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authorMunyoki Kilyungi2023-10-24 16:59:46 +0300
committerMunyoki Kilyungi2023-10-24 16:59:46 +0300
commit6b9866b77814ad6312665dd67d62c7319cc4a72a (patch)
treee50d1747c27c905e6cea710466953ef620f3e0d8
parentda978ab9a240f9650972cabbbf4d4ce04f00f48c (diff)
downloadgn-docs-6b9866b77814ad6312665dd67d62c7319cc4a72a.tar.gz
Update GN3 API documentation.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
-rw-r--r--api/GN2-API-documentation.md655
1 files changed, 655 insertions, 0 deletions
diff --git a/api/GN2-API-documentation.md b/api/GN2-API-documentation.md
index 70342dc..c7e6a0e 100644
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@@ -305,3 +305,658 @@ Example Results:
"type": "resultItem"
}
```
+
+## GET /metadata/datasets/search/:term
+Search datasets based of it's title.
+
+*Parameters:* page(default=0), per-page(default=10)
+
+```
+curl "localhost:8080/api/metadata/datasets/search/BXD?page=2&limit=3"
+```
+
+Example Results:
+
+```
+{
+ "@context": {
+ "classifiedUnder": "xkos:classifiedUnder",
+ "currentPage": "ex:currentPage",
+ "data": "@graph",
+ "dataset": "rdfs:label",
+ "dct": "http://purl.org/dc/terms/",
+ "ex": "http://example.org/stuff/1.0/",
+ "id": "@id",
+ "inbredSet": "ex:belongsToInbredSet",
+ "pages": "ex:totalCount",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "result": "ex:result",
+ "resultItem": "ex:resultType",
+ "results": "ex:items",
+ "title": "dct:title",
+ "type": "@type",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#"
+ },
+ "data": [
+ {
+ "currentPage": 2,
+ "id": "ex:result",
+ "pages": 46,
+ "results": [
+ {
+ "classifiedUnder": "Phenotype",
+ "dataset": "BXD-AEPublish",
+ "inbredSet": "BXD Adult and Aged Eye",
+ "title": "BXD Adult and Aged Eye Phenotypes"
+ },
+ {
+ "classifiedUnder": "Phenotype",
+ "dataset": "BXD-AEPublish",
+ "inbredSet": "BXD Adult and Aged Eye",
+ "title": "BXD Adult and Aged Eye Phenotypes"
+ },
+ {
+ "classifiedUnder": "Phenotype",
+ "dataset": "BXD-BonePublish",
+ "inbredSet": "BXD Bone Individual Data",
+ "title": "BXD Bone Individual Data"
+ }
+ ],
+ "type": "resultItem"
+ }
+ ]
+}
+```
+
+## GET /metadata/datasets/search/:term
+Search datasets based of it's title.
+
+*Parameters:* page(default=0), per-page(default=10)
+
+```
+curl "localhost:8080/api/metadata/datasets/search/BXD?page=2&limit=3"
+```
+
+## GET /metadata/publication/:name
+
+Get a publication given it's name. Name can be a pubmedId or a GN-specific identifier for unpublished work.
+
+```
+curl localhost:8080/api/metadata/publications/2760876
+```
+
+Example Result:
+
+```
+{
+ "@context": {
+ "abstract": "dct:abstract",
+ "creator": "dct:creator",
+ "dct": "http://purl.org/dc/terms/",
+ "fabio": "http://purl.org/spar/fabio/",
+ "id": "@id",
+ "journal": "fabio:Journal",
+ "month": {
+ "@id": "prism:publicationDate",
+ "@type": "xsd:gMonth"
+ },
+ "page": "fabio:page",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "title": "dct:title",
+ "type": "@type",
+ "volume": "prism:volume",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+ "year": {
+ "@id": "fabio:hasPublicationYear",
+ "@type": "xsd:gYear"
+ }
+ },
+ "abstract": "Fetal gonadal size [...]",
+ "creator": [
+ "Argyropoulos G",
+ "Shire JG"
+ ],
+ "id": "http://rdf.ncbi.nlm.nih.gov/pubmed/2760876",
+ "journal": "J Reprod Fertil",
+ "month": "July",
+ "page": "473-478",
+ "title": "Genotypic effects on gonadal size in fetal mice",
+ "type": "fabio:ResearchPaper",
+ "volume": "86(2)",
+ "year": "1989"
+}
+```
+
+## GET /metadata/publications/search/:term
+
+Search publications using :term.
