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TogoVar API version 0.9.1 specification Base URLs: - https://grch38.togovar.org/api search post__search_variant Code samples # You can also use wget curl -X POST https://grch38.togovar.org/api/search/variant \ -H 'Content-Type: application/json' \ -H 'Accept: application/json' POST https://grch38.togovar.org/api/search/variant HTTP/1.1 Host: grch38.togovar.org Content-Type: application/json Accept: application/json const inputBody = '{ "query": { "type": { "relation": "eq", "terms": [ "ins", "del", "indel" ] } } }'; const headers = { 'Content-Type':'application/json', 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/search/variant', { method: 'POST', body: inputBody, headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Content-Type' => 'application/json', 'Accept' => 'application/json' } result = RestClient.post 'https://grch38.togovar.org/api/search/variant', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } r = requests.post('https://grch38.togovar.org/api/search/variant', headers = headers) print(r.json()) 'application/json', 'Accept' => 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('POST','https://grch38.togovar.org/api/search/variant', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/search/variant"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("POST"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Content-Type": []string{"application/json"}, "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("POST", "https://grch38.togovar.org/api/search/variant", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } POST /search/variant Body parameter { "query": { "type": { "relation": "eq", "terms": [ "ins", "del", "indel" ] } } } Parameters ----------------------------------------------------------------------------------------- Name In Type Required Description --------------- -------------- ---------------------- -------------- -------------------- pretty query boolean false If set, response body will be nicely formatted. stat query integer false If set to 0, do not collect statistics data query integer false If set to 0, do not return result records body body object false Schema for searching variant » version body string false (Optional) Set version number if you would like to use old version. » formatter body string false (Optional) Formatter for response data. » query body any false none »» anonymous body ID false none »»» id body [string] true none »» anonymous body Location false none »»» location body object true none »»»» chromosome body string true chromosome name »»»» position body any true none »»»»» anonymous body integer false none »»»»» anonymous body any false Available keys »»»»»» body object false Both-closed(a, b) = anonymous {x »»»»»»» gte body number true none »»»»»»» lte body number true none »»»»»» body object false Both-open(a, b) = {x anonymous »»»»»»» gt body number true none »»»»»»» lt body number true none »»»»»» body object false Left-open, anonymous right-closed(a, b) = {x »»»»»»» gt body number true none »»»»»»» lte body number true none »»»»»» body object false Left-closed, anonymous right-open(a, b) = {x »»»»»»» gte body number true none »»»»»»» lt body number true none »»»»»» body object false Left-closed, anonymous right-unbounded(a, +∞) = {x »»»»»»» gte body number true none »»»»»» body object false Left-open, anonymous right-unbounded(a, +∞) = {x »»»»»»» gt body number true none »»»»»» body object false Right-closed, anonymous left-unbounded(-∞, b) = {x »»»»»»» lte body number true none »»»»»» body object false Right-open, anonymous left-unbounded(-∞, b) = {x »»»»»»» lt body number true none »» anonymous body VariantType false none »»» type body object true none »»»» relation body string true Available values »»»» terms body [string] true none »» anonymous body VariantConsequence false none »»» consequence body object true none »»»» relation body string true Available values »»»» terms body [string] true none »» anonymous body VariantFrequency false none »»» frequency body object true none »»»» anonymous body object false none »»»»» dataset body Dataset false none »»»»»» name body string true Available values »»»»» frequency body any true Available keys »»»»» filtered body boolean false if true, exclude variants with a FILTER flag other than PASS »»»» anonymous body object false none »»»»» dataset body Dataset false none »»»»» count body any true Available keys »»»»» filtered body boolean false if true, exclude variants with a FILTER flag other than PASS »» anonymous body ClinicalSignificance false none »»» body object true none significance »»»» relation body string true Available values »»»» terms body [string] true none »»»» source body [string] false none »» anonymous body Sift false none »»» sift body object true none »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body Polyphen false none »»» polyphen body object true none »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body AlphaMissense false none »»» body object true none alphamissense »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body Gene false none »»» gene body object true none »»»» relation body string true Available values »»»» terms body [integer] true none »» anonymous body Disease false none »»» disease body object true none »»»» relation body string true Available values »»»» terms body [string] true none »»»» body boolean false Include diseases of sub_concepts subordinate concepts in the Mondo Disease Ontology (default: true) »»»» source body [string] false none »» anonymous body And false none »»» and body [oneOf] true none »»»» anonymous body ID false none »»»» anonymous body Location false none »»»» anonymous body VariantType false none »»»» anonymous body VariantConsequence false none »»»» anonymous body VariantFrequency false none »»»» anonymous body ClinicalSignificance false none »»»» anonymous body Sift false none »»»» anonymous body Polyphen false none »»»» anonymous body AlphaMissense false none »»»» anonymous body Gene false none »»»» anonymous body Disease false none »»»» anonymous body And false none »»»» anonymous body Or false none »»»»» or body [oneOf] true none »»»»»» body ID false none anonymous »»»»»» body Location false none anonymous »»»»»» body VariantType false none anonymous »»»»»» body VariantConsequence false none anonymous »»»»»» body VariantFrequency false none anonymous »»»»»» body ClinicalSignificance false none anonymous »»»»»» body Sift false none anonymous »»»»»» body Polyphen false none anonymous »»»»»» body AlphaMissense false none anonymous »»»»»» body Gene false none anonymous »»»»»» body Disease false none anonymous »»»»»» body And false none anonymous »»»»»» body Or false none anonymous »»»»»» body any false none anonymous »»»» anonymous body any false none »» anonymous body Or false none » limit body integer false (Optional) Default is 100. » offset body any false none »» anonymous body integer false none »» anonymous body array false Set [{chromosome}, {position}, {reference}, {alternative}] in case you would like to paginate over 10,000 records. {reference} and {alternative} can be omitted. » column body [string] false This option is only valid for the download API. ----------------------------------------------------------------------------------------- Detailed descriptions »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»»»» name: Available values * gem_j_wga - GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel * jga_wgs - ** DDBJ account required ** * jga_wes - Japanese Genotype-phenotype Archive (JGA) * jga_snp - SNP-chip data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA) * tommo - ToMMo 54KJPN Allele Frequency Panel * ncbn - * gnomad_genomes - The Genome Aggregation Database (gnomAD Genomes) * gnomad_exomes - The Genome Aggregation Database (gnomAD Exomes) »»»»» frequency: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» count: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list Enumerated Values Parameter Value ----------------- ---------------------------------------------- stat 1 stat 0 data 1 data 0 » version 1 » formatter html »»»» chromosome 1 »»»» chromosome 2 »»»» chromosome 3 »»»» chromosome 4 »»»» chromosome 5 »»»» chromosome 6 »»»» chromosome 7 »»»» chromosome 8 »»»» chromosome 9 »»»» chromosome 10 »»»» chromosome 11 »»»» chromosome 12 »»»» chromosome 13 »»»» chromosome 14 »»»» chromosome 15 »»»» chromosome 16 »»»» chromosome 17 »»»» chromosome 18 »»»» chromosome 19 »»»» chromosome 20 »»»» chromosome 21 »»»» chromosome 22 »»»» chromosome X »»»» chromosome Y »»»» chromosome MT »»»» relation eq »»»» relation ne »»»» terms SO_0001483 »»»» terms SO_0000667 »»»» terms SO_0000159 »»»» terms SO_1000032 »»»» terms SO_1000002 »»»» terms snv »»»» terms ins »»»» terms del »»»» terms indel »»»» terms sub »»»» relation eq »»»» relation ne »»»» terms SO_0001893 »»»» terms SO_0001574 »»»» terms SO_0001575 »»»» terms SO_0001587 »»»» terms SO_0001589 »»»» terms SO_0001578 »»»» terms SO_0002012 »»»» terms SO_0001889 »»»» terms SO_0001821 »»»» terms SO_0001822 »»»» terms SO_0001583 »»»» terms SO_0001818 »»»» terms SO_0001630 »»»» terms SO_0001626 »»»» terms SO_0002019 »»»» terms SO_0001567 »»»» terms SO_0001819 »»»» terms SO_0001580 »»»» terms SO_0001620 »»»» terms SO_0001623 »»»» terms SO_0001624 »»»» terms SO_0001792 »»»» terms SO_0001627 »»»» terms SO_0001621 »»»» terms SO_0001619 »»»» terms SO_0001631 »»»» terms SO_0001632 »»»» terms SO_0001895 »»»» terms SO_0001892 »»»» terms SO_0001782 »»»» terms SO_0001894 »»»» terms SO_0001891 »»»» terms SO_0001907 »»»» terms SO_0001566 »»»» terms SO_0001906 »»»» terms SO_0001628 »»»» terms transcript_ablation »»»» terms splice_acceptor_variant »»»» terms splice_donor_variant »»»» terms stop_gained »»»» terms frameshift_variant »»»» terms stop_lost »»»» terms start_lost »»»» terms transcript_amplification »»»» terms inframe_insertion »»»» terms