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diff --git a/api/GN2-API-documentation.md b/api/GN2-API-documentation.md index 70342dc..c7e6a0e 100644 --- a/api/GN2-API-documentation.md +++ b/api/GN2-API-documentation.md @@ -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 Name can be a pubmedId or a GN-specific identifier for unpublished work.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": { + "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" + }, + { + "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" + } + ] +} +``` |