+
+```
+curl "localhost:8080/api/metadata/publications/search/BXD?page=0&limit=3"
+```
+
+
+Example Results:
+
+```
+{
+ "@context": {
+ "currentPage": "ex:currentPage",
+ "data": "@graph",
+ "dcat": "http://www.w3.org/ns/dcat#",
+ "dct": "http://purl.org/dc/terms/",
+ "ex": "http://example.org/stuff/1.0/",
+ "fabio": "http://purl.org/spar/fabio/",
+ "foaf": "http://xmlns.com/foaf/0.1/",
+ "generif": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=",
+ "genotype": "http://genenetwork.org/genotype/",
+ "gn": "http://genenetwork.org/id/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "owl": "http://www.w3.org/2002/07/owl#",
+ "pages": "ex:totalCount",
+ "phenotype": "http://genenetwork.org/phenotype/",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "publication": "http://genenetwork.org/publication/",
+ "pubmed": "fabio:hasPubMedId",
+ "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "result": "ex:result",
+ "resultItem": "ex:resultType",
+ "results": "ex:items",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "taxon": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=",
+ "title": "dct:title",
+ "type": "@type",
+ "up": "http://purl.uniprot.org/core/",
+ "url": "rdfs:label",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+ "xsd": "http://www.w3.org/2001/XMLSchema#"
+ },
+ "data": [
+ {
+ "currentPage": 0,
+ "id": "ex:result",
+ "pages": 2740,
+ "results": [
+ {
+ "title": "A QTL on chromosome 1 modulates inter-male aggression in mice",
+ "url": "http://genenetwork.org/id/unpublished14159"
+ },
+ {
+ "title": "\tSystems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits",
+ "url": "http://genenetwork.org/id/unpublished14051"
+ },
+ {
+ "title": "3a,5a-THP in BXD CIE study",
+ "url": "http://genenetwork.org/id/unpublished12780"
+ }
+ ],
+ "type": "resultItem"
+ }
+ ]
+}
+```
+
+## GET /metadata/phenotypes/:name
+Fetch metadata about a given phenotype given it's name.
+
+```
+curl "localhost:8080/api/metadata/phenotypes/BXD_10007"
+```
+
+Example Result:
+
+```
+{
+ "@context": {
+ "LRS": "gnt:LRS",
+ "abbreviation": "dct:abbreviation",
+ "abstract": "dct:abstract",
+ "additive": "gnt:additive",
+ "altName": "rdfs:altLabel",
+ "contributor": "dct:contributor",
+ "creator": "dct:creator",
+ "data": "@graph",
+ "dct": "http://purl.org/dc/terms/",
+ "description": "dct:description",
+ "fabio": "http://purl.org/spar/fabio/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "journal": "fabio:Journal",
+ "labCode": "gnt:labCode",
+ "locus": "gnt:locus",
+ "mean": "gnt:mean",
+ "month": {
+ "@id": "prism:publicationDate",
+ "@type": "xsd:gMonth"
+ },
+ "page": "fabio:page",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "references": "dct:isReferencedBy",
+ "sequence": "gnt:sequence",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "submitter": "gnt:submitter",
+ "title": "dct:title",
+ "trait": "rdfs:label",
+ "traitName": "skos:altLabel",
+ "type": "@type",
+ "volume": "prism:volume",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+ "year": {
+ "@id": "fabio:hasPublicationYear",
+ "@type": "xsd:gYear"
+ }
+ },
+ "LRS": 14.3203,
+ "abstract": "To discover [...]",
+ "additive": 1.24101,
+ "creator": [
+ "Airey DC",
+ "Williams RW",
+ "Lu L"
+ ],
+ "description": "Central nervous system, morphology: Internal granule layer IGL of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]",
+ "gnt:abbreviation": "AdjIGLVol",
+ "http://example.org/stuff/1.0/inbredSet": "BXD Family",
+ "http://example.org/stuff/1.0/species": "Mouse (Mus musculus, mm10)",
+ "id": "http://genenetwork.org/id/traitBxd_10007",
+ "journal": "J Neurosci",
+ "locus": "rsm10000005700",
+ "mean": 18.2129,
+ "month": "Jul",
+ "page": "5099-5109",
+ "references": {
+ "id": "http://rdf.ncbi.nlm.nih.gov/pubmed/11438585"
+ },
+ "sequence": 1,
+ "submitter": "robwilliams",
+ "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture",
+
+ "trait": "10007",
+ "traitName": "BXD_10007",
+ "type": "gnc:Phenotype",
+ "volume": "21(14)",
+ "year": "2001"
+}
+```
+
+## GET /metadata/phenotypes/:group/:name
+Fetch metadata about a given phenotype given it's group and name.
