diff --git a/openapi.schema.yaml b/openapi.schema.yaml index 9cebe5d..9f2b2b2 100644 --- a/openapi.schema.yaml +++ b/openapi.schema.yaml @@ -9,6 +9,36 @@ info: name: Apache-2.0 version: 0.41.3 paths: + /api/v1/genes/info: + get: + tags: + - genes_info + summary: Query for annotations for one or more genes. + operationId: genesInfo + parameters: + - name: hgnc_id + in: query + description: The HGNC IDs to search for. + required: false + schema: + type: + - array + - 'null' + items: + type: string + responses: + '200': + description: Per-gene information. + content: + application/json: + schema: + $ref: '#/components/schemas/GenesInfoResponse' + '500': + description: Internal server error. + content: + application/json: + schema: + $ref: '#/components/schemas/CustomError' /api/v1/versionsInfo: get: tags: @@ -54,6 +84,2067 @@ components: properties: err: type: string + GenesAcmgSecondaryFindingRecord: + type: object + description: Information from ACMG secondary findings list. + required: + - hgnc_id + - ensembl_gene_id + - ncbi_gene_id + - gene_symbol + - mim_gene_id + - disease_phenotype + - disorder_mim + - phenotype_category + - inheritance + - sf_list_version + - variants_to_report + properties: + hgnc_id: + type: string + description: The HGNC ID. + ensembl_gene_id: + type: string + description: The Ensembl gene ID. + ncbi_gene_id: + type: string + description: The NCBI gene ID. + gene_symbol: + type: string + description: The HGNC gene symbol. + mim_gene_id: + type: string + description: The MIM gene ID. + disease_phenotype: + type: string + description: The disease phenotype. + disorder_mim: + type: string + description: The disease MIM id. + phenotype_category: + type: string + description: The phenotype category. + inheritance: + type: string + description: The mode of inheritance. + sf_list_version: + type: string + description: The version of the ACMG SF list of first appearance. + variants_to_report: + type: string + description: The variants to report according to ACMG SF. + GenesClingenDosageRecord: + type: object + description: '`ClinGen` gene dosage sensitivity record.' + required: + - gene_symbol + - ncbi_gene_id + - genomic_location_37 + - genomic_location_38 + properties: + gene_symbol: + type: string + description: Gene symbol. + ncbi_gene_id: + type: string + description: NCBI gene ID. + genomic_location_37: + type: string + description: Genomic location GRCh37. + genomic_location_38: + type: string + description: Genomic location GRCh38. + haploinsufficiency_score: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesClingenDosageScore' + description: Haploinsufficiency score. + triplosensitivity_score: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesClingenDosageScore' + description: Triplosensitivity score. + haploinsufficiency_disease_id: + type: + - string + - 'null' + description: Haploinsufficiency Disease ID. + triplosensitivity_disease_id: + type: + - string + - 'null' + description: Haploinsufficiency Disease ID. + GenesClingenDosageScore: + type: string + description: Enumeration for Haploinsufficiency / Triplosensitivity scores. + enum: + - SufficientEvidenceAvailable + - SomeEvidenceAvailable + - LittleEvidence + - NoEvidenceAvailable + - Recessive + - Unlikely + GenesConditionsRecord: + type: object + description: Record from the integrated conditions computation. + required: + - hgnc_id + - disease_associations + - panelapp_associations + properties: + hgnc_id: + type: string + description: The HGNC ID. + disease_associations: + type: array + items: + $ref: '#/components/schemas/GenesDiseaseAssociation' + description: The gene-disease associations. + panelapp_associations: + type: array + items: + $ref: '#/components/schemas/GenesPanelappAssociation' + description: The PanelApp associations. + GenesDbnsfpRecord: + type: object + description: Code for data from the dbNSFP database. + required: + - gene_name + - gene_old_names + - gene_other_names + - ccds_id + - refseq_id + - mim_id + - omim_id + - pathway_biocarta_short + - pathway_biocarta_full + - pathway_consensus_path_db + - pathway_kegg_id + - pathway_kegg_full + - function_description + - disease_description + - mim_phenotype_id + - mim_disease + - orphanet_disorder_id + - orphanet_disorder + - orphanet_association_type + - trait_association_gwas + - hpo_id + - hpo_name + - go_biological_process + - go_cellular_component + - go_molecular_function + - tissue_specificity_uniprot + - expression_egenetics + - expression_gnf_atlas + - interactions_intact + - interactions_biogrid + - interactions_consensus_path_db + properties: + gene_name: + type: string + description: Gene symbol from HGNC. + ensembl_gene: + type: + - string + - 'null' + description: Ensembl gene id (from HGNC). + chr: + type: + - string + - 'null' + description: Chromosome number (from HGNC). + gene_old_names: + type: array + items: + type: string + description: Old gene symbol (from HGNC). + gene_other_names: + type: array + items: + type: string + description: Other gene names (from HGNC). + uniprot_acc: + type: + - string + - 'null' + description: Uniprot acc (from HGNC). + uniprot_id: + type: + - string + - 'null' + description: Uniprot id (from HGNC). + entrez_gene_id: + type: + - string + - 'null' + description: Uniprot id (from HGNC). + ccds_id: + type: array + items: + type: string + description: CCDS id (from HGNC). + refseq_id: + type: array + items: + type: string + description: Refseq gene id (from HGNC). + ucsc_id: + type: + - string + - 'null' + description: UCSC gene id (from HGNC). + mim_id: + type: array + items: + type: string + description: MIM gene id (from OMIM). + omim_id: + type: array + items: + type: string + description: MIM gene id from OMIM. + gene_full_name: + type: + - string + - 'null' + description: Gene full name (from HGNC). + pathway_uniprot: + type: + - string + - 'null' + description: Pathway