inframe_deletion »»»» terms missense_variant »»»» terms protein_altering_variant »»»» terms splice_region_variant »»»» terms incomplete_terminal_codon_variant »»»» terms start_retained_variant »»»» terms stop_retained_variant »»»» terms synonymous_variant »»»» terms coding_sequence_variant »»»» terms mature_miRNA_variant »»»» terms 5_prime_UTR_variant »»»» terms 3_prime_UTR_variant »»»» terms non_coding_transcript_exon_variant »»»» terms intron_variant »»»» terms NMD_transcript_variant »»»» terms non_coding_transcript_variant »»»» terms upstream_gene_variant »»»» terms downstream_gene_variant »»»» terms TFBS_ablation »»»» terms TFBS_amplification »»»» terms TF_binding_site_variant »»»» terms regulatory_region_ablation »»»» terms regulatory_region_amplification »»»» terms feature_elongation »»»» terms regulatory_region_variant »»»» terms feature_truncation »»»» terms intergenic_variant »»»»»» name gem_j_wga »»»»»» name jga_wgs »»»»»» name jga_wgs.jgad000670 »»»»»» name jga_wgs.jgad000687 »»»»»» name jga_wgs.jgad000688 »»»»»» name jga_wgs.jgad000689 »»»»»» name jga_wes »»»»»» name jga_snp »»»»»» name bbj_riken.mpheno1 »»»»»» name bbj_riken.mpheno1.male »»»»»» name bbj_riken.mpheno1.female »»»»»» name bbj_riken.mpheno2 »»»»»» name bbj_riken.mpheno2.male »»»»»» name bbj_riken.mpheno2.female »»»»»» name bbj_riken.mpheno3 »»»»»» name bbj_riken.mpheno3.male »»»»»» name bbj_riken.mpheno3.female »»»»»» name bbj_riken.mpheno4 »»»»»» name bbj_riken.mpheno4.male »»»»»» name bbj_riken.mpheno4.female »»»»»» name bbj_riken.mpheno5 »»»»»» name bbj_riken.mpheno5.male »»»»»» name bbj_riken.mpheno5.female »»»»»» name bbj_riken.mpheno6 »»»»»» name bbj_riken.mpheno6.male »»»»»» name bbj_riken.mpheno6.female »»»»»» name bbj_riken.mpheno7 »»»»»» name bbj_riken.mpheno7.male »»»»»» name bbj_riken.mpheno7.female »»»»»» name bbj_riken.mpheno8 »»»»»» name bbj_riken.mpheno8.male »»»»»» name bbj_riken.mpheno9 »»»»»» name bbj_riken.mpheno9.female »»»»»» name bbj_riken.mpheno10 »»»»»» name bbj_riken.mpheno10.female »»»»»» name bbj_riken.mpheno11 »»»»»» name bbj_riken.mpheno11.female »»»»»» name bbj_riken.mpheno12 »»»»»» name bbj_riken.mpheno12.female »»»»»» name bbj_riken.mpheno13 »»»»»» name bbj_riken.mpheno13.male »»»»»» name bbj_riken.mpheno13.female »»»»»» name bbj_riken.mpheno14 »»»»»» name bbj_riken.mpheno14.male »»»»»» name bbj_riken.mpheno14.female »»»»»» name bbj_riken.mpheno15 »»»»»» name bbj_riken.mpheno15.male »»»»»» name bbj_riken.mpheno15.female »»»»»» name bbj_riken.mpheno16 »»»»»» name bbj_riken.mpheno16.male »»»»»» name bbj_riken.mpheno16.female »»»»»» name bbj_riken.mpheno17 »»»»»» name bbj_riken.mpheno17.male »»»»»» name bbj_riken.mpheno17.female »»»»»» name bbj_riken.mpheno18 »»»»»» name bbj_riken.mpheno18.male »»»»»» name bbj_riken.mpheno18.female »»»»»» name bbj_riken.mpheno19 »»»»»» name bbj_riken.mpheno19.male »»»»»» name bbj_riken.mpheno19.female »»»»»» name bbj_riken.mpheno20 »»»»»» name bbj_riken.mpheno20.male »»»»»» name bbj_riken.mpheno20.female »»»»»» name bbj_riken.mpheno21 »»»»»» name bbj_riken.mpheno21.male »»»»»» name bbj_riken.mpheno21.female »»»»»» name bbj_riken.mpheno22 »»»»»» name bbj_riken.mpheno22.male »»»»»» name bbj_riken.mpheno22.female »»»»»» name bbj_riken.mpheno23 »»»»»» name bbj_riken.mpheno23.male »»»»»» name bbj_riken.mpheno23.female »»»»»» name bbj_riken.mpheno24 »»»»»» name bbj_riken.mpheno24.male »»»»»» name bbj_riken.mpheno24.female »»»»»» name bbj_riken.mpheno25 »»»»»» name bbj_riken.mpheno25.male »»»»»» name bbj_riken.mpheno25.female »»»»»» name bbj_riken.mpheno26 »»»»»» name bbj_riken.mpheno26.male »»»»»» name bbj_riken.mpheno26.female »»»»»» name bbj_riken.mpheno27 »»»»»» name bbj_riken.mpheno27.male »»»»»» name bbj_riken.mpheno27.female »»»»»» name bbj_riken.mpheno28 »»»»»» name bbj_riken.mpheno28.male »»»»»» name bbj_riken.mpheno28.female »»»»»» name bbj_riken.mpheno29 »»»»»» name bbj_riken.mpheno29.male »»»»»» name bbj_riken.mpheno29.female »»»»»» name bbj_riken.mpheno30 »»»»»» name bbj_riken.mpheno30.male »»»»»» name bbj_riken.mpheno30.female »»»»»» name bbj_riken.mpheno31 »»»»»» name bbj_riken.mpheno31.male »»»»»» name bbj_riken.mpheno31.female »»»»»» name bbj_riken.mpheno32 »»»»»» name bbj_riken.mpheno32.male »»»»»» name bbj_riken.mpheno32.female »»»»»» name bbj_riken.mpheno33 »»»»»» name bbj_riken.mpheno33.male »»»»»» name bbj_riken.mpheno33.female »»»»»» name bbj_riken.mpheno34 »»»»»» name bbj_riken.mpheno34.male »»»»»» name bbj_riken.mpheno34.female »»»»»» name bbj_riken.mpheno35 »»»»»» name bbj_riken.mpheno35.male »»»»»» name bbj_riken.mpheno35.female »»»»»» name bbj_riken.mpheno36 »»»»»» name bbj_riken.mpheno36.male »»»»»» name bbj_riken.mpheno36.female »»»»»» name bbj_riken.mpheno37 »»»»»» name bbj_riken.mpheno37.male »»»»»» name bbj_riken.mpheno37.female »»»»»» name bbj_riken.mpheno38 »»»»»» name bbj_riken.mpheno38.male »»»»»» name bbj_riken.mpheno38.female »»»»»» name bbj_riken.mpheno39 »»»»»» name bbj_riken.mpheno39.male »»»»»» name bbj_riken.mpheno39.female »»»»»» name bbj_riken.mpheno40 »»»»»» name bbj_riken.mpheno40.male »»»»»» name bbj_riken.mpheno40.female »»»»»» name bbj_riken.mpheno41 »»»»»» name bbj_riken.mpheno41.female »»»»»» name bbj_riken.mpheno42 »»»»»» name bbj_riken.mpheno42.female »»»»»» name bbj_riken.mpheno44 »»»»»» name bbj_riken.mpheno44.male »»»»»» name bbj_riken.mpheno44.female »»»»»» name bbj_riken.mpheno45 »»»»»» name bbj_riken.mpheno45.male »»»»»» name bbj_riken.mpheno45.female »»»»»» name bbj_riken.mpheno46 »»»»»» name bbj_riken.mpheno46.male »»»»»» name bbj_riken.mpheno46.female »»»»»» name tommo »»»»»» name ncbn »»»»»» name ncbn.jpn »»»»»» name ncbn.jpn.hondo »»»»»» name ncbn.jpn.ryukyu »»»»»» name ncbn.acb »»»»»» name ncbn.asw »»»»»» name ncbn.beb »»»»»» name ncbn.gbr »»»»»» name ncbn.cdx »»»»»» name ncbn.ceu »»»»»» name ncbn.clm »»»»»» name ncbn.esn »»»»»» name ncbn.fin »»»»»» name ncbn.gwd »»»»»» name ncbn.gih »»»»»» name ncbn.chb »»»»»» name ncbn.chs »»»»»» name ncbn.ibs »»»»»» name ncbn.itu »»»»»» name ncbn.jpt »»»»»» name ncbn.khv »»»»»» name ncbn.lwk »»»»»» name ncbn.msl »»»»»» name ncbn.mxl »»»»»» name ncbn.pel »»»»»» name ncbn.pur »»»»»» name ncbn.pjl »»»»»» name ncbn.stu »»»»»» name ncbn.tsi »»»»»» name ncbn.yri »»»»»» name gnomad_genomes »»»»»» name gnomad_genomes.afr »»»»»» name gnomad_genomes.ami »»»»»» name gnomad_genomes.amr »»»»»» name gnomad_genomes.asj »»»»»» name gnomad_genomes.eas »»»»»» name gnomad_genomes.fin »»»»»» name gnomad_genomes.mid »»»»»» name gnomad_genomes.nfe »»»»»» name gnomad_genomes.remaining »»»»»» name gnomad_genomes.sas »»»»»» name gnomad_exomes »»»»»» name gnomad_exomes.afr »»»»»» name gnomad_exomes.amr »»»»»» name gnomad_exomes.asj »»»»»» name gnomad_exomes.eas »»»»»» name gnomad_exomes.fin »»»»»» name gnomad_exomes.mid »»»»»» name gnomad_exomes.nfe »»»»»» name gnomad_exomes.remaining »»»»»» name gnomad_exomes.sas »»»» relation eq »»»» relation ne »»»» terms NC »»»» terms P »»»» terms PLP »»»» terms LP »»»» terms LPLP »»»» terms DR »»»» terms ERA »»»» terms LRA »»»» terms URA »»»» terms CS »»»» terms A »»»» terms RF »»»» terms AF »»»» terms PR »»»» terms B »»»» terms LB »»»» terms CI »»»» terms AN »»»» terms O »»»» terms US »»»» terms NP »»»» terms not_in_clinvar »»»» terms pathogenic »»»» terms pathogenic_low_penetrance »»»» terms likely_pathogenic »»»» terms likely_pathogenic_low_penetrance »»»» terms drug_response »»»» terms established_risk_allele »»»» terms likely_risk_allele »»»» terms uncertain_risk_allele »»»» terms confers_sensitivity »»»» terms association »»»» terms risk_factor »»»» terms affects »»»» terms protective »»»» terms benign »»»» terms likely_benign »»»» terms conflicting_interpretations_of_pathogenicity »»»» terms association_not_found »»»» terms other »»»» terms uncertain_significance »»»» terms not_provided »»»» source clinvar »»»» source mgend »»»»» anonymous unassigned »»»»» anonymous unassigned »»»»» anonymous unknown »»»»» anonymous unassigned »»»» relation eq »»»» relation ne »»»» relation eq »»»» relation ne »»»» source clinvar »»»» source mgend » column id » column rs » column position » column ref_alt » column type » column gene » column frequency » column consequence » column condition » column sift » column polyphen » column alphamissense Example responses 200 Response { "scroll": { "offset": 0, "limit": 0, "max_rows": 0 }, "statistics": { "total": 0, "filtered": 0, "dataset": { "dataset_name": 0 }, "type": { "so_term": 0 }, "significance": { "significance_key": 0 }, "consequence": { "so_term": 0 } }, "data": [ { "id": "string", "type": "string", "chromosome": "string", "start": 0, "stop": 0, "reference": "string", "alternative": "string", "most_severe_consequence": "string", "sift": 0, "polyphen": 0, "existing_variations": [ "string" ], "external_link": [ { "db_name": [ "string" ] } ], "significance": [ { "condition": "string", "interpretations": [ "string" ] } ], "transcripts": { "transcript_id": "string", "gene_id": "string", "consequence": [ "string" ], "sift": 0, "polyphen": 0, "hgnc_id": 0, "symbol": { "source": "string", "label": "string" }, "hgvs_p": "string", "hgvs_c": "string", "hgvs_g": "string" }, "frequencies": { "source": "string", "filter": [ "string" ], "quality": 0, "allele": { "number": 0, "count": 0, "frequency": 0 }, "genotype": { "ref_homo_count": 0, "hetero_count": 0, "alt_homo_count": 0 } } } ] } 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK SearchVariant 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication get__search_gene Code samples # You can also use wget curl -X GET https://grch38.togovar.org/api/search/gene?term=ALDH2 \ -H 'Accept: application/json' GET https://grch38.togovar.org/api/search/gene?term=ALDH2 HTTP/1.1 Host: grch38.togovar.org Accept: application/json const headers = { 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/search/gene?term=ALDH2', { method: 'GET', headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Accept' => 'application/json' } result = RestClient.get 