix
@pytest.fixture(scope="module")
@@ -104,3 +104,10 @@ def test_gene(gene, sequence_location):
symbol="BRAF",
locations=sequence_location,
)
+
+
+def test_namespace_to_system_uri():
+ """Ensure that each NamespacePrefix is included in NAMESPACE_TO_SYSTEM_URI"""
+ for v in NamespacePrefix.__members__.values():
+ assert v in NAMESPACE_TO_SYSTEM_URI, v
+ assert NAMESPACE_TO_SYSTEM_URI[v].startswith("http"), v