description from Uniprot. + pathway_biocarta_short: + type: array + items: + type: string + description: Short name of the Pathway(s) the gene belongs to (from BioCarta). + pathway_biocarta_full: + type: array + items: + type: string + description: Full name(s) of the Pathway(s) the gene belongs to (from BioCarta). + pathway_consensus_path_db: + type: array + items: + type: string + description: Pathway(s) the gene belongs to (from ConsensusPathDB). + pathway_kegg_id: + type: array + items: + type: string + description: ID(s) of the Pathway(s) the gene belongs to (from KEGG). + pathway_kegg_full: + type: array + items: + type: string + description: Full name(s) of the Pathway(s) the gene belongs to (from KEGG). + function_description: + type: array + items: + type: string + description: Function description of the gene (from Uniprot). + disease_description: + type: array + items: + type: string + description: Disease(s) the gene caused or associated with (from Uniprot). + mim_phenotype_id: + type: array + items: + type: string + description: MIM id(s) of the phenotype the gene caused or associated with (from Uniprot). + mim_disease: + type: array + items: + type: string + description: MIM disease name(s) with MIM id(s) in \[\] (from Uniprot). + orphanet_disorder_id: + type: array + items: + type: string + description: Orphanet Number of the disorder the gene caused or associated with. + orphanet_disorder: + type: array + items: + type: string + description: Disorder name from Orphanet. + orphanet_association_type: + type: array + items: + type: string + description: The type of association beteen the gene and the disorder in Orphanet. + trait_association_gwas: + type: array + items: + type: string + description: Trait(s) the gene associated with (from GWAS catalog). + hpo_id: + type: array + items: + type: string + description: ID of the mapped Human Phenotype Ontology. + hpo_name: + type: array + items: + type: string + description: Name of the mapped Human Phenotype Ontology. + go_biological_process: + type: array + items: + type: string + description: GO terms for biological process. + go_cellular_component: + type: array + items: + type: string + description: GO terms for cellular component. + go_molecular_function: + type: array + items: + type: string + description: GO terms for molecular function. + tissue_specificity_uniprot: + type: array + items: + type: string + description: Tissue specificity description from Uniprot. + expression_egenetics: + type: array + items: + type: string + description: Tissues/organs the gene expressed in (egenetics data from BioMart). + expression_gnf_atlas: + type: array + items: + type: string + description: Tissues/organs the gene expressed in (GNF/Atlas data from BioMart). + interactions_intact: + type: array + items: + type: string + description: The interacting genes from IntAct. + interactions_biogrid: + type: array + items: + type: string + description: The interacting genes from BioGRID. + interactions_consensus_path_db: + type: array + items: + type: string + description: The interacting genes from ConsensusPathDB. + haploinsufficiency: + type: + - number + - 'null' + format: double + description: |- + Estimated probability of haploinsufficiency of the gene (from + doi:10.1371/journal.pgen.1001154). + hipred_score: + type: + - number + - 'null' + format: double + description: |- + Estimated probability of haploinsufficiency of the gene (from + doi:10.1093/bioinformatics/btx028). + hipred: + type: + - string + - 'null' + description: |- + HIPred prediction of haploinsufficiency of the gene. Y(es) or N(o). (from + doi:10.1093/bioinformatics/btx028). + ghis: + type: + - number + - 'null' + format: double + description: |- + A score predicting the gene haploinsufficiency. The higher the score the more likely the + gene is haploinsufficient (from doi: 10.1093/nar/gkv474). + prec: + type: + - number + - 'null' + format: double + description: |- + Estimated probability that gene is a recessive disease gene (from + DOI:10.1126/science.1215040). + known_rec_info: + type: + - string + - 'null' + description: |- + Known recessive status of the gene (from DOI:10.1126/science.1215040) "lof-tolerant = + seen in homozygous state in at least one 1000G individual" "recessive = known OMIM + recessive disease" (original annotations from DOI:10.1126/science.1215040). + rvis_evs: + type: + - number + - 'null' + format: double + description: |- + Residual Variation Intolerance Score, a measure of intolerance of mutational burden, the + higher the score the more tolerant to mutational burden the gene is. Based on EVS + (ESP6500) data. from doi:10.1371/journal.pgen.1003709. + rvis_percentile_evs: + type: + - number + - 'null' + format: double + description: |- + The percentile rank of the gene based on RVIS, the higher the percentile the more + tolerant to mutational burden the gene is. Based on EVS (ESP6500) data. + lof_fdr_exac: + type: + - number + - 'null' + format: double + description: |- + "A gene's corresponding FDR p-value for preferential LoF depletion among the ExAC + population. Lower FDR corresponds with genes that are increasingly depleted of LoF + variants." cited from RVIS document. + rvis_exac: + type: + - number + - 'null' + format: double + description: |- + "ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six + individual ethnic strata from ExAC." cited from RVIS document. + rvis_percentile_exac: + type: + - number + - 'null' + format: double + description: |- + "Genome-Wide percentile for the new ExAC-based RVIS; setting 'common' MAF filter at 0.05% + in at least one of the six individual ethnic strata from ExAC." cited from RVIS document. + exac_pli: + type: + - number + - 'null' + format: double + description: |- + "the probability of being loss-of-function intolerant (intolerant of both heterozygous + and homozygous lof variants)" based