+
+```
+curl "localhost:8080/api/metadata/phenotypes/BXD/10007"
+```
+
+Example Result:
+
+```
+{
+ "@context": {
+ "LRS": "gnt:LRS",
+ "abbreviation": "dct:abbreviation",
+ "abstract": "dct:abstract",
+ "additive": "gnt:additive",
+ "altName": "rdfs:altLabel",
+ "contributor": "dct:contributor",
+ "creator": "dct:creator",
+ "data": "@graph",
+ "dct": "http://purl.org/dc/terms/",
+ "description": "dct:description",
+ "fabio": "http://purl.org/spar/fabio/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "journal": "fabio:Journal",
+ "labCode": "gnt:labCode",
+ "locus": "gnt:locus",
+ "mean": "gnt:mean",
+ "month": {
+ "@id": "prism:publicationDate",
+ "@type": "xsd:gMonth"
+ },
+ "page": "fabio:page",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "references": "dct:isReferencedBy",
+ "sequence": "gnt:sequence",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "submitter": "gnt:submitter",
+ "title": "dct:title",
+ "trait": "rdfs:label",
+ "traitName": "skos:altLabel",
+ "type": "@type",
+ "volume": "prism:volume",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+ "year": {
+ "@id": "fabio:hasPublicationYear",
+ "@type": "xsd:gYear"
+ }
+ },
+ "LRS": 14.3203,
+ "abstract": "To discover [...]",
+ "additive": 1.24101,
+ "creator": [
+ "Airey DC",
+ "Williams RW",
+ "Lu L"
+ ],
+ "description": "Central nervous system, morphology: Internal granule layer IGL of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]",
+ "gnt:abbreviation": "AdjIGLVol",
+ "http://example.org/stuff/1.0/inbredSet": "BXD Family",
+ "http://example.org/stuff/1.0/species": "Mouse (Mus musculus, mm10)",
+ "id": "http://genenetwork.org/id/traitBxd_10007",
+ "journal": "J Neurosci",
+ "locus": "rsm10000005700",
+ "mean": 18.2129,
+ "month": "Jul",
+ "page": "5099-5109",
+ "references": {
+ "id": "http://rdf.ncbi.nlm.nih.gov/pubmed/11438585"
+ },
+ "sequence": 1,
+ "submitter": "robwilliams",
+ "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture",
+ "trait": "10007",
+ "traitName": "BXD_10007",
+ "type": "gnc:Phenotype",
+ "volume": "21(14)",
+ "year": "2001"
+}
+```
+
+## GET /metadata/genotypes/:name
+Fetch metadata about a given genotype given it's name.
+
+```
+curl "localhost:8080/api/metadata/genotypes/D1Mit3"
+```
+
+Example Result
+
+```
+{
+ "@context": {
+ "alternateSource": "gnt:hasAltSourceName",
+ "chr": "gnt:chr",
+ "chrNum": {
+ "@id": "gnt:chrNum",
+ "@type": "xsd:int"
+ },
+ "comments": "rdfs:comments",
+ "data": "@graph",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "mb": "gnt:mb",
+ "mb2016": "gnt:mb2016",
+ "mbMm8": "gnt:mbMm8",
+ "name": "rdfs:label",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "sequence": "gnt:hasSequence",
+ "source": "gnt:hasSource",
+ "species": "xkos:classifiedUnder",
+ "type": "@type",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+ "xsd": "http://www.w3.org/2001/XMLSchema#"
+ },
+ "chr": "1",
+ "chrNum": "1",
+ "id": "http://genenetwork.org/id/D1mit3",
+ "mb": 19.812,
+ "mb2016": 19.8021,
+ "mbMm8": 19.7972,
+ "name": "D1Mit3",
+ "sequence": "TTTAGCAATGGGTANCGGGGATCTTCCACTGTCTTTGTGTCTTAGGACCCAGAATTTACTTTTCTTTTTGTTTTCTTTTCTTTTCCCTGTCTTTTTTTTTTTTTGCTTCTTTTATTTTAAAAATCTATTCATGTTTAAAGTCTCCCTCTCTGTCTCTCTGTCTGTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCAGTACATGTGGAAACCAGAAGAGGGCATCAGATTCCTAGGAACTGGAGCTACAGAT",
+ "source": "Mit",
+ "species": {
+ "id": "http://genenetwork.org/id/Mus_musculus",
+ "name": "Mus musculus"
+ },
+ "type": "gnc:Genotype"
+}
+```
+
+## GET /genewiki/gn/:symbol
+Get genewiki entries from Genetwork about a given symbol
+
+*Parameters:* page(default=0), per-page(default=10)
+
+```
+curl "localhost:8080/api/metadata/genewikis/gn/Lpl"
+```
+
+Example Result
+
+```
+{
+ "@context": {
+ "author": "dct:creator",
+ "category": "gnt:belongsToCategory",
+ "comment": "rdfs:comment",
+ "created": {
+ "@id": "dct:created",
+ "@type": "xsd:datetime"
+ },
+ "currentPage": "ex:currentPage",
+ "data": "@graph",
+ "dct": "http://purl.org/dc/terms/",
+ "entries": "ex:entries",
+ "ex": "http://example.org/stuff/1.0/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "pages": "ex:totalCount",
+ "pubmed": "dct:references",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "type": "@type",
+ "xsd": "http://www.w3.org/2001/XMLSchema#"
+ },
+ "currentPage": 0,
+ "entries": [
+ {
+ "category": "Genetic variation and alleles",
+ "comment": "Individual probe analysis:probably true cisQTL",
