From 0c00a5f5153f6c3cf4199586bf7dfe6dd87850af Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 24 Oct 2023 17:09:22 +0300
Subject: Update GN3 API documentation.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
api/GN3-REST-API-Implementation.md | 224 +++++++++++++------------------------
1 file changed, 76 insertions(+), 148 deletions(-)
(limited to 'api')
diff --git a/api/GN3-REST-API-Implementation.md b/api/GN3-REST-API-Implementation.md
index 4f02bf0..d759e94 100644
--- a/api/GN3-REST-API-Implementation.md
+++ b/api/GN3-REST-API-Implementation.md
@@ -836,61 +836,62 @@ Example Result
"pages": "ex:totalCount",
"pubmed": "dct:references",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "species": "ex:species",
"type": "@type",
"xsd": "http://www.w3.org/2001/XMLSchema#"
},
"currentPage": 0,
"entries": [
{
+ "author": "Robert Williams",
"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": ""
+ "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",
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
- "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": "Genetic variation and alleles",
+ "comment": "Individual probe analysis:probably true cisQTL",
+ "created": "2007-10-05T09:09:52",
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
"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"
+ "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/15084669",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
"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": ""
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
- "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": "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",
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
"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": ""
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
},
{
"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": ""
+ "pubmed": "",
+ "species": "Mouse (Mus musculus, mm10)"
}
],
"id": "http://genenetwork.org/id/symbolLpl",
@@ -899,13 +900,13 @@ Example Result
}
```
-## GET /genewiki/ncbi/:symol
+## GET /genewiki/ncbi/:symbol
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"
+curl "localhost:8080/api/metadata/genewikis/ncbi/Lpl?per-page=3"
```
Example Result
@@ -913,134 +914,61 @@ Example Result
```
{
"@context": {
- "author": "dct:creator",
- "category": "gnt:belongsToCategory",
- "comment": "rdfs:comment",
+ "author": "dct:creator",
+ "category": "gnt:belongsToCategory",
+ "comment": "rdfs:comment",
"created": {
- "@id": "dct: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",
+ },
+ "currentPage": "ex:currentPage",
+ "data": "@graph",
+ "dct": "http://purl.org/dc/terms/",
+ "entries": "ex:entries",
+ "ex": "http://example.org/stuff/1.0/",
+ "geneId": "gnt:hasGeneId",
+ "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#",
+ "species": "ex:species",
+ "type": "@type",
"xsd": "http://www.w3.org/2001/XMLSchema#"
- },
- "data": [
+ },
+ "currentPage": 0,
+ "entries": [
{
- "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": {
- "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
- },
- "pubmed": ""
- }
- ],
- "id": "http://genenetwork.org/id/symbolLPL",
- "pages": 48,
- "type": "gnc:GNWikiEntry"
- },
+ "comment": "LPL gene variant is involved in carotid atherosclerotic lesions.",
+ "created": "2010-01-20T18:00:00",
+ "geneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": "",
+ "species": "Human (Homo sapiens, hg19)"
+ },
{
- "currentPage": 0,
- "entries": [
- {
- "comment": "LPL activity can be inhibited by endogenous apoC-I in apoE-knockout mice.",
- "created": "2010-01-20T18:00:00",
- "ex:species": "Mouse (Mus musculus, mm10)",
- "gnt:hasGeneId": {
- "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=16956"
- },
- "pubmed": ""
- },
- {
- "comment": "STZ-induced diabetes causes a decrease in LPL activity in the sciatic nerve that is reversible with insulin treatment",
- "created": "2010-01-20T18:00:00",
- "ex:species": "Rat (Rattus norvegicus, rn7.2)",
- "gnt:hasGeneId": {
- "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=24539"
- },
- "pubmed": ""
- }
- ],
- "id": "http://genenetwork.org/id/symbolLpl",
- "pages": 48,
- "type": "gnc:GNWikiEntry"
+ "comment": "LPL 44X alleles were associated with moderately increased LDL peak particle size.",
+ "created": "2010-01-20T18:00:00",
+ "geneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": "",
+ "species": "Human (Homo sapiens, hg19)"
+ },
+ {
+ "comment": "Observational study of gene-disease association and pharmacogenomic / toxicogenomic. HuGE Navigator",
+ "created": "2009-02-11T15:30:00",
+ "geneId": {
+ "id": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=4023"
+ },
+ "pubmed": "",
+ "species": "Human (Homo sapiens, hg19)"
}
- ]
+ ],
+ "id": "http://genenetwork.org/id/symbolLPL",
+ "pages": 158,
+ "type": "gnc:GNWikiEntry"
}
```
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