on ExAC r0.3 data. + exac_prec: + type: + - number + - 'null' + format: double + description: |- + "the probability of being intolerant of homozygous, but not heterozygous lof variants" + based on ExAC r0.3 data. + exac_pnull: + type: + - number + - 'null' + format: double + description: |- + "the probability of being tolerant of both heterozygous and homozygous lof variants" + based on ExAC r0.3 data. + exac_nontcga_pli: + type: + - number + - 'null' + format: double + description: |- + "the probability of being loss-of-function intolerant (intolerant of both heterozygous + and homozygous lof variants)" based on ExAC r0.3 nonTCGA subset. + exac_nontcga_prec: + type: + - number + - 'null' + format: double + description: |- + "the probability of being intolerant of homozygous, but not heterozygous lof variants" + based on ExAC r0.3 nonTCGA subset. + exac_nontcga_pnull: + type: + - number + - 'null' + format: double + description: |- + "the probability of being tolerant of both heterozygous and homozygous lof variants" + based on ExAC r0.3 nonTCGA subset. + exac_nonpsych_pli: + type: + - number + - 'null' + format: double + description: |- + "the probability of being loss-of-function intolerant (intolerant of both heterozygous + and homozygous lof variants)" based on ExAC r0.3 nonpsych subset. + exac_nonpsych_prec: + type: + - number + - 'null' + format: double + description: |- + "the probability of being intolerant of homozygous, but not heterozygous lof variants" + based on ExAC r0.3 nonpsych subset. + exac_nonpsych_pnull: + type: + - number + - 'null' + format: double + description: |- + "the probability of being tolerant of both heterozygous and homozygous lof variants" + based on ExAC r0.3 nonpsych subset/ + gnomad_pli: + type: + - number + - 'null' + format: double + description: |- + "the probability of being loss-of-function intolerant (intolerant of both heterozygous + and homozygous lof variants)" based on gnomAD 2.1 data. + gnomad_prec: + type: + - number + - 'null' + format: double + description: |- + "the probability of being intolerant of homozygous, but not heterozygous lof variants" + based on gnomAD 2.1 data. + gnomad_pnull: + type: + - number + - 'null' + format: double + description: |- + "the probability of being tolerant of both heterozygous and homozygous lof variants" + based on gnomAD 2.1 data. + exac_del_score: + type: + - number + - 'null' + format: double + description: '"Winsorised deletion intolerance z-score" based on ExAC r0.3.1 CNV data.' + exac_dup_score: + type: + - number + - 'null' + format: double + description: '"Winsorised duplication intolerance z-score" based on ExAC r0.3.1 CNV data.' + exac_cnv_score: + type: + - number + - 'null' + format: double + description: '"Winsorised cnv intolerance z-score" based on ExAC r0.3.1 CNV data.' + exac_cnv_flag: + type: + - string + - 'null' + description: |- + "Gene is in a known region of recurrent CNVs mediated by tandem segmental duplications + and intolerance scores are more likely to be biased or noisy." from ExAC r0.3.1 CNV + release. + gdi: + type: + - number + - 'null' + format: double + description: |- + gene damage index score, "a genome-wide, gene-level metric of the mutational damage that + has accumulated in the general population" from doi: 10.1073/pnas.1518646112. The higher + the score the less likely the gene is to be responsible for monogenic diseases. + gdi_phred: + type: + - number + - 'null' + format: double + description: Phred-scaled GDI scores. + gdp_all_disease_causing: + type: + - string + - 'null' + description: gene damage prediction (low/medium/high) by GDI for all diseases., + gdp_all_mendelian: + type: + - string + - 'null' + description: gene damage prediction (low/medium/high) by GDI for all Mendelian diseases. + gdp_all_mendelian_ad: + type: + - string + - 'null' + description: |- + gene damage prediction (low/medium/high) by GDI for Mendelian autosomal dominant + diseases. + gdp_mendelian_ar: + type: + - string + - 'null' + description: |- + gene damage prediction (low/medium/high) by GDI for Mendelian autosomal recessive + diseases. + gdp_pid: + type: + - string + - 'null' + description: |- + gene damage prediction (low/medium/high) by GDI for all primary immunodeficiency + diseases. + gdp_pid_ad: + type: + - string + - 'null' + description: |- + gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal + dominant diseases. + gdp_pid_ar: + type: + - string + - 'null' + description: |- + gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal + recessive diseases. + gdp_cancer: + type: + - string + - 'null' + description: gene damage prediction (low/medium/high) by GDI for all cancer disease. + gdb_cancer_rec: + type: + - string + - 'null' + description: gene damage prediction (low/medium/high) by GDI for cancer recessive disease. + gdp_cancer_dom: + type: + - string + - 'null' + description: gene damage prediction (low/medium/high) by GDI for cancer dominant disease. + loftool_score: + type: + - number + - 'null' + format: double + description: |- + A percentile score for gene intolerance to functional change. The lower the score the + higher gene intolerance to functional change. For details see doi: + 10.1093/bioinformatics/btv602. + sorva_lof_maf_5_het_or_hom: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method + for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_maf_5_hom_or_comphet: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a + method for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_maf_1_het_or_hom: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method + for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_maf_1_hom_or_comphet: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a + method for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_or_mis_maf_5_het_or_hom: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from + a method for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_or_mis_maf_5_hom_or_comphet: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This + fraction is from a method for ranking genes based on mutational burden called SORVA + (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_or_mis_maf_1_het_or_hom: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from + a method for ranking genes based on mutational burden called SORVA (Significance Of Rare + VAriants). Please see doi: 10.1101/103218 for details. + sorva_lof_or_mis_maf_1_hom_or_comphet: + type: + - number + - 'null' + format: double + description: |- + The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either + Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This + fraction is from a method for ranking genes based on mutational burden called SORVA + (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. + essential_gene: + type: + - string + - 'null' + description: |- + Essential ("E") or Non-essential phenotype-changing ("N") based on Mouse Genome + Informatics database. from doi:10.1371/journal.pgen.1003484. + essential_gene_crispr: + type: + - string + - 'null' + description: |- + Essential ("E") or Non-essential phenotype-changing ("N") based on large scale CRISPR + experiments. from doi: 10.1126/science.aac7041. + essential_gene_crispr2: + type: + - string + - 'null' + description: |- + Essential ("E"), context-Specific essential ("S"), or Non-essential phenotype-changing + ("N") based on large scale CRISPR experiments. from + + essential_gene_gene_trap: + type: + - string + - 'null' + description: |- + Essential ("E"), HAP1-Specific essential ("H"), KBM7-Specific essential ("K"), or + Non-essential phenotype-changing ("N"), based on large scale mutagenesis experiments. + from doi: 10.1126/science.aac7557. + gene_indispensability_score: + type: + - number + - 'null' + format: double + description: |- + A probability prediction of the gene being essential. From + doi:10.1371/journal.pcbi.1002886. + gene_indispensability_pred: + type: + - string + - 'null' + description: Essential ("E") or loss-of-function tolerant ("N") based on Gene_indispensability_score. + mgi_mouse_gene: + type: + - string + - 'null' + description: Homolog mouse gene name from MGI. + mgi_mouse_phenotype: + type: + - string + - 'null' + description: Phenotype description for the homolog mouse gene from MGI. + zfin_zebrafish_gene: + type: + - string + - 'null' + description: Homolog zebrafish gene name from ZFIN. + zfin_zebrafish_structure: + type: + - string + - 'null' + description: Affected structure of the homolog zebrafish gene from ZFIN. + zfin_zebrafish_phenotype_quality: + type: + - string + - 'null' + description: Phenotype description for the homolog zebrafish gene from ZFIN. + zfin_zebrafish_phenotype_tag: + type: + - string + - 'null' + description: Phenotype tag for the homolog zebrafish gene from ZFIN" + GenesDecipherHiRecord: + type: object + description: Decipher HI Predictions + required: + - hgnc_id + - hgnc_symbol + - p_hi + - hi_index + properties: + hgnc_id: + type: string + description: HGNC identifier. + hgnc_symbol: + type: string + description: Official HGNC gene symbol. + p_hi: + type: number + format: double + description: P(HI) prediction from DECIPHER HI. + hi_index: + type: number + format: double + description: Percent HI index. + GenesDiseaseAssociation: + type: object + description: A gene-disease association. + required: + - hgnc_id + - labeled_disorders + - sources + - confidence + properties: + hgnc_id: + type: string + description: The HGNC ID. + labeled_disorders: + type: array + items: + $ref: '#/components/schemas/GenesLabeledDisorder' + description: The gene-disease association entries. + disease_name: + type: + - string + - 'null' + description: Overall disease name. + disease_definition: + type: + - string + - 'null' + description: Disease definition. + sources: + type: array + items: + $ref: '#/components/schemas/GenesDiseaseAssociationSource' + description: The gene-disease association sources. + confidence: + $ref: '#/components/schemas/GenesDiseaseAssociationConfidenceLevel' + description: Overall disease-gene association confidence level. + GenesDiseaseAssociationConfidenceLevel: + type: string + description: Enumeration for confidence levels. + enum: + - High + - Medium + - Low + GenesDiseaseAssociationEntryConfidenceLevel: + type: string + description: Enumeration for confidence levels. + enum: + - High + - Medium + - Low + GenesDiseaseAssociationSource: + type: string + description: Enumeration for sources. + enum: + - Omim + - Orphanet + - Panelapp + GenesDominoRecord: + type: object + description: Information from DOMINO. + required: + - gene_symbol + - score + properties: + gene_symbol: + type: string + description: Gene symbol. + score: + type: number + format: double + description: The score. + GenesEntityType: + type: string + description: Enumeration for entity types. + enum: + - Gene + - Str + - Region + GenesGeneData: + type: object + description: Gene identity information. + properties: + hgnc_id: + type: + - string + - 'null' + description: HGNC ID. + hgnc_symbol: + type: + - string + - 'null' + description: HGNC gene symbol. + gene_symbol: + type: + - string + - 'null' + description: Gene symbol. + GenesGeneDiseaseAssociationEntry: + type: object + description: A gene-disease association entry. + required: + - source + - confidence + properties: + source: + $ref: '#/components/schemas/GenesDiseaseAssociationSource' + description: The gene-disease association source. + confidence: + $ref: '#/components/schemas/GenesDiseaseAssociationEntryConfidenceLevel' + description: The gene-disease association confidence level. + GenesGeneInfoRecord: + type: object + description: Information about a gene. + required: + - panelapp + properties: + acmg_sf: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord' + description: Information from the ACMG secondary finding list. + clingen: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesClingenDosageRecord' + description: Information from ClinGen dosage curation. + dbnsfp: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDbnsfpRecord' + description: Information from dbNSFP. + gnomad_constraints: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesGnomadConstraintsRecord' + description: Information from the gnomAD constraints database. + hgnc: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesHgncRecord' + description: Information from the HGNC database. + ncbi: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesNcbiRecord' + description: Information from the NCBI gene database (aka "Entrez"). + omim: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesOmimRecord' + description: Information about gene to OMIM term annotation, composed from clingen and HPO. + orpha: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesOrphaRecord' + description: Information about gene to Orphanet annotation, derived from Orphapacket. + rcnv: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesRcnvRecord' + description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022). + shet: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesShetRecord' + description: Information from the sHet score (Weghor et al., 2019) + gtex: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesGtexRecord' + description: Information from GTEx data + domino: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDominoRecord' + description: Information from DOMINO. + decipher_hi: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDecipherHiRecord' + description: DECIPHER HI score. + panelapp: + type: array + items: + $ref: '#/components/schemas/GenesPanelAppRecord' + description: GenomicsEngland PanelApp gene information. + conditions: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesConditionsRecord' + description: Conditions record. + GenesGeneRecord: + type: object + description: Entry in the genes RocksDB database. + required: + - panelapp + properties: + acmg_sf: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord' + description: Information from the ACMG secondary finding list. + clingen: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesClingenDosageRecord' + description: Information from ClinGen dosage curation. + dbnsfp: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDbnsfpRecord' + description: Information from dbNSFP. + gnomad_constraints: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesGnomadConstraintsRecord' + description: Information from the gnomAD constraints database. + hgnc: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesHgncRecord' + description: Information from the HGNC database. + ncbi: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesNcbiRecord' + description: Information from the NCBI gene database (aka "Entrez"). + omim: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesOmimRecord' + description: Information about gene to OMIM term annotation, composed from clingen and HPO. + orpha: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesOrphaRecord' + description: Information about gene to Orphanet annotation, derived from Orphapacket. + rcnv: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesRcnvRecord' + description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022). + shet: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesShetRecord' + description: Information from the sHet score (Weghor et al., 2019) + gtex: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesGtexRecord' + description: Information from GTEx data + domino: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDominoRecord' + description: Information from DOMINO. + decipher_hi: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesDecipherHiRecord' + description: DECIPHER HI score. + panelapp: + type: array + items: + $ref: '#/components/schemas/GenesPanelAppRecord' + description: GenomicsEngland PanelApp gene information. + conditions: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesConditionsRecord' + description: Conditions record. + GenesGnomadConstraintsRecord: + type: object + description: Code for data from the gnomAD constraints. + required: + - ensembl_gene_id + - entrez_id + - gene_symbol + properties: + ensembl_gene_id: + type: string + description: The Ensembl gene ID. + entrez_id: + type: string + description: The NCBI gene ID. + gene_symbol: + type: string + description: The HGNC gene symbol. + exp_lof: + type: + - number + - 'null' + format: double + description: The expected number of loss-of-function variants. + exp_mis: + type: + - number + - 'null' + format: double + description: The expected number of missense variants. + exp_syn: + type: + - number + - 'null' + format: double + description: The expected number of synonymous variants. + mis_z: + type: + - number + - 'null' + format: double + description: The missense-related Z-score. + obs_lof: + type: + - integer + - 'null' + format: int32 + description: The observed number of loss-of-function variants. + minimum: 0 + obs_mis: + type: + - integer + - 'null' + format: int32 + description: The observed number of missense variants. + minimum: 0 + obs_syn: + type: + - integer + - 'null' + format: int32 + description: The observed number of synonymous variants. + minimum: 0 + oe_lof: + type: + - number + - 'null' + format: double + description: The loss-of-function observed/expected ratio. + oe_lof_lower: + type: + - number + - 'null' + format: double + description: The lower bound of the loss-of-function observed/expected ratio. + oe_lof_upper: + type: + - number + - 'null' + format: double + description: The upper bound of the loss-of-function observed/expected ratio. + oe_mis: + type: + - number + - 'null' + format: double + description: The missense observed/expected ratio. + oe_mis_lower: + type: + - number + - 'null' + format: double + description: The lower bound of the missense observed/expected ratio. + oe_mis_upper: + type: + - number + - 'null' + format: double + description: The upper bound of the missense observed/expected ratio. + oe_syn: + type: + - number + - 'null' + format: double + description: The synonymous observed/expected ratio. + oe_syn_lower: + type: + - number + - 'null' + format: double + description: The lower bound of the synonymous observed/expected ratio. + oe_syn_upper: + type: + - number + - 'null' + format: double + description: The upper bound of the synonymous observed/expected ratio. + pli: + type: + - number + - 'null' + format: double + description: The probability of loss-of-function intolerance (pLI score). + syn_z: + type: + - number + - 'null' + format: double + description: The synonymous-related Z-score. + exac_pli: + type: + - number + - 'null' + format: double + description: The probability of loss-of-function intolerance (pLI score) from ExAC. + exac_obs_lof: + type: + - number + - 'null' + format: double + description: The observed number of loss-of-function variants from ExAC. + exac_exp_lof: + type: + - number + - 'null' + format: double + description: The expected number of loss-of-function variants from ExAC. + exac_oe_lof: + type: + - number + - 'null' + format: double + description: The loss-of-function observed/expected ratio from ExAC. + GenesGtexRecord: + type: object + description: Entry with the GTEx information. + required: + - hgnc_id + - ensembl_gene_id + - ensembl_gene_version + - records + properties: + hgnc_id: + type: string + description: The HGNC ID. + ensembl_gene_id: + type: string + description: ENSEMBL gene ID. + ensembl_gene_version: + type: string + description: ENSEMBL gene version. + records: + type: array + items: + $ref: '#/components/schemas/GenesGtexTissueRecord' + description: Counts per tissue + GenesGtexTissue: + type: string + description: Enumeration for GTEx V8 tissue + enum: + - AdiposeTissue + - AdrenalGland + - Bladder + - Blood + - BloodVessel + - BoneMarrow + - Brain + - Breast + - CervixUteri + - Colon + - Esophagus + - FallopianTube + - Heart + - Kidney + - Liver + - Lung + - Muscle + - Nerve + - Ovary + - Pancreas + - Pituitary + - Prostate + - SalivaryGland + - Skin + - SmallIntestine + - Spleen + - Stomach + - Testis + - Thyroid + - Uterus + - Vagina + GenesGtexTissueDetailed: + type: string + description: Enumeration for GTEx V8 tissue details + enum: + - AdiposeSubcutaneous + - AdiposeVisceralOmentum + - AdrenalGland + - ArteryAorta + - ArteryCoronary + - ArteryTibial + - Bladder + - BrainAmygdala + - BrainAnteriorCingulateCortex + - BrainCaudateBasalGanglia + - BrainCerebellarHemisphere + - BrainCerebellum + - BrainCortex + - BrainFrontalCortex + - BrainHippocampus + - BrainHypothalamus + - BrainNucleusAccumbens + - BrainPutamenBasalGanglia + - BrainSpinalCord + - BrainSubstantiaNigra + - BreastMammaryTissue + - CellsCulturedFibroblasts + - CellsEbvTransformedLymphocytes + - CellsLeukemiaCellLine + - CervixEctocervix + - CervixEndocervix + - ColonSigmoid + - ColonTransverse + - EsophagusGastroesophagealJunction + - EsophagusMucosa + - EsophagusMuscularis + - FallopianTube + - HeartAtrialAppendage + - HeartLeftVentricle + - KidneyCortex + - KidneyMedulla + - Liver + - Lung + - MinorSalivaryGland + - MuscleSkeletal + - NerveTibial + - Ovary + - Pancreas + - Pituitary + - Prostate + - SalivaryGland + - SkinNotSunExposedSuprapubic + - SkinSunExposedLowerLeg + - SmallIntestineTerminalIleum + - Spleen + - Stomach + - Testis + - Thyroid + - Uterus + - Vagina + - WholeBlood + GenesGtexTissueRecord: + type: object + description: Entry with the tissue-specific information for a gene. + required: + - tissue + - tissue_detailed + - tpms + properties: + tissue: + $ref: '#/components/schemas/GenesGtexTissue' + description: The tissue type + tissue_detailed: + $ref: '#/components/schemas/GenesGtexTissueDetailed' + description: The detailed tissue type + tpms: + type: array + items: + type: number + format: float + description: TPM counts + GenesHgncLsdb: + type: object + description: Information from the locus-specific dabase. + required: + - name + - url + properties: + name: + type: string + description: The name of the Locus Specific Mutation Database. + url: + type: string + description: The URL for the gene. + GenesHgncRecord: + type: object + description: A record from the HGNC database. + required: + - hgnc_id + - symbol + - name + - status + - alias_symbol + - alias_name + - prev_symbol + - prev_name + - gene_group + - gene_group_id + - ena + - refseq_accession + - ccds_id + - uniprot_ids + - pubmed_id + - mgd_id + - rgd_id + - lsdb + - omim_id + - enzyme_id + - mane_select + properties: + hgnc_id: + type: string + description: HGNC ID. A unique ID created by the HGNC for every approved symbol. + symbol: + type: string + description: The HGNC approved gene symbol. + name: + type: string + description: HGNC approved name for the gene. + locus_group: + type: + - string + - 'null' + description: |- + A group name for a set of related locus types as defined by the HGNC + (e.g. non-coding RNA). + locus_type: + type: + - string + - 'null' + description: The locus type as defined by the HGNC (e.g. RNA, transfer). + status: + type: integer + format: int32 + description: Status of the symbol report. + location: + type: + - string + - 'null' + description: Cytogenetic location of the gene (e.g. 2q34). + location_sortable: + type: + - string + - 'null' + description: Sortable cytogenic location of the gene (e.g. 02q34). + alias_symbol: + type: array + items: + type: string + description: Other symbols used to refer to this gene. + alias_name: + type: array + items: + type: string + description: Other names used to refer