Index

_

__init__() (civic.CivicRecord method)

_CivicGksAssertionRecord (class in civicpy.exports.civic_gks_record)

A

abstract (civic.Source attribute) acmg_codes (civic.Assertion attribute) AcmgCode (class in civic) aliases (civic.Disease attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile attribute) (civic.Region attribute) (civic.Therapy attribute) (civic.Variant property) allele_registry_id (civic.GeneVariant attribute) amp_level (civic.Assertion attribute) Approval (class in civic)

approvals (civic.Assertion property) (civic.Organization property) asco_abstract_id (civic.Source attribute) assertion (civic.Approval property) Assertion (class in civic) assertion_direction (civic.Assertion attribute) assertion_id (civic.Approval attribute) assertion_ids (civic.Evidence attribute) assertion_type (civic.Assertion attribute) assertions (civic.Disease property) (civic.Evidence property) (civic.MolecularProfile property) (civic.Phenotype property) (civic.Therapy property) author_string (civic.Source attribute)

B

bulk_search_variants_by_coordinates() (in module civic)

C

chromosome (civic.Coordinate attribute) (civic.ExonCoordinate attribute) citation (civic.Source attribute) citation_id (civic.Source attribute) civic module CivicGksDiagnosticAssertion (class in civicpy.exports.civic_gks_record) CivicGksPredictiveAssertion (class in civicpy.exports.civic_gks_record) CivicGksPrognosticAssertion (class in civicpy.exports.civic_gks_record) CivicGksWriter (class in civicpy.exports.civic_gks_writer) CivicRecord (class in civic)

CivicVcfRecord (class in civicpy.exports.civic_vcf_record) CivicVcfWriter (class in civicpy.exports.civic_vcf_writer) clingen_codes (civic.Assertion attribute) ClingenCode (class in civic) clinical_trials (civic.Source attribute) ClinicalTrial (class in civic) clinvar_entries (civic.GeneVariant attribute) code (civic.AcmgCode attribute) (civic.ClingenCode attribute) Coordinate (class in civic) CoordinateQuery (class in civic) coordinates (civic.GeneVariant attribute)

D

description (civic.AcmgCode attribute) (civic.Assertion attribute) (civic.ClingenCode attribute) (civic.ClinicalTrial attribute) (civic.Evidence attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile attribute) (civic.Organization attribute) (civic.Region attribute) (civic.VariantType attribute)

disease (civic.Assertion property) (civic.Evidence property) Disease (class in civic) disease_id (civic.Assertion attribute) (civic.Evidence attribute) disease_url (civic.Disease attribute) doid (civic.Disease attribute)

E

ensembl_id (civic.ExonCoordinate attribute) ensembl_version (civic.Coordinate attribute) (civic.ExonCoordinate attribute) entrez_id (civic.Gene attribute) (civic.GeneVariant attribute) entrez_name (civic.GeneVariant attribute) evidence (civic.Assertion property) (civic.Disease property) (civic.MolecularProfile property) (civic.Phenotype property) (civic.Source property) (civic.Therapy property) Evidence (class in civic) evidence_direction (civic.Evidence attribute) evidence_ids (civic.Assertion attribute)

evidence_items (civic.Assertion property) (civic.Disease property) (civic.MolecularProfile property) (civic.Phenotype property) (civic.Source property) (civic.Therapy property) evidence_level (civic.Evidence attribute) evidence_