'https://grch38.togovar.org/api/search/gene', params: { 'term' => 'string' }, headers: headers p JSON.parse(result) import requests headers = { 'Accept': 'application/json' } r = requests.get('https://grch38.togovar.org/api/search/gene', params={ 'term': 'ALDH2' }, headers = headers) print(r.json()) 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('GET','https://grch38.togovar.org/api/search/gene', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/search/gene?term=ALDH2"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("GET"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("GET", "https://grch38.togovar.org/api/search/gene", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } GET /search/gene Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. term query string true A term to search -------------------------------------------------------------------------- Example responses 200 Response [ { "id": 404, "symbol": "ALDH2", "name": "aldehyde dehydrogenase 2 family member", "alias_of": null, "highlight": "ALDH2" } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK SearchGene 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication post__search_gene Code samples # You can also use wget curl -X POST https://grch38.togovar.org/api/search/gene \ -H 'Content-Type: application/json' \ -H 'Accept: application/json' POST https://grch38.togovar.org/api/search/gene HTTP/1.1 Host: grch38.togovar.org Content-Type: application/json Accept: application/json const inputBody = '{ "term": "ALDH2" }'; const headers = { 'Content-Type':'application/json', 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/search/gene', { method: 'POST', body: inputBody, headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Content-Type' => 'application/json', 'Accept' => 'application/json' } result = RestClient.post 'https://grch38.togovar.org/api/search/gene', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } r = requests.post('https://grch38.togovar.org/api/search/gene', headers = headers) print(r.json()) 'application/json', 'Accept' => 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('POST','https://grch38.togovar.org/api/search/gene', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/search/gene"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("POST"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Content-Type": []string{"application/json"}, "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("POST", "https://grch38.togovar.org/api/search/gene", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } POST /search/gene Body parameter { "term": "ALDH2" } Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. body body object false Schema for searching gene » term body string true A term to search -------------------------------------------------------------------------- Example responses 200 Response [ { "id": 404, "symbol": "ALDH2", "name": "aldehyde dehydrogenase 2 family member", "alias_of": null, "highlight": "ALDH2" } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK SearchGene 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication get__search_disease Code samples # You can also use wget curl -X GET https://grch38.togovar.org/api/search/disease?term=breast%20ovarian%20cancer \ -H 'Accept: application/json' GET https://grch38.togovar.org/api/search/disease?term=breast%20ovarian%20cancer HTTP/1.1 Host: grch38.togovar.org Accept: application/json const headers = { 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/search/disease?term=breast%20ovarian%20cancer', { method: 'GET', headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Accept' => 'application/json' } result = RestClient.get 'https://grch38.togovar.org/api/search/disease', params: { 'term' => 'string' }, headers: headers p JSON.parse(result) import requests headers = { 'Accept': 'application/json' } r = requests.get('https://grch38.togovar.org/api/search/disease', params={ 'term': 'breast ovarian cancer' }, headers = headers) print(r.json()) 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('GET','https://grch38.togovar.org/api/search/disease', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/search/disease?term=breast%20ovarian%20cancer"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("GET"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("GET", "https://grch38.togovar.org/api/search/disease", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } GET /search/disease Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. term query string true A term to search -------------------------------------------------------------------------- Example responses 200 Response [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "highlight": "Hereditary breast and ovarian cancer syndrome" } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK SearchDisease 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication post__search_disease Code samples # You can also use wget curl -X POST https://grch38.togovar.org/api/search/disease \ -H 'Content-Type: application/json' \ -H 'Accept: application/json' POST https://grch38.togovar.org/api/search/disease HTTP/1.1 Host: grch38.togovar.org Content-Type: application/json Accept: application/json const inputBody = '{ "term": "breast ovarian cancer" }'; const headers = { 'Content-Type':'application/json', 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/search/disease', { method: 'POST', body: inputBody, headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Content-Type' => 'application/json', 'Accept' => 'application/json' } result = RestClient.post 'https://grch38.togovar.org/api/search/disease', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } r = requests.post('https://grch38.togovar.org/api/search/disease', headers = headers) print(r.json()) 'application/json', 'Accept' => 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('POST','https://grch38.togovar.org/api/search/disease', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/search/disease"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("POST"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Content-Type": []string{"application/json"}, "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("POST", "https://grch38.togovar.org/api/search/disease", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } POST /search/disease Body parameter { "term": "breast ovarian cancer" } Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. body body object false Schema for searching disease » term body string true A term to search -------------------------------------------------------------------------- Example responses 200 Response [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "highlight": "Hereditary breast and ovarian cancer syndrome" } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK SearchDisease 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication inspect get__inspect_disease Code samples # You can also use wget curl -X GET https://grch38.togovar.org/api/inspect/disease \ -H 'Accept: application/json' GET https://grch38.togovar.org/api/inspect/disease HTTP/1.1 Host: grch38.togovar.org Accept: application/json const headers = { 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/inspect/disease', { method: 'GET', headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Accept' => 'application/json' } result = RestClient.get 'https://grch38.togovar.org/api/inspect/disease', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Accept': 'application/json' } r = requests.get('https://grch38.togovar.org/api/inspect/disease', headers = headers) print(r.json()) 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('GET','https://grch38.togovar.org/api/inspect/disease', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/inspect/disease"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("GET"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("GET", "https://grch38.togovar.org/api/inspect/disease", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } GET /inspect/disease Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. node query string false A node ID -------------------------------------------------------------------------- Example responses 200 Response [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "root": false, "leaf": false, "parents": [ { "id": "MONDO_0016248", "cui": "CN201036", "label": "Familial ovarian cancer", "root": false } ], "children": [ { "id": "MONDO_0012933", "cui": "C2675520", "label": "Breast-ovarian cancer, familial 2", "leaf": true } ] } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK InspectDisease 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication post__inspect_disease Code samples # You can also use wget curl -X POST https://grch38.togovar.org/api/inspect/disease \ -H 'Content-Type: application/json' \ -H 'Accept: application/json' POST https://grch38.togovar.org/api/inspect/disease HTTP/1.1 Host: grch38.togovar.org Content-Type: application/json Accept: application/json const inputBody = '{ "node": "MONDO_0003582" }'; const headers = { 'Content-Type':'application/json', 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/inspect/disease', { method: 'POST', body: inputBody, headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Content-Type' => 'application/json', 'Accept' => 'application/json' } result = RestClient.post 'https://grch38.togovar.org/api/inspect/disease', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } r = requests.post('https://grch38.togovar.org/api/inspect/disease', headers = headers) print(r.json()) 'application/json', 'Accept' => 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('POST','https://grch38.togovar.org/api/inspect/disease', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/inspect/disease"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("POST"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Content-Type": []string{"application/json"}, "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("POST", "https://grch38.togovar.org/api/inspect/disease", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } POST /inspect/disease Body parameter { "node": "MONDO_0003582" } Parameters -------------------------------------------------------------------------- Name In Type Required Description -------------- -------------- -------------- -------------- -------------- pretty query boolean false If set, response body will be nicely formatted. body body object false Schema for inspecting disease » node body string false A node ID -------------------------------------------------------------------------- Example responses 200 Response [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "root": false, "leaf": false, "parents": [ { "id": "MONDO_0016248", "cui": "CN201036", "label": "Familial ovarian cancer", "root": false } ], "children": [ { "id": "MONDO_0012933", "cui": "C2675520", "label": "Breast-ovarian cancer, familial 2", "leaf": true } ] } ] 501 Response "Not implemented" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK InspectDisease 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication download post__download_variant Code samples # You can also use wget curl -X POST https://grch38.togovar.org/api/download/variant \ -H 'Content-Type: application/json' \ -H 'Accept: application/json' POST https://grch38.togovar.org/api/download/variant HTTP/1.1 Host: grch38.togovar.org Content-Type: application/json Accept: application/json const inputBody = '{ "query": { "type": { "relation": "eq", "terms": [ "ins", "del", "indel" ] } } }'; const headers = { 'Content-Type':'application/json', 'Accept':'application/json' }; fetch('https://grch38.togovar.org/api/download/variant', { method: 'POST', body: inputBody, headers: headers }) .then(function(res) { return res.json(); }).then(function(body) { console.log(body); }); require 'rest-client' require 'json' headers = { 'Content-Type' => 'application/json', 'Accept' => 'application/json' } result = RestClient.post 'https://grch38.togovar.org/api/download/variant', params: { }, headers: headers p JSON.parse(result) import requests headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } r = requests.post('https://grch38.togovar.org/api/download/variant', headers = headers) print(r.json()) 'application/json', 'Accept' => 'application/json', ); $client = new \GuzzleHttp\Client(); // Define array of request body. $request_body = array(); try { $response = $client->request('POST','https://grch38.togovar.org/api/download/variant', array( 'headers' => $headers, 'json' => $request_body, ) ); print_r($response->getBody()->getContents()); } catch (\GuzzleHttp\Exception\BadResponseException $e) { // handle exception or api errors. print_r($e->getMessage()); } // ... URL obj = new URL("https://grch38.togovar.org/api/download/variant"); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); con.setRequestMethod("POST"); int responseCode = con.getResponseCode(); BufferedReader in = new BufferedReader( new InputStreamReader(con.getInputStream())); String inputLine; StringBuffer response = new StringBuffer(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); System.out.println(response.toString()); package main import ( "bytes" "net/http" ) func main() { headers := map[string][]string{ "Content-Type": []string{"application/json"}, "Accept": []string{"application/json"}, } data := bytes.NewBuffer([]byte{jsonReq}) req, err := http.NewRequest("POST", "https://grch38.togovar.org/api/download/variant", data) req.Header = headers client := &http.Client{} resp, err := client.Do(req) // ... } POST /download/variant Body parameter { "query": { "type": { "relation": "eq", "terms": [ "ins", "del", "indel" ] } } } Parameters ----------------------------------------------------------------------------------------- Name In Type Required Description --------------- -------------- ---------------------- -------------- -------------------- body body object false Schema for searching variant » version body string false (Optional) Set version number if you would like to use old version. » formatter body string false (Optional) Formatter for response data. » query body any false none »» anonymous body ID false none »»» id body [string] true none »» anonymous body Location false none »»» location body object true none »»»» chromosome body string true chromosome name »»»» position body any true none »»»»» anonymous body integer false none »»»»» anonymous body any false Available keys »»»»»» body object false Both-closed(a, b) = anonymous {x »»»»»»» gte body number true none »»»»»»» lte body number true none »»»»»» body object false Both-open(a, b) = {x anonymous »»»»»»» gt body number true none »»»»»»» lt body number true none »»»»»» body object false Left-open, anonymous right-closed(a, b) = {x »»»»»»» gt body number true none »»»»»»» lte body number true none »»»»»» body object false Left-closed, anonymous right-open(a, b) = {x »»»»»»» gte body number true none »»»»»»» lt body number true none »»»»»» body object false Left-closed, anonymous right-unbounded(a, +∞) = {x »»»»»»» gte body number true none »»»»»» body object false Left-open, anonymous right-unbounded(a, +∞) = {x »»»»»»» gt body number true none »»»»»» body object false Right-closed, anonymous left-unbounded(-∞, b) = {x »»»»»»» lte body number true none »»»»»» body object false Right-open, anonymous left-unbounded(-∞, b) = {x »»»»»»» lt body number true none »» anonymous body VariantType false none »»» type body object true none »»»» relation body string true Available values »»»» terms body [string] true none »» anonymous body VariantConsequence false none »»» consequence body object true none »»»» relation body string true Available values »»»» terms body [string] true none »» anonymous body VariantFrequency false none »»» frequency body object true none »»»» anonymous body object false none »»»»» dataset body Dataset false none »»»»»» name body string true Available values »»»»» frequency body any true Available keys »»»»» filtered body boolean false if true, exclude variants with a FILTER flag other than PASS »»»» anonymous body object false none »»»»» dataset body Dataset false none »»»»» count body any true Available keys »»»»» filtered body boolean false if true, exclude variants with a FILTER flag other than PASS »» anonymous body ClinicalSignificance false none »»» body object true none significance »»»» relation body string true Available values »»»» terms body [string] true none »»»» source body [string] false none »» anonymous body Sift false none »»» sift body object true none »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body Polyphen false none »»» polyphen body object true none »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body AlphaMissense false none »»» body object true none alphamissense »»»» score body any true none »»»»» anonymous body any false Available keys »»»»» anonymous body [string] false none »» anonymous body Gene false none »»» gene body object true none »»»» relation body string true Available values »»»» terms body [integer] true none »» anonymous body Disease false none »»» disease body object true none »»»» relation body string true Available values »»»» terms body [string] true none »»»» body boolean false Include diseases of sub_concepts subordinate concepts in the Mondo Disease Ontology (default: true) »»»» source body [string] false none »» anonymous body And false none »»» and body [oneOf] true none »»»» anonymous body ID false none »»»» anonymous body Location false none »»»» anonymous body VariantType false none »»»» anonymous body VariantConsequence false none »»»» anonymous body VariantFrequency false none »»»» anonymous body ClinicalSignificance false none »»»» anonymous body Sift false none »»»» anonymous body Polyphen false none »»»» anonymous body AlphaMissense false none »»»» anonymous body Gene false none »»»» anonymous body Disease false none »»»» anonymous body And false none »»»» anonymous body Or false none »»»»» or body [oneOf] true none »»»»»» body ID false none anonymous »»»»»» body Location false none anonymous »»»»»» body VariantType false none anonymous »»»»»» body VariantConsequence false none anonymous »»»»»» body VariantFrequency false none anonymous »»»»»» body ClinicalSignificance false none anonymous »»»»»» body Sift false none anonymous »»»»»» body Polyphen false none anonymous »»»»»» body AlphaMissense false none anonymous »»»»»» body Gene false none anonymous »»»»»» body Disease false none anonymous »»»»»» body And false none anonymous »»»»»» body Or false none anonymous »»»»»» body any false none anonymous »»»» anonymous body any false none »» anonymous body Or false none » limit body integer false (Optional) Default is 100. » offset body any false none »» anonymous body integer false none »» anonymous body array false Set [{chromosome}, {position}, {reference}, {alternative}] in case you would like to paginate over 10,000 records. {reference} and {alternative} can be omitted. » column body [string] false This option is only valid for the download API. ----------------------------------------------------------------------------------------- Detailed descriptions »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»»»» name: Available values * gem_j_wga - GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel * jga_wgs - ** DDBJ account required ** * jga_wes - Japanese Genotype-phenotype Archive (JGA) * jga_snp - SNP-chip data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA) * tommo - ToMMo 54KJPN Allele Frequency Panel * ncbn - * gnomad_genomes - The Genome Aggregation Database (gnomAD Genomes) * gnomad_exomes - The Genome Aggregation Database (gnomAD Exomes) »»»»» frequency: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» count: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»»» anonymous: Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list »»»» relation: Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list Enumerated Values Parameter Value ----------------- ---------------------------------------------- » version 1 » formatter html »»»» chromosome 1 »»»» chromosome 2 »»»» chromosome 3 »»»» chromosome 4 »»»» chromosome 5 »»»» chromosome 6 »»»» chromosome 7 »»»» chromosome 8 »»»» chromosome 9 »»»» chromosome 10 »»»» chromosome 11 »»»» chromosome 12 »»»» chromosome 13 »»»» chromosome 14 »»»» chromosome 15 »»»» chromosome 16 »»»» chromosome 17 »»»» chromosome 18 »»»» chromosome 19 »»»» chromosome 20 »»»» chromosome 21 »»»» chromosome 22 »»»» chromosome X »»»» chromosome Y »»»» chromosome MT »»»» relation eq »»»» relation ne »»»» terms SO_0001483 »»»» terms SO_0000667 »»»» terms SO_0000159 »»»» terms SO_1000032 »»»» terms SO_1000002 »»»» terms snv »»»» terms ins »»»» terms del »»»» terms indel »»»» terms sub »»»» relation eq »»»» relation ne »»»» terms SO_0001893 »»»» terms SO_0001574 »»»» terms SO_0001575 »»»» terms SO_0001587 »»»» terms SO_0001589 »»»» terms SO_0001578 »»»» terms SO_0002012 »»»» terms SO_0001889 »»»» terms SO_0001821 »»»» terms SO_0001822 »»»» terms SO_0001583 »»»» terms SO_0001818 »»»» terms SO_0001630 »»»» terms SO_0001626 »»»» terms SO_0002019 »»»» terms SO_0001567 »»»» terms SO_0001819 »»»» terms SO_0001580 »»»» terms SO_0001620 »»»» terms SO_0001623 »»»» terms SO_0001624 »»»» terms SO_0001792 »»»» terms SO_0001627 »»»» terms SO_0001621 »»»» terms SO_0001619 »»»» terms SO_0001631 »»»» terms SO_0001632 »»»» terms SO_0001895 »»»» terms SO_0001892 »»»» terms SO_0001782 »»»» terms SO_0001894 »»»» terms SO_0001891 »»»» terms SO_0001907 »»»» terms SO_0001566 »»»» terms SO_0001906 »»»» terms SO_0001628 »»»» terms transcript_ablation »»»» terms splice_acceptor_variant »»»» terms splice_donor_variant »»»» terms stop_gained »»»» terms frameshift_variant »»»» terms stop_lost »»»» terms start_lost »»»» terms transcript_amplification »»»» terms inframe_insertion »»»» terms inframe_deletion »»»» terms missense_variant »»»» terms protein_altering_variant »»»» terms splice_region_variant »»»» terms incomplete_terminal_codon_variant »»»» terms start_retained_variant »»»» terms stop_retained_variant »»»» terms synonymous_variant »»»» terms coding_sequence_variant »»»» terms mature_miRNA_variant »»»» terms 5_prime_UTR_variant »»»» terms 3_prime_UTR_variant »»»» terms non_coding_transcript_exon_variant »»»» terms intron_variant »»»» terms NMD_transcript_variant »»»» terms non_coding_transcript_variant »»»» terms upstream_gene_variant »»»» terms downstream_gene_variant »»»» terms TFBS_ablation »»»» terms TFBS_amplification »»»» terms TF_binding_site_variant »»»» terms regulatory_region_ablation »»»» terms regulatory_region_amplification »»»» terms feature_elongation »»»» terms regulatory_region_variant »»»» terms feature_truncation »»»» terms intergenic_variant »»»»»» name gem_j_wga »»»»»» name jga_wgs »»»»»» name jga_wgs.jgad000670 »»»»»» name jga_wgs.jgad000687 »»»»»» name jga_wgs.jgad000688 »»»»»» name jga_wgs.jgad000689 »»»»»» name jga_wes »»»»»» name jga_snp »»»»»» name bbj_riken.mpheno1 »»»»»» name bbj_riken.mpheno1.male »»»»»» name bbj_riken.mpheno1.female »»»»»» name bbj_riken.mpheno2 »»»»»» name bbj_riken.mpheno2.male »»»»»» name bbj_riken.mpheno2.female »»»»»» name bbj_riken.mpheno3 »»»»»» name bbj_riken.mpheno3.male »»»»»» name bbj_riken.mpheno3.female »»»»»» name bbj_riken.mpheno4 »»»»»» name bbj_riken.mpheno4.male »»»»»» name bbj_riken.mpheno4.female »»»»»» name bbj_riken.mpheno5 »»»»»» name bbj_riken.mpheno5.male »»»»»» name bbj_riken.mpheno5.female »»»»»» name bbj_riken.mpheno6 »»»»»» name bbj_riken.mpheno6.male »»»»»» name bbj_riken.mpheno6.female »»»»»» name bbj_riken.mpheno7 »»»»»» name bbj_riken.mpheno7.male »»»»»» name bbj_riken.mpheno7.female »»»»»» name bbj_riken.mpheno8 »»»»»» name bbj_riken.mpheno8.male »»»»»» name bbj_riken.mpheno9 »»»»»» name bbj_riken.mpheno9.female »»»»»» name bbj_riken.mpheno10 »»»»»» name bbj_riken.mpheno10.female »»»»»» name bbj_riken.mpheno11 »»»»»» name bbj_riken.mpheno11.female »»»»»» name bbj_riken.mpheno12 »»»»»» name bbj_riken.mpheno12.female »»»»»» name bbj_riken.mpheno13 »»»»»» name bbj_riken.mpheno13.male »»»»»» name bbj_riken.mpheno13.female »»»»»» name bbj_riken.mpheno14 »»»»»» name bbj_riken.mpheno14.male »»»»»» name bbj_riken.mpheno14.female »»»»»» name bbj_riken.mpheno15 »»»»»» name bbj_riken.mpheno15.male »»»»»» name bbj_riken.mpheno15.female »»»»»» name bbj_riken.mpheno16 »»»»»» name bbj_riken.mpheno16.male »»»»»» name bbj_riken.mpheno16.female »»»»»» name bbj_riken.mpheno17 »»»»»» name bbj_riken.mpheno17.male »»»»»» name bbj_riken.mpheno17.female »»»»»» name bbj_riken.mpheno18 »»»»»» name bbj_riken.mpheno18.male »»»»»» name bbj_riken.mpheno18.female »»»»»» name bbj_riken.mpheno19 »»»»»» name bbj_riken.mpheno19.male »»»»»» name bbj_riken.mpheno19.female »»»»»» name bbj_riken.mpheno20 »»»»»» name bbj_riken.mpheno20.male »»»»»» name bbj_riken.mpheno20.female »»»»»» name bbj_riken.mpheno21 »»»»»» name bbj_riken.mpheno21.male »»»»»» name bbj_riken.mpheno21.female »»»»»» name bbj_riken.mpheno22 »»»»»» name bbj_riken.mpheno22.male »»»»»» name bbj_riken.mpheno22.female »»»»»» name bbj_riken.mpheno23 »»»»»» name bbj_riken.mpheno23.male »»»»»» name bbj_riken.mpheno23.female »»»»»» name bbj_riken.mpheno24 »»»»»» name bbj_riken.mpheno24.male »»»»»» name bbj_riken.mpheno24.female »»»»»» name bbj_riken.mpheno25 »»»»»» name bbj_riken.mpheno25.male »»»»»» name bbj_riken.mpheno25.female »»»»»» name bbj_riken.mpheno26 »»»»»» name bbj_riken.mpheno26.male »»»»»» name bbj_riken.mpheno26.female »»»»»» name bbj_riken.mpheno27 »»»»»» name bbj_riken.mpheno27.male »»»»»» name bbj_riken.mpheno27.female »»»»»» name bbj_riken.mpheno28 »»»»»» name bbj_riken.mpheno28.male »»»»»» name bbj_riken.mpheno28.female »»»»»» name bbj_riken.mpheno29 »»»»»» name bbj_riken.mpheno29.male »»»»»» name bbj_riken.mpheno29.female »»»»»» name bbj_riken.mpheno30 »»»»»» name bbj_riken.mpheno30.male »»»»»» name bbj_riken.mpheno30.female »»»»»» name bbj_riken.mpheno31 »»»»»» name bbj_riken.mpheno31.male »»»»»» name bbj_riken.mpheno31.female »»»»»» name bbj_riken.mpheno32 »»»»»» name bbj_riken.mpheno32.male »»»»»» name bbj_riken.mpheno32.female »»»»»» name bbj_riken.mpheno33 »»»»»» name bbj_riken.mpheno33.male »»»»»» name bbj_riken.mpheno33.female »»»»»» name bbj_riken.mpheno34 »»»»»» name bbj_riken.mpheno34.male »»»»»» name bbj_riken.mpheno34.female »»»»»» name bbj_riken.mpheno35 »»»»»» name bbj_riken.mpheno35.male »»»»»» name bbj_riken.mpheno35.female »»»»»» name bbj_riken.mpheno36 »»»»»» name bbj_riken.mpheno36.male »»»»»» name bbj_riken.mpheno36.female »»»»»» name bbj_riken.mpheno37 »»»»»» name bbj_riken.mpheno37.male »»»»»» name bbj_riken.mpheno37.female »»»»»» name bbj_riken.mpheno38 »»»»»» name bbj_riken.mpheno38.male »»»»»» name bbj_riken.mpheno38.female »»»»»» name bbj_riken.mpheno39 »»»»»» name bbj_riken.mpheno39.male »»»»»» name bbj_riken.mpheno39.female »»»»»» name bbj_riken.mpheno40 »»»»»» name bbj_riken.mpheno40.male »»»»»» name bbj_riken.mpheno40.female »»»»»» name bbj_riken.mpheno41 »»»»»» name bbj_riken.mpheno41.female »»»»»» name bbj_riken.mpheno42 »»»»»» name bbj_riken.mpheno42.female »»»»»» name bbj_riken.mpheno44 »»»»»» name bbj_riken.mpheno44.male »»»»»» name bbj_riken.mpheno44.female »»»»»» name bbj_riken.mpheno45 »»»»»» name bbj_riken.mpheno45.male »»»»»» name bbj_riken.mpheno45.female »»»»»» name bbj_riken.mpheno46 »»»»»» name bbj_riken.mpheno46.male »»»»»» name bbj_riken.mpheno46.female »»»»»» name tommo »»»»»» name ncbn »»»»»» name ncbn.jpn »»»»»» name ncbn.jpn.hondo »»»»»» name ncbn.jpn.ryukyu »»»»»» name ncbn.acb »»»»»» name ncbn.asw »»»»»» name ncbn.beb »»»»»» name ncbn.gbr »»»»»» name ncbn.cdx »»»»»» name ncbn.ceu »»»»»» name ncbn.clm »»»»»» name ncbn.esn »»»»»» name ncbn.fin »»»»»» name ncbn.gwd »»»»»» name ncbn.gih »»»»»» name ncbn.chb »»»»»» name ncbn.chs »»»»»» name ncbn.ibs »»»»»» name ncbn.itu »»»»»» name ncbn.jpt »»»»»» name ncbn.khv »»»»»» name ncbn.lwk »»»»»» name ncbn.msl »»»»»» name ncbn.mxl »»»»»» name ncbn.pel »»»»»» name ncbn.pur »»»»»» name ncbn.pjl »»»»»» name ncbn.stu »»»»»» name ncbn.tsi »»»»»» name ncbn.yri »»»»»» name gnomad_genomes »»»»»» name gnomad_genomes.afr »»»»»» name gnomad_genomes.ami »»»»»» name gnomad_genomes.amr »»»»»» name gnomad_genomes.asj »»»»»» name gnomad_genomes.eas »»»»»» name gnomad_genomes.fin »»»»»» name gnomad_genomes.mid »»»»»» name gnomad_genomes.nfe »»»»»» name gnomad_genomes.remaining »»»»»» name gnomad_genomes.sas »»»»»» name gnomad_exomes »»»»»» name gnomad_exomes.afr »»»»»» name gnomad_exomes.amr »»»»»» name gnomad_exomes.asj »»»»»» name gnomad_exomes.eas »»»»»» name gnomad_exomes.fin »»»»»» name gnomad_exomes.mid »»»»»» name gnomad_exomes.nfe »»»»»» name gnomad_exomes.remaining »»»»»» name gnomad_exomes.sas »»»» relation eq »»»» relation ne »»»» terms NC »»»» terms P »»»» terms PLP »»»» terms LP »»»» terms LPLP »»»» terms DR »»»» terms ERA »»»» terms LRA »»»» terms URA »»»» terms CS »»»» terms A »»»» terms RF »»»» terms AF »»»» terms PR »»»» terms B »»»» terms LB »»»» terms CI »»»» terms AN »»»» terms O »»»» terms US »»»» terms NP »»»» terms not_in_clinvar »»»» terms pathogenic »»»» terms pathogenic_low_penetrance »»»» terms likely_pathogenic »»»» terms likely_pathogenic_low_penetrance »»»» terms drug_response »»»» terms established_risk_allele »»»» terms likely_risk_allele »»»» terms uncertain_risk_allele »»»» terms confers_sensitivity »»»» terms association »»»» terms risk_factor »»»» terms affects »»»» terms protective »»»» terms benign »»»» terms likely_benign »»»» terms conflicting_interpretations_of_pathogenicity »»»» terms association_not_found »»»» terms other »»»» terms uncertain_significance »»»» terms not_provided »»»» source clinvar »»»» source mgend »»»»» anonymous unassigned »»»»» anonymous unassigned »»»»» anonymous unknown »»»»» anonymous unassigned »»»» relation eq »»»» relation ne »»»» relation eq »»»» relation ne »»»» source clinvar »»»» source mgend » column id » column rs » column position » column ref_alt » column type » column gene » column frequency » column consequence » column condition » column sift » column polyphen » column alphamissense Example responses 200 Response { "data": [ { "tgv_id": "string", "rs": [ "string" ], "chromosome": "string", "position_grch38": 0, "reference": "string", "alternate": "string", "type": "string", "gene": { "name": "string", "id": "string", "synonyms": [ "string" ] }, "consequence": [ "string" ], "condition": [ {} ], "sift_qualitative_prediction": "string", "sift_score": 0, "polyphen2_qualitative_prediction": "string", "polyphen_score": 0, "alphamissense_pathogenicity": "string", "alphamissense_score": 0, "jga_wgs_allele_alt": 0, "jga_wgs_allele_total": 0, "jga_wgs_alt_allele_freq": 0, "jga_wgs_qc_status": [ "string" ], "jga_wes_allele_alt": 0, "jga_wes_allele_total": 0, "jga_wes_alt_allele_freq": 0, "jga_wes_qc_status": [ "string" ], "jga_snp_allele_alt": 0, "jga_snp_allele_total": 0, "jga_snp_alt_allele_freq": 0, "jga_snp_genotype_alt_alt": 0, "jga_snp_genotype_ref_alt": 0, "jga_snp_genotype_ref_ref": 0, "jga_snp_qc_status": [ "string" ], "tommo_allele_alt": 0, "tommo_allele_total": 0, "tommo_alt_allele_freq": 0, "tommo_qc_status": [ "string" ], "hgvd_allele_alt": 0, "hgvd_allele_total": 0, "hgvd_alt_allele_freq": 0, "hgvd_qc_status": [ "string" ], "gem_j_wga_allele_alt": 0, "gem_j_wga_allele_total": 0, "gem_j_wga_alt_allele_freq": 0, "gem_j_wga_qc_status": [ "string" ], "gnomad_genomes_allele_alt": 0, "gnomad_genomes_allele_total": 0, "gnomad_genomes_alt_allele_freq": 0, "gnomad_genomes_qc_status": [ "string" ] } ] } "string" Responses ---------------------------------------------------------------------------------------- Status Meaning Description Schema ----------------- ----------------- ---------------------------------- ----------------- 200 OK OK string 400 Bad Request Bad Request Your query contains Error grammatical mistakes. See errors in the response. 500 Internal Server Internal Server Error Unexpected Error Error errors occurred. 501 Not Implemented Not Implemented Responder for string given mime type are not implemented. Provide the correct accept header (e.g. Accept: application/json). ---------------------------------------------------------------------------------------- This operation does not require authentication Schemas ID { "id": [ "string" ] } Properties Name Type Required Restrictions Description ------ ---------- ---------- -------------- ------------- id [string] true none none Location { "location": { "chromosome": "1", "position": 0 } } Properties Name Type Required Restrictions Description -------------- -------- ---------- -------------- ----------------- location object true none none » chromosome string true none chromosome name » position any true none none oneOf Name Type Required Restrictions Description -------------- --------- ---------- -------------- ------------- »» anonymous integer false none none xor -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- »» anonymous Range false none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than -------------------------------------------------------------------------- Enumerated Values Property Value ------------ ------- chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12 chromosome 13 chromosome 14 chromosome 15 chromosome 16 chromosome 17 chromosome 18 chromosome 19 chromosome 20 chromosome 21 chromosome 22 chromosome X chromosome Y chromosome MT VariantType { "type": { "relation": "eq", "terms": [ "SO_0001483" ] } } Properties -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- type object true none none » relation string true none Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list » terms [string] true none none -------------------------------------------------------------------------- Enumerated Values Property Value ---------- ------- relation eq relation ne VariantConsequence { "consequence": { "relation": "eq", "terms": [ "SO_0001893" ] } } Properties -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- consequence object true none none » relation string true none Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list » terms [string] true none none -------------------------------------------------------------------------- Enumerated Values Property Value ---------- ------- relation eq relation ne VariantFrequency { "frequency": { "dataset": { "name": "gem_j_wga" }, "frequency": { "gte": 0, "lte": 0 }, "filtered": true } } Properties Name Type Required Restrictions Description ----------- -------- ---------- -------------- ------------- frequency object true none none oneOf -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- » anonymous object false none none »» dataset Dataset false none none »» frequency Range true none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »» filtered boolean false none if true, exclude variants with a FILTER flag other than PASS -------------------------------------------------------------------------- xor -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- » anonymous object false none none »» dataset Dataset false none none »» count Range true none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than »» filtered boolean false none if true, exclude variants with a FILTER flag other than PASS -------------------------------------------------------------------------- ClinicalSignificance { "significance": { "relation": "eq", "terms": [ "NC" ], "source": [ "clinvar" ] } } Properties -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- significance object true none none » relation string true none Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list » terms [string] true none none » source [string] false none none -------------------------------------------------------------------------- Enumerated Values Property Value ---------- ------- relation eq relation ne Sift { "sift": { "score": { "gte": 0, "lte": 0 } } } Properties Name Type Required Restrictions Description --------- -------- ---------- -------------- ------------- sift object true none none » score any true none none oneOf -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- »» anonymous Range false none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than -------------------------------------------------------------------------- xor Name Type Required Restrictions Description -------------- ---------- ---------- -------------- ------------- »» anonymous [string] false none none Polyphen { "polyphen": { "score": { "gte": 0, "lte": 0 } } } Properties Name Type Required Restrictions Description ---------- -------- ---------- -------------- ------------- polyphen object true none none » score any true none none oneOf -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- »» anonymous Range false none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than -------------------------------------------------------------------------- xor Name Type Required Restrictions Description -------------- ---------- ---------- -------------- ------------- »» anonymous [string] false none none AlphaMissense { "alphamissense": { "score": { "gte": 0, "lte": 0 } } } Properties Name Type Required Restrictions Description --------------- -------- ---------- -------------- ------------- alphamissense object true none none » score any true none none oneOf -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- »» anonymous Range false none Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than -------------------------------------------------------------------------- xor Name Type Required Restrictions Description -------------- ---------- ---------- -------------- ------------- »» anonymous [string] false none none Gene { "gene": { "relation": "eq", "terms": [ 0 ] } } Properties -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- gene object true none none » relation string true none Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list » terms [integer] true none none -------------------------------------------------------------------------- Enumerated Values Property Value ---------- ------- relation eq relation ne Disease { "disease": { "relation": "eq", "terms": [ "string" ], "sub_concepts": true, "source": [ "clinvar" ] } } Properties -------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------- disease object true none none » relation string true none Available values * eq - Equals to any of term in the list * ne - Not equals to all of term in the list » terms [string] true none none » sub_concepts boolean false none Include diseases of subordinate concepts in the Mondo Disease Ontology (default: true) » source [string] false none none -------------------------------------------------------------------------- Enumerated Values Property Value ---------- ------- relation eq relation ne Dataset { "name": "gem_j_wga" } Properties -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------------- name string true none Available values* gem_j_wga - GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel* jga_wgs - ** DDBJ account required *** jga_wes - Japanese Genotype-phenotype Archive (JGA)* jga_snp - SNP-chip data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA)* tommo - ToMMo 54KJPN Allele Frequency Panel* ncbn - * gnomad_genomes - The Genome Aggregation Database (gnomAD Genomes)* gnomad_exomes - The Genome Aggregation Database (gnomAD Exomes) -------------------------------------------------------------------------------- Enumerated Values Property Value ---------- --------------------------- name gem_j_wga name jga_wgs name jga_wgs.jgad000670 name jga_wgs.jgad000687 name jga_wgs.jgad000688 name jga_wgs.jgad000689 name jga_wes name jga_snp name bbj_riken.mpheno1 name bbj_riken.mpheno1.male name bbj_riken.mpheno1.female name bbj_riken.mpheno2 name