to this gene. + prev_symbol: + type: array + items: + type: string + description: Prevous symbols used to refer to this gene. + prev_name: + type: array + items: + type: string + description: Previous names used to refer to this gene. + gene_group: + type: array + items: + type: string + description: Name given to a gene group. + gene_group_id: + type: array + items: + type: integer + format: int32 + minimum: 0 + description: ID used to designate a gene group. + date_approved_reserved: + type: + - string + - 'null' + description: The date the entry was first approved. + date_symbol_changed: + type: + - string + - 'null' + description: The date the gene symbol was last changed. + date_name_changed: + type: + - string + - 'null' + description: The date the gene name was last changed. + date_modified: + type: + - string + - 'null' + description: Date the entry was last modified. + entrez_id: + type: + - string + - 'null' + description: Entrez gene id. + ensembl_gene_id: + type: + - string + - 'null' + description: Ensembl gene id. + vega_id: + type: + - string + - 'null' + description: Vega gene id. + ucsc_id: + type: + - string + - 'null' + description: UCSC gene id. + ena: + type: array + items: + type: string + description: ENA accession number(s). + refseq_accession: + type: array + items: + type: string + description: RefSeq nucleotide accession(s). + ccds_id: + type: array + items: + type: string + description: Consensus CDS ID(ds). + uniprot_ids: + type: array + items: + type: string + description: Uniprot IDs. + pubmed_id: + type: array + items: + type: integer + format: int32 + minimum: 0 + description: Pubmed IDs. + mgd_id: + type: array + items: + type: string + description: Mouse genome informatics database ID(s). + rgd_id: + type: array + items: + type: string + description: Rat genome database gene ID(s). + lsdb: + type: array + items: + $ref: '#/components/schemas/GenesHgncLsdb' + description: The name of the Locus Specific Mutation Database and URL for the gene. + cosmic: + type: + - string + - 'null' + description: Symbol used within COSMIC. + omim_id: + type: array + items: + type: string + description: OMIM ID(s). + mirbase: + type: + - string + - 'null' + description: miRBase ID. + homeodb: + type: + - integer + - 'null' + format: int32 + description: Homeobox Database ID. + minimum: 0 + snornabase: + type: + - string + - 'null' + description: snoRNABase ID. + bioparadigms_slc: + type: + - string + - 'null' + description: |- + Symbol used to link to the SLC tables database at bioparadigms.org + for the gene. + orphanet: + type: + - integer + - 'null' + format: int32 + description: Orphanet ID. + minimum: 0 + pseudogene_org: + type: + - string + - 'null' + description: Pseudogene.org. + horde_id: + type: + - string + - 'null' + description: Symbol used within HORDE for the gene. + merops: + type: + - string + - 'null' + description: ID used to link to the MEROPS peptidase database. + imgt: + type: + - string + - 'null' + description: Symbol used within international ImMunoGeneTics information system. + iuphar: + type: + - string + - 'null' + description: |- + The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY + database. + cd: + type: + - string + - 'null' + description: Symbol used within the Human Cell Differentiation Molecule database. + mamit_trnadb: + type: + - integer + - 'null' + format: int32 + description: ID to link to the Mamit-tRNA database + minimum: 0 + lncrnadb: + type: + - string + - 'null' + description: lncRNA Database ID. + enzyme_id: + type: array + items: + type: string + description: ENZYME EC accession number. + intermediate_filament_db: + type: + - string + - 'null' + description: ID used to link to the Human Intermediate Filament Database. + agr: + type: + - string + - 'null' + description: The HGNC ID that the Alliance of Genome Resources (AGR) use. + mane_select: + type: array + items: + type: string + description: |- + NCBI and Ensembl transcript IDs/acessions including the version + number. + GenesHgncStatus: + type: string + description: Status of the symbol report, which can be either "Approved" or "Entry Withdrawn". + enum: + - Approved + - Withdrawn + GenesInfoResponse: + type: object + description: Query response for `handle_with_openapi()`. + required: + - genes + properties: + genes: + type: array + items: + $ref: '#/components/schemas/GenesGeneInfoRecord' + description: Version information of the genes. + GenesLabeledDisorder: + type: object + description: A labeled disorder. + required: + - term_id + properties: + term_id: + type: string + description: The disorder ID. + title: + type: + - string + - 'null' + description: The disorder name. + GenesNcbiRecord: + type: object + description: A record from the NCBI gene database. + required: + - gene_id + - rif_entries + properties: + gene_id: + type: string + description: NCBI Gene ID. + summary: + type: + - string + - 'null' + description: Gene summary. + rif_entries: + type: array + items: + $ref: '#/components/schemas/GenesRifEntry' + description: '"Reference Into Function" entry.' + GenesOmimRecord: + type: object + description: A record from the OMIM gene association. + required: + - hgnc_id + - omim_diseases + properties: + hgnc_id: + type: string + description: The HGNC gene ID. + omim_diseases: + type: array + items: + $ref: '#/components/schemas/GenesOmimTerm' + description: The associated OMIM records. + GenesOmimTerm: + type: object + description: Description of an OMIM record. + required: + - omim_id + - label + properties: + omim_id: + type: string + description: The OMIM ID. + label: + type: string + description: The OMIM label. + GenesOrphaRecord: + type: object + description: A record from the ORDO gene association. + required: + - hgnc_id + - orpha_diseases + properties: + hgnc_id: + type: string + description: The HGNC gene ID. + orpha_diseases: + type: array + items: + $ref: '#/components/schemas/GenesOrphaTerm' + description: The associated ORPHA diseases. + GenesOrphaTerm: + type: object + description: Description of an ORDO record. + required: + - orpha_id + - label + properties: + orpha_id: + type: string + description: The ORPHA ID. + label: + type: string + description: The disease name. + GenesPanel: + type: object + description: Message for panel information. + required: + - id + - name + - disease_group + - disease_sub_group + - version + - version_created + - relevant_disorders + - types + properties: + id: + type: integer + format: int32 + description: Panel ID. + minimum: 0 + hash_id: + type: + - string + - 'null' + description: Panel hash ID. + name: + type: string + description: Panel name. + disease_group: + type: string + description: Disease group. + disease_sub_group: + type: string + description: Disease subgroup. + version: + type: string + description: Version + version_created: + type: string + description: Creation date of version. + relevant_disorders: + type: array + items: + type: string + description: Relevant disorders. + stats: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesPanelStats' + description: Stats. + types: + type: array + items: + $ref: '#/components/schemas/GenesPanelType' + description: Panel types. + GenesPanelAppRecord: + type: object + description: Entry in PanelApp. + required: + - entity_type + - entity_name + - confidence_level + - publications + - evidence + - phenotypes + - mode_of_inheritance + properties: + gene_data: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesGeneData' + description: Gene identity information. + entity_type: + $ref: '#/components/schemas/GenesEntityType' + description: Entity type. + entity_name: + type: string + description: Entity name. + confidence_level: + $ref: '#/components/schemas/GenesPanelappRecordConfidenceLevel' + description: Confidence level. + penetrance: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesPenetrance' + description: Penetrance. + publications: + type: array + items: + type: string + description: Publications. + evidence: + type: array + items: + type: string + description: Evidence. + phenotypes: + type: array + items: + type: string + description: Phenotypes. + mode_of_inheritance: + type: string + description: Mode of inheritance. + panel: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesPanel' + description: Panel. + GenesPanelStats: + type: object + description: Message for panel statistics. + required: + - number_of_genes + - number_of_strs + - number_of_regions + properties: + number_of_genes: + type: integer + format: int32 + description: Number of genes. + minimum: 0 + number_of_strs: + type: integer + format: int32 + description: Number of STRs. + minimum: 0 + number_of_regions: + type: integer + format: int32 + description: Number of regions. + minimum: 0 + GenesPanelType: + type: object + description: Message for panel types. + required: + - name + - slug + - description + properties: + name: + type: string + description: Type name. + slug: + type: string + description: Slug. + description: + type: string + description: Description. + GenesPanelappAssociation: + type: object + description: An association of a gene by HGNC with a panel from PanelApp. + required: + - hgnc_id + - confidence_level + - entity_type + - phenotypes + properties: + hgnc_id: + type: string + description: The HGNC ID. + confidence_level: + $ref: '#/components/schemas/GenesPanelappAssociationConfidenceLevel' + description: The PanelApp confidence level. + entity_type: + $ref: '#/components/schemas/GenesPanelappEntityType' + description: The PanelApp entity type. + mode_of_inheritance: + type: + - string + - 'null' + description: The PanelApp entity name. + phenotypes: + type: array + items: + type: string + description: The PanelApp publications. + panel: + oneOf: + - type: 'null' + - $ref: '#/components/schemas/GenesPanelappPanel' + description: The PanelApp panel. + GenesPanelappAssociationConfidenceLevel: + type: string + description: Enumeration for PanelApp confidence level. + enum: + - Green + - Amber + - Red + - None + GenesPanelappEntityType: + type: string + description: Enumeration for entity type. + enum: + - Gene + - Region + - Str + GenesPanelappPanel: + type: object + description: A panel from PanelApp. + required: + - id + - name + - version + properties: + id: + type: integer + format: int32 + description: PanelApp panel ID. + name: + type: string + description: PanelApp panel name. + version: + type: string + description: PanelApp panel version. + GenesPanelappRecordConfidenceLevel: + type: string + description: Enumeration for PanelApp confidence level. + enum: + - Green + - Amber + - Red + - None + GenesPenetrance: + type: string + description: Enumeration for penetrance. + enum: + - Complete + - Incomplete + GenesRcnvRecord: + type: object + description: Entry in the rCNV dosage sensitivity scores (Collins et al., 2022). + required: + - hgnc_id + - p_haplo + - p_triplo + properties: + hgnc_id: + type: string + description: The HGNC ID. + p_haplo: + type: number + format: double + description: The pHaplo value. + p_triplo: + type: number + format: double + description: The pTriplo value. + GenesRifEntry: + type: object + description: Reference into function record. + required: + - text + - pmids + properties: + text: + type: string + description: The RIF text. + pmids: + type: array + items: + type: integer + format: int32 + minimum: 0 + description: PubMed IDs. + GenesShetRecord: + type: object + description: Entry with sHet information (Weghorn et al., 2019). + required: + - hgnc_id + - s_het + properties: + hgnc_id: + type: string + description: The HGNC ID. + s_het: + type: number + format: double + description: The sHet value. GenomeRelease: type: string description: Local genome release for command line arguments.