+ "created": "2007-10-05T09:09:52",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ },
+ {
+ "category": "Expression patterns: mature cells, tissues; Gene structure and organization; Genetic variation and alleles",
+ "comment": "cis QTL present in hippocampus LXS, ILM2970706 distal 3' UTR, 121.4 LRS, ISS increases the trait;",
+ "created": "2007-05-10T05:52:22",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ },
+ {
+ "category": "",
+ "comment": "hippocampal CA1-3 expression signature",
+ "created": "2005-12-16T15:23:23",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/15084669"
+ },
+ {
+ "category": "Probes and probe sets; Transcriptional and translation control",
+ "comment": "Validated strong cis-QTL in CNS using allele-specific expression ASE SNaPshot assay Daniel Ciobanu and al., 2007. Possible 3' UTR variants.",
+ "created": "2007-05-08T09:46:07",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ },
+ {
+ "author": "Robert Williams",
+ "category": "Genetic variation and alleles",
+ "comment": "cis eQTL in BXD brain RNA-seq data with LRS of 33 and high D allele. No obvious trans target transcripts.",
+ "created": "2012-11-10T07:30:09",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ },
+ {
+ "category": "Health and disease associations",
+ "comment": "Merck, Rosetta, Schadt, Lusis target gene associated with obesity, diabetes and atherosclerosis.",
+ "created": "2008-05-13T08:48:50",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ },
+ {
+ "author": "Robert Williams",
+ "category": "",
+ "comment": "Of interest to Lu Lu and colleagues 2015 due to modulation of expression of this gene in hippocampus following stress or ethanol BXD Illumina Hippocampus data sets.",
+ "created": "2015-05-26T11:37:57",
+ "ex:species": "Mouse (Mus musculus, mm10)",
+ "pubmed": ""
+ }
+ ],
+ "id": "http://genenetwork.org/id/symbolLpl",
+ "pages": 1,
+ "type": "gnc:GNWikiEntry"
+}
+```
+
+## GET /genewiki/ncbi/:symol
+Get genewiki entries from NCBI about a given symbol
+
+*Parameters:* page(default=0), per-page(default=10)
+
+```
+curl "localhost:8080/api/metadata/genewikis/ncbi/Lpl"
+```
+
+Example Result
+
+```
+{
+ "@context": {
+ "author": "dct:creator",
+ "category": "gnt:belongsToCategory",
+ "comment": "rdfs:comment",
+ "created": {
+ "@id": "dct:created",
+ "@type": "xsd:datetime"
+ },
+ "currentPage": "ex:currentPage",
+ "data": "@graph",
+ "dct": "http://purl.org/dc/terms/",
+ "entries": "ex:entries",
+ "ex": "http://example.org/stuff/1.0/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "id": "@id",
+ "pages": "ex:totalCount",
+ "pubmed": "dct:references",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "type": "@type",
+ "xsd": "http://www.w3.org/2001/XMLSchema#"
+ },
+ "data": [
+ {
+ "currentPage": 0,
+ "entries": [
+ {
+ "comment": "Results support the use of LPL and ADAM29 gene expression associated to IGHV mutational status for predicting the clinical outcome of patients treated by oral fludarabine + cyclophosphamide and could be considered for treatment strategies.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "Observational study of gene-disease association and pharmacogenomic / toxicogenomic. HuGE Navigator",
+ "created": "2009-02-11T15:30:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "analysis of human placental lipoprotein lipase gestational and hormonal regulation",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "LPL 44X alleles were associated with moderately increased LDL peak particle size.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "LPL gene variant is involved in carotid atherosclerotic lesions.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "Metformin may increase LPL production, thereby increasing low density lipoprotein particle size which may be independent of the hypoglycemic effect of metforminin type 2 diabetes.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "LPL may represent a link between low adiponectin levels and dyslipidemia in both nondiabetic individuals and patients with type 2 diabetes.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": ""
+ },
+ {
+ "comment": "The PvuII polymorphism cannot be used as independent genetic risk factor for coronary artery disease in patients of Saudi Arabic descent.",
+ "created": "2010-01-20T18:00:00",
+ "ex:species": "Human (Homo sapiens, hg19)",
+ "gnt:hasGeneId": {
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+ },
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+}
+```