From 291a0eab8d5585e599d97a28c4b5e1a7653b7cfc Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 24 Oct 2023 17:01:17 +0300 Subject: Rename GN2-API-documentation.md -> GN3-REST-API-Implementation.md. Signed-off-by: Munyoki Kilyungi --- api/GN2-API-documentation.md | 962 ------------------------------------- api/GN3-REST-API-Implementation.md | 962 +++++++++++++++++++++++++++++++++++++ 2 files changed, 962 insertions(+), 962 deletions(-) delete mode 100644 api/GN2-API-documentation.md create mode 100644 api/GN3-REST-API-Implementation.md diff --git a/api/GN2-API-documentation.md b/api/GN2-API-documentation.md deleted file mode 100644 index c7e6a0e..0000000 --- a/api/GN2-API-documentation.md +++ /dev/null @@ -1,962 +0,0 @@ -# API Endpoints - -The following end-points are available to all users. The result of every query is json-ld. - -## GET /metadata/species - -Returns a list of species. - -``` -curl localhost:8080/api/metadata/species -``` - -Example Result: - -``` -{ - "@context": { - "alternateName": "skos:altLabel", - "data": "@graph", - "family": "gnt:family", - "fullName": "skos:prefLabel", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "shortName": "gnt:shortName", - "skos": "http://www.w3.org/2004/02/skos/core#", - "taxonomicId": "skos:notation", - "type": "@type" - }, - "data": [ - { - "alternateName": "Human", - "family": "Vertebrates", - "fullName": "Human (Homo sapiens, hg19)", - "id": "http://genenetwork.org/id/Homo_sapiens", - "name": "Homo sapiens", - "shortName": "human", - "taxonomicId": { - "id": "http://purl.uniprot.org/taxonomy/9606" - } - }, - [...] - { - "alternateName": "Soybean", - "family": "Plants", - "fullName": "Soybean (Glycine max, US DOE JGI-PGF v2 2021)", - "id": "http://genenetwork.org/id/Glycine_max", - "name": "Glycine max", - "shortName": "soybean", - "taxonomicId": { - "id": "http://purl.uniprot.org/taxonomy/3847" - } - } - ] -} -``` - -## GET /metadata/species/:name - -Get a list of species with data available in GN. - -``` -curl "localhost:8080/api/metadata/species/bat" -``` - -Example Result: - -``` -{ - "@context": { - "alternateName": "skos:altLabel", - "data": "@graph", - "family": "gnt:family", - "fullName": "skos:prefLabel", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "shortName": "gnt:shortName", - "skos": "http://www.w3.org/2004/02/skos/core#", - "taxonomicId": "skos:notation", - "type": "@type" - }, - "alternateName": "Bat (Glossophaga soricina)", - "family": "Vertebrates", - "fullName": "Bat (Glossophaga soricina, gsor23)", - "id": "http://genenetwork.org/id/Glossophaga_soricina", - "name": "Glossophaga soricina", - "shortName": "bat", - "taxonomicId": { - "id": "http://purl.uniprot.org/taxonomy/27638" - } -} - -``` - -## GET /metadata/groups - -Fetch all groups. - -``` -curl "localhost:8080/api/metadata/groups" -``` - -Example Results: - -``` -{ - "@context": { - "code": "gnt:code", - "data": "@graph", - "family": "gnt:family", - "fullName": "skos:prefLabel", - "geneticType": "gnt:geneticType", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "mappingMethod": "gnt:mappingMethod", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "shortName": "gnt:shortName", - "skos": "http://www.w3.org/2004/02/skos/core#", - "type": "@type" - }, - "data": [ - { - "code": "BDG", - "family": "BXD Individual Data", - "fullName": "DOD-BXD-GWI", - "geneticType": "intercross", - "id": "http://genenetwork.org/id/setDod-bxd-gwi", - "mappingMethod": "qtlreaper", - "name": "BXD DOD Gulf War Illness" - }, - [...] - { - "code": "CAN", - "fullName": "CANDLE", - "id": "http://genenetwork.org/id/setCandle", - "name": "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" - } - ] -} -``` - -## GET /metadata/groups/:name - -Fetch information about a given group given a species' name. - -``` -curl "localhost:8080/api/metadata/groups/bat" -``` - -Example Results: - -``` -{ - "@context": { - "code": "gnt:code", - "data": "@graph", - "family": "gnt:family", - "fullName": "skos:prefLabel", - "geneticType": "gnt:geneticType", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "mappingMethod": "gnt:mappingMethod", - "name": "rdfs:label", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "shortName": "gnt:shortName", - "skos": "http://www.w3.org/2004/02/skos/core#", - "type": "@type" - }, - "code": "GSO", - "fullName": "GSO", - "id": "http://genenetwork.org/id/setGso", - "mappingMethod": "qtlreaper", - "name": "HUB Winter Gsor families (2014-2022)" -} -``` - - -## GET /metadata/datasets/:name - -Fetch information about a given dataset given it's name. - -``` -curl "localhost:8080/api/metadata/datasets/IBR_M_0204_M" -``` - -or - -``` -curl "localhost:8080/api/metadata/datasets/GN11" -``` - -Example Results: - -``` -{ - "@context": { - "accessRights": "dct:accessRights", - "accessionId": "dct:identifier", - "acknowledgement": "gnt:hasAcknowledgement", - "altLabel": "skos:altLabel", - "caseInfo": "gnt:hasCaseInfo", - "classifiedUnder": "xkos:classifiedUnder", - "contactPoint": "dcat:contactPoint", - "created": "dct:created", - "data": "@graph", - "dcat": "http://www.w3.org/ns/dcat#", - "dct": "http://purl.org/dc/terms/", - "description": "dct:description", - "ex": "http://example.org/stuff/1.0/", - "experimentDesignInfo": "gnt:hasExperimentDesignInfo", - "foaf": "http://xmlns.com/foaf/0.1/", - "geoSeriesId": "gnt:hasGeoSeriesId", - "gnt": "http://genenetwork.org/term/", - "id": "@id", - "inbredSet": "ex:belongsToInbredSet", - "info": "ex:info", - "label": "rdfs:label", - "normalization": "gnt:usesNormalization", - "notes": "gnt:hasNotes", - "organization": "foaf:Organization", - "platform": "ex:platform", - "prefLabel": "skos:prefLabel", - "processingInfo": "gnt:hasDataProcessingInfo", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "skos": "http://www.w3.org/2004/02/skos/core#", - "tissue": "ex:tissue", - "title": "dct:title", - "type": "@type", - "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#" - }, - "accessionId": "GN11", - "contactPoint": "Michael Miles", - "id": "http://genenetwork.org/id/Ibr_m_0204_m", - "inbredSet": "BXD Family", - "label": "IBR_M_0204_M", - "normalization": "MAS5", - "platform": { - "id": "http://genenetwork.org/id/platformMoe430", - "info": "[...]", - "label": "Affy Mouse Genome 430A, 430B, 430A 2.0 (GPL339,GPL340)", - "prefLabel": "MOE430", - "type": "http://genenetwork.org/category/geneChip" - }, - "tissue": { - "id": "http://genenetwork.org/id/tissueBrn", - "info": "[...]", - "label": "Brain mRNA", - "type": "http://genenetwork.org/category/tissue" - }, - "type": "dcat:Dataset" -} -``` - -## GET /metadata/datasets/:group/list - -List datasets that belong to a given group. - -*Parameters:* page(default=0), per-page(default=10) - -``` -curl "localhost:8080/api/metadata/datasets/BXD/list" -``` - -Example Results: - -``` -{ - "@context": { - "classifiedUnder": "xkos:classifiedUnder", - "created": "dct:created", - "currentPage": "ex:currentPage", - "data": "@graph", - "dct": "http://purl.org/dc/terms/", - "ex": "http://example.org/stuff/1.0/", - "id": "@id", - "name": "rdfs:label", - "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#" - }, - "currentPage": 0, - "id": "ex:result", - "pages": 42, - "results": [ - { - "created": "2001-09-22", - "name": "DBA2J-ONH-1212", - "title": "Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma." - }, - [...] - { - "created": "2003-06-01", - "name": "Br_U_0603_M" - } - ], - "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" - } - ] -} -``` diff --git a/api/GN3-REST-API-Implementation.md b/api/GN3-REST-API-Implementation.md new file mode 100644 index 0000000..c7e6a0e --- /dev/null +++ b/api/GN3-REST-API-Implementation.md @@ -0,0 +1,962 @@ +# API Endpoints + +The following end-points are available to all users. The result of every query is json-ld. + +## GET /metadata/species + +Returns a list of species. + +``` +curl localhost:8080/api/metadata/species +``` + +Example Result: + +``` +{ + "@context": { + "alternateName": "skos:altLabel", + "data": "@graph", + "family": "gnt:family", + "fullName": "skos:prefLabel", + "gnt": "http://genenetwork.org/term/", + "id": "@id", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "shortName": "gnt:shortName", + "skos": "http://www.w3.org/2004/02/skos/core#", + "taxonomicId": "skos:notation", + "type": "@type" + }, + "data": [ + { + "alternateName": "Human", + "family": "Vertebrates", + "fullName": "Human (Homo sapiens, hg19)", + "id": "http://genenetwork.org/id/Homo_sapiens", + "name": "Homo sapiens", + "shortName": "human", + "taxonomicId": { + "id": "http://purl.uniprot.org/taxonomy/9606" + } + }, + [...] + { + "alternateName": "Soybean", + "family": "Plants", + "fullName": "Soybean (Glycine max, US DOE JGI-PGF v2 2021)", + "id": "http://genenetwork.org/id/Glycine_max", + "name": "Glycine max", + "shortName": "soybean", + "taxonomicId": { + "id": "http://purl.uniprot.org/taxonomy/3847" + } + } + ] +} +``` + +## GET /metadata/species/:name + +Get a list of species with data available in GN. + +``` +curl "localhost:8080/api/metadata/species/bat" +``` + +Example Result: + +``` +{ + "@context": { + "alternateName": "skos:altLabel", + "data": "@graph", + "family": "gnt:family", + "fullName": "skos:prefLabel", + "gnt": "http://genenetwork.org/term/", + "id": "@id", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "shortName": "gnt:shortName", + "skos": "http://www.w3.org/2004/02/skos/core#", + "taxonomicId": "skos:notation", + "type": "@type" + }, + "alternateName": "Bat (Glossophaga soricina)", + "family": "Vertebrates", + "fullName": "Bat (Glossophaga soricina, gsor23)", + "id": "http://genenetwork.org/id/Glossophaga_soricina", + "name": "Glossophaga soricina", + "shortName": "bat", + "taxonomicId": { + "id": "http://purl.uniprot.org/taxonomy/27638" + } +} + +``` + +## GET /metadata/groups + +Fetch all groups. + +``` +curl "localhost:8080/api/metadata/groups" +``` + +Example Results: + +``` +{ + "@context": { + "code": "gnt:code", + "data": "@graph", + "family": "gnt:family", + "fullName": "skos:prefLabel", + "geneticType": "gnt:geneticType", + "gnt": "http://genenetwork.org/term/", + "id": "@id", + "mappingMethod": "gnt:mappingMethod", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "shortName": "gnt:shortName", + "skos": "http://www.w3.org/2004/02/skos/core#", + "type": "@type" + }, + "data": [ + { + "code": "BDG", + "family": "BXD Individual Data", + "fullName": "DOD-BXD-GWI", + "geneticType": "intercross", + "id": "http://genenetwork.org/id/setDod-bxd-gwi", + "mappingMethod": "qtlreaper", + "name": "BXD DOD Gulf War Illness" + }, + [...] + { + "code": "CAN", + "fullName": "CANDLE", + "id": "http://genenetwork.org/id/setCandle", + "name": "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" + } + ] +} +``` + +## GET /metadata/groups/:name + +Fetch information about a given group given a species' name. + +``` +curl "localhost:8080/api/metadata/groups/bat" +``` + +Example Results: + +``` +{ + "@context": { + "code": "gnt:code", + "data": "@graph", + "family": "gnt:family", + "fullName": "skos:prefLabel", + "geneticType": "gnt:geneticType", + "gnt": "http://genenetwork.org/term/", + "id": "@id", + "mappingMethod": "gnt:mappingMethod", + "name": "rdfs:label", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "shortName": "gnt:shortName", + "skos": "http://www.w3.org/2004/02/skos/core#", + "type": "@type" + }, + "code": "GSO", + "fullName": "GSO", + "id": "http://genenetwork.org/id/setGso", + "mappingMethod": "qtlreaper", + "name": "HUB Winter Gsor families (2014-2022)" +} +``` + + +## GET /metadata/datasets/:name + +Fetch information about a given dataset given it's name. + +``` +curl "localhost:8080/api/metadata/datasets/IBR_M_0204_M" +``` + +or + +``` +curl "localhost:8080/api/metadata/datasets/GN11" +``` + +Example Results: + +``` +{ + "@context": { + "accessRights": "dct:accessRights", + "accessionId": "dct:identifier", + "acknowledgement": "gnt:hasAcknowledgement", + "altLabel": "skos:altLabel", + "caseInfo": "gnt:hasCaseInfo", + "classifiedUnder": "xkos:classifiedUnder", + "contactPoint": "dcat:contactPoint", + "created": "dct:created", + "data": "@graph", + "dcat": "http://www.w3.org/ns/dcat#", + "dct": "http://purl.org/dc/terms/", + "description": "dct:description", + "ex": "http://example.org/stuff/1.0/", + "experimentDesignInfo": "gnt:hasExperimentDesignInfo", + "foaf": "http://xmlns.com/foaf/0.1/", + "geoSeriesId": "gnt:hasGeoSeriesId", + "gnt": "http://genenetwork.org/term/", + "id": "@id", + "inbredSet": "ex:belongsToInbredSet", + "info": "ex:info", + "label": "rdfs:label", + "normalization": "gnt:usesNormalization", + "notes": "gnt:hasNotes", + "organization": "foaf:Organization", + "platform": "ex:platform", + "prefLabel": "skos:prefLabel", + "processingInfo": "gnt:hasDataProcessingInfo", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "tissue": "ex:tissue", + "title": "dct:title", + "type": "@type", + "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#" + }, + "accessionId": "GN11", + "contactPoint": "Michael Miles", + "id": "http://genenetwork.org/id/Ibr_m_0204_m", + "inbredSet": "BXD Family", + "label": "IBR_M_0204_M", + "normalization": "MAS5", + "platform": { + "id": "http://genenetwork.org/id/platformMoe430", + "info": "[...]", + "label": "Affy Mouse Genome 430A, 430B, 430A 2.0 (GPL339,GPL340)", + "prefLabel": "MOE430", + "type": "http://genenetwork.org/category/geneChip" + }, + "tissue": { + "id": "http://genenetwork.org/id/tissueBrn", + "info": "[...]", + "label": "Brain mRNA", + "type": "http://genenetwork.org/category/tissue" + }, + "type": "dcat:Dataset" +} +``` + +## GET /metadata/datasets/:group/list + +List datasets that belong to a given group. + +*Parameters:* page(default=0), per-page(default=10) + +``` +curl "localhost:8080/api/metadata/datasets/BXD/list" +``` + +Example Results: + +``` +{ + "@context": { + "classifiedUnder": "xkos:classifiedUnder", + "created": "dct:created", + "currentPage": "ex:currentPage", + "data": "@graph", + "dct": "http://purl.org/dc/terms/", + "ex": "http://example.org/stuff/1.0/", + "id": "@id", + "name": "rdfs:label", + "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#" + }, + "currentPage": 0, + "id": "ex:result", + "pages": 42, + "results": [ + { + "created": "2001-09-22", + "name": "DBA2J-ONH-1212", + "title": "Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma." + }, + [...] + { + "created": "2003-06-01", + "name": "Br_U_0603_M" + } + ], + "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" + } + ] +} +``` -- cgit v1.2.3