bbj_riken.mpheno2.male name bbj_riken.mpheno2.female name bbj_riken.mpheno3 name bbj_riken.mpheno3.male name bbj_riken.mpheno3.female name bbj_riken.mpheno4 name bbj_riken.mpheno4.male name bbj_riken.mpheno4.female name bbj_riken.mpheno5 name bbj_riken.mpheno5.male name bbj_riken.mpheno5.female name bbj_riken.mpheno6 name bbj_riken.mpheno6.male name bbj_riken.mpheno6.female name bbj_riken.mpheno7 name bbj_riken.mpheno7.male name bbj_riken.mpheno7.female name bbj_riken.mpheno8 name bbj_riken.mpheno8.male name bbj_riken.mpheno9 name bbj_riken.mpheno9.female name bbj_riken.mpheno10 name bbj_riken.mpheno10.female name bbj_riken.mpheno11 name bbj_riken.mpheno11.female name bbj_riken.mpheno12 name bbj_riken.mpheno12.female name bbj_riken.mpheno13 name bbj_riken.mpheno13.male name bbj_riken.mpheno13.female name bbj_riken.mpheno14 name bbj_riken.mpheno14.male name bbj_riken.mpheno14.female name bbj_riken.mpheno15 name bbj_riken.mpheno15.male name bbj_riken.mpheno15.female name bbj_riken.mpheno16 name bbj_riken.mpheno16.male name bbj_riken.mpheno16.female name bbj_riken.mpheno17 name bbj_riken.mpheno17.male name bbj_riken.mpheno17.female name bbj_riken.mpheno18 name bbj_riken.mpheno18.male name bbj_riken.mpheno18.female name bbj_riken.mpheno19 name bbj_riken.mpheno19.male name bbj_riken.mpheno19.female name bbj_riken.mpheno20 name bbj_riken.mpheno20.male name bbj_riken.mpheno20.female name bbj_riken.mpheno21 name bbj_riken.mpheno21.male name bbj_riken.mpheno21.female name bbj_riken.mpheno22 name bbj_riken.mpheno22.male name bbj_riken.mpheno22.female name bbj_riken.mpheno23 name bbj_riken.mpheno23.male name bbj_riken.mpheno23.female name bbj_riken.mpheno24 name bbj_riken.mpheno24.male name bbj_riken.mpheno24.female name bbj_riken.mpheno25 name bbj_riken.mpheno25.male name bbj_riken.mpheno25.female name bbj_riken.mpheno26 name bbj_riken.mpheno26.male name bbj_riken.mpheno26.female name bbj_riken.mpheno27 name bbj_riken.mpheno27.male name bbj_riken.mpheno27.female name bbj_riken.mpheno28 name bbj_riken.mpheno28.male name bbj_riken.mpheno28.female name bbj_riken.mpheno29 name bbj_riken.mpheno29.male name bbj_riken.mpheno29.female name bbj_riken.mpheno30 name bbj_riken.mpheno30.male name bbj_riken.mpheno30.female name bbj_riken.mpheno31 name bbj_riken.mpheno31.male name bbj_riken.mpheno31.female name bbj_riken.mpheno32 name bbj_riken.mpheno32.male name bbj_riken.mpheno32.female name bbj_riken.mpheno33 name bbj_riken.mpheno33.male name bbj_riken.mpheno33.female name bbj_riken.mpheno34 name bbj_riken.mpheno34.male name bbj_riken.mpheno34.female name bbj_riken.mpheno35 name bbj_riken.mpheno35.male name bbj_riken.mpheno35.female name bbj_riken.mpheno36 name bbj_riken.mpheno36.male name bbj_riken.mpheno36.female name bbj_riken.mpheno37 name bbj_riken.mpheno37.male name bbj_riken.mpheno37.female name bbj_riken.mpheno38 name bbj_riken.mpheno38.male name bbj_riken.mpheno38.female name bbj_riken.mpheno39 name bbj_riken.mpheno39.male name bbj_riken.mpheno39.female name bbj_riken.mpheno40 name bbj_riken.mpheno40.male name bbj_riken.mpheno40.female name bbj_riken.mpheno41 name bbj_riken.mpheno41.female name bbj_riken.mpheno42 name bbj_riken.mpheno42.female name bbj_riken.mpheno44 name bbj_riken.mpheno44.male name bbj_riken.mpheno44.female name bbj_riken.mpheno45 name bbj_riken.mpheno45.male name bbj_riken.mpheno45.female name bbj_riken.mpheno46 name bbj_riken.mpheno46.male name bbj_riken.mpheno46.female name tommo name ncbn name ncbn.jpn name ncbn.jpn.hondo name ncbn.jpn.ryukyu name ncbn.acb name ncbn.asw name ncbn.beb name ncbn.gbr name ncbn.cdx name ncbn.ceu name ncbn.clm name ncbn.esn name ncbn.fin name ncbn.gwd name ncbn.gih name ncbn.chb name ncbn.chs name ncbn.ibs name ncbn.itu name ncbn.jpt name ncbn.khv name ncbn.lwk name ncbn.msl name ncbn.mxl name ncbn.pel name ncbn.pur name ncbn.pjl name ncbn.stu name ncbn.tsi name ncbn.yri name gnomad_genomes name gnomad_genomes.afr name gnomad_genomes.ami name gnomad_genomes.amr name gnomad_genomes.asj name gnomad_genomes.eas name gnomad_genomes.fin name gnomad_genomes.mid name gnomad_genomes.nfe name gnomad_genomes.remaining name gnomad_genomes.sas name gnomad_exomes name gnomad_exomes.afr name gnomad_exomes.amr name gnomad_exomes.asj name gnomad_exomes.eas name gnomad_exomes.fin name gnomad_exomes.mid name gnomad_exomes.nfe name gnomad_exomes.remaining name gnomad_exomes.sas Range { "gte": 0, "lte": 0 } Available keys * gte - Greater than or equal to * te - Greater than * lte - Less than or equal to * le - Less than Properties oneOf Name Type Required Restrictions Description ----------- -------- ---------- -------------- ------------------------ anonymous object false none Both-closed(a, b) = {x » gte number true none none » lte number true none none xor Name Type Required Restrictions Description ----------- -------- ---------- -------------- ---------------------- anonymous object false none Both-open(a, b) = {x » gt number true none none » lt number true none none xor Name Type Required Restrictions Description ----------- -------- ---------- -------------- ------------------------------------ anonymous object false none Left-open, right-closed(a, b) = {x » gt number true none none » lte number true none none xor Name Type Required Restrictions Description ----------- -------- ---------- -------------- ------------------------------------ anonymous object false none Left-closed, right-open(a, b) = {x » gte number true none none » lt number true none none xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------------- anonymous object false none Left-closed, right-unbounded(a, +∞) = {x » gte number true none none -------------------------------------------------------------------------------- xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------------- anonymous object false none Left-open, right-unbounded(a, +∞) = {x » gt number true none none -------------------------------------------------------------------------------- xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------------- anonymous object false none Right-closed, left-unbounded(-∞, b) = {x » lte number true none none -------------------------------------------------------------------------------- xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------- -------------- -------------- -------------------- anonymous object false none Right-open, left-unbounded(-∞, b) = {x » lt number true none none -------------------------------------------------------------------------------- And { "and": [ { "id": [ "string" ] }, { "id": [ "string" ] } ] } Properties Name Type Required Restrictions Description ------ --------- ---------- -------------- ------------- and [oneOf] true none none oneOf Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous ID false none none xor Name Type Required Restrictions Description ------------- ---------- ---------- -------------- ------------- » anonymous Location false none none xor Name Type Required Restrictions Description ------------- ------------- ---------- -------------- ------------- » anonymous VariantType false none none xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------------- -------------- -------------- -------------- » anonymous VariantConsequence false none none -------------------------------------------------------------------------------- xor ------------------------------------------------------------------------------ Name Type Required Restrictions Description -------------- ------------------ -------------- -------------- -------------- » anonymous VariantFrequency false none none ------------------------------------------------------------------------------ xor ---------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- ---------------------- -------------- -------------- -------------- » anonymous ClinicalSignificance false none none ---------------------------------------------------------------------------------- xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Sift false none none xor Name Type Required Restrictions Description ------------- ---------- ---------- -------------- ------------- » anonymous Polyphen false none none xor Name Type Required Restrictions Description ------------- --------------- ---------- -------------- ------------- » anonymous AlphaMissense false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Gene false none none xor Name Type Required Restrictions Description ------------- --------- ---------- -------------- ------------- » anonymous Disease false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous And false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Or false none none Or { "or": [ { "id": [ "string" ] }, { "id": [ "string" ] } ] } Properties Name Type Required Restrictions Description ------ --------- ---------- -------------- ------------- or [oneOf] true none none oneOf Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous ID false none none xor Name Type Required Restrictions Description ------------- ---------- ---------- -------------- ------------- » anonymous Location false none none xor Name Type Required Restrictions Description ------------- ------------- ---------- -------------- ------------- » anonymous VariantType false none none xor -------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- -------------------- -------------- -------------- -------------- » anonymous VariantConsequence false none none -------------------------------------------------------------------------------- xor ------------------------------------------------------------------------------ Name Type Required Restrictions Description -------------- ------------------ -------------- -------------- -------------- » anonymous VariantFrequency false none none ------------------------------------------------------------------------------ xor ---------------------------------------------------------------------------------- Name Type Required Restrictions Description -------------- ---------------------- -------------- -------------- -------------- » anonymous ClinicalSignificance false none none ---------------------------------------------------------------------------------- xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Sift false none none xor Name Type Required Restrictions Description ------------- ---------- ---------- -------------- ------------- » anonymous Polyphen false none none xor Name Type Required Restrictions Description ------------- --------------- ---------- -------------- ------------- » anonymous AlphaMissense false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Gene false none none xor Name Type Required Restrictions Description ------------- --------- ---------- -------------- ------------- » anonymous Disease false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous And false none none xor Name Type Required Restrictions Description ------------- ------ ---------- -------------- ------------- » anonymous Or false none none SearchVariant { "scroll": { "offset": 0, "limit": 0, "max_rows": 0 }, "statistics": { "total": 0, "filtered": 0, "dataset": { "dataset_name": 0 }, "type": { "so_term": 0 }, "significance": { "significance_key": 0 }, "consequence": { "so_term": 0 } }, "data": [ { "id": "string", "type": "string", "chromosome": "string", "start": 0, "stop": 0, "reference": "string", "alternative": "string", "most_severe_consequence": "string", "sift": 0, "polyphen": 0, "existing_variations": [ "string" ], "external_link": [ { "db_name": [ "string" ] } ], "significance": [ { "condition": "string", "interpretations": [ "string" ] } ], "transcripts": { "transcript_id": "string", "gene_id": "string", "consequence": [ "string" ], "sift": 0, "polyphen": 0, "hgnc_id": 0, "symbol": { "source": "string", "label": "string" }, "hgvs_p": "string", "hgvs_c": "string", "hgvs_g": "string" }, "frequencies": { "source": "string", "filter": [ "string" ], "quality": 0, "allele": { "number": 0, "count": 0, "frequency": 0 }, "genotype": { "ref_homo_count": 0, "hetero_count": 0, "alt_homo_count": 0 } } } ] } Properties Name Type Required Restrictions Description --------------------------- ---------- ---------- -------------- ------------- scroll object false none none » offset integer false none none » limit integer false none none » max_rows integer false none none statistics object false none none » total integer false none none » filtered integer false none none » dataset object false none none »» dataset_name integer false none none » type object false none none »» so_term integer false none none » significance object false none none »» significance_key integer false none none » consequence object false none none »» so_term integer false none none data [object] false none none » id string false none none » type string false none none » chromosome string false none none » start integer false none none » stop integer false none none » reference string false none none » alternative string false none none » most_severe_consequence string false none none » sift number false none none » polyphen number false none none » existing_variations [string] false none none » external_link [object] false none none »» db_name [string] false none none » significance [object] false none none »» condition string false none none »» interpretations [string] false none none » transcripts object false none none »» transcript_id string false none none »» gene_id string false none none »» consequence [string] false none none »» sift number false none none »» polyphen number false none none »» hgnc_id integer false none none »» symbol object false none none »»» source string false none none »»» label string false none none »» hgvs_p string false none none »» hgvs_c string false none none »» hgvs_g string false none none » frequencies object false none none »» source string false none none »» filter [string] false none none »» quality number false none none »» allele object false none none »»» number integer false none none »»» count integer false none none »»» frequency number false none none »» genotype object false none none »»» ref_homo_count integer false none none »»» hetero_count integer false none none »»» alt_homo_count integer false none none DownloadVariant { "data": [ { "tgv_id": "string", "rs": [ "string" ], "chromosome": "string", "position_grch38": 0, "reference": "string", "alternate": "string", "type": "string", "gene": { "name": "string", "id": "string", "synonyms": [ "string" ] }, "consequence": [ "string" ], "condition": [ {} ], "sift_qualitative_prediction": "string", "sift_score": 0, "polyphen2_qualitative_prediction": "string", "polyphen_score": 0, "alphamissense_pathogenicity": "string", "alphamissense_score": 0, "jga_wgs_allele_alt": 0, "jga_wgs_allele_total": 0, "jga_wgs_alt_allele_freq": 0, "jga_wgs_qc_status": [ "string" ], "jga_wes_allele_alt": 0, "jga_wes_allele_total": 0, "jga_wes_alt_allele_freq": 0, "jga_wes_qc_status": [ "string" ], "jga_snp_allele_alt": 0, "jga_snp_allele_total": 0, "jga_snp_alt_allele_freq": 0, "jga_snp_genotype_alt_alt": 0, "jga_snp_genotype_ref_alt": 0, "jga_snp_genotype_ref_ref": 0, "jga_snp_qc_status": [ "string" ], "tommo_allele_alt": 0, "tommo_allele_total": 0, "tommo_alt_allele_freq": 0, "tommo_qc_status": [ "string" ], "hgvd_allele_alt": 0, "hgvd_allele_total": 0, "hgvd_alt_allele_freq": 0, "hgvd_qc_status": [ "string" ], "gem_j_wga_allele_alt": 0, "gem_j_wga_allele_total": 0, "gem_j_wga_alt_allele_freq": 0, "gem_j_wga_qc_status": [ "string" ], "gnomad_genomes_allele_alt": 0, "gnomad_genomes_allele_total": 0, "gnomad_genomes_alt_allele_freq": 0, "gnomad_genomes_qc_status": [ "string" ] } ] } Properties Name Type Required Restrictions Description ------------------------------------ ---------- ---------- -------------- ------------- data [object] false none none » tgv_id string false none none » rs [string] false none none » chromosome string false none none » position_grch38 integer false none none » reference string false none none » alternate string false none none » type string false none none » gene object false none none »» name string false none none »» id string false none none »» synonyms [string] false none none » consequence [string] false none none » condition [object] false none none » sift_qualitative_prediction string false none none » sift_score number false none none » polyphen2_qualitative_prediction string false none none » polyphen_score number false none none » alphamissense_pathogenicity string false none none » alphamissense_score number false none none » jga_wgs_allele_alt number false none none » jga_wgs_allele_total number false none none » jga_wgs_alt_allele_freq number false none none » jga_wgs_qc_status [string] false none none » jga_wes_allele_alt number false none none » jga_wes_allele_total number false none none » jga_wes_alt_allele_freq number false none none » jga_wes_qc_status [string] false none none » jga_snp_allele_alt number false none none » jga_snp_allele_total number false none none » jga_snp_alt_allele_freq number false none none » jga_snp_genotype_alt_alt number false none none » jga_snp_genotype_ref_alt number false none none » jga_snp_genotype_ref_ref number false none none » jga_snp_qc_status [string] false none none » tommo_allele_alt number false none none » tommo_allele_total number false none none » tommo_alt_allele_freq number false none none » tommo_qc_status [string] false none none » hgvd_allele_alt number false none none » hgvd_allele_total number false none none » hgvd_alt_allele_freq number false none none » hgvd_qc_status [string] false none none » gem_j_wga_allele_alt number false none none » gem_j_wga_allele_total number false none none » gem_j_wga_alt_allele_freq number false none none » gem_j_wga_qc_status [string] false none none » gnomad_genomes_allele_alt number false none none » gnomad_genomes_allele_total number false none none » gnomad_genomes_alt_allele_freq number false none none » gnomad_genomes_qc_status [string] false none none SearchGene [ { "id": 404, "symbol": "ALDH2", "name": "aldehyde dehydrogenase 2 family member", "alias_of": null, "highlight": "ALDH2" } ] Properties Name Type Required Restrictions Description ----------- --------- ---------- -------------- ------------- id integer false none none symbol string false none none name string false none none alias_of string false none none highlight string false none none SearchDisease [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "highlight": "Hereditary breast and ovarian cancer syndrome" } ] Properties Name Type Required Restrictions Description ----------- -------- ---------- -------------- ------------- id string false none none cui string false none none label string false none none highlight string false none none InspectDisease [ { "id": "MONDO_0003582", "cui": "C0677776", "label": "Hereditary breast and ovarian cancer syndrome", "root": false, "leaf": false, "parents": [ { "id": "MONDO_0016248", "cui": "CN201036", "label": "Familial ovarian cancer", "root": false } ], "children": [ { "id": "MONDO_0012933", "cui": "C2675520", "label": "Breast-ovarian cancer, familial 2", "leaf": true } ] } ] Properties Name Type Required Restrictions Description ---------- ---------- ---------- -------------- ------------- id string false none none cui string false none none label string false none none root boolean false none none leaf boolean false none none parents [object] false none none » id string false none none » cui string false none none » label string false none none » root boolean false none none children [object] false none none » id string false none none » cui string false none none » label string false none none » leaf boolean false none none Error { "errors": [ "error message" ] } Properties Name Type Required Restrictions Description -------- ---------- ---------- -------------- ------------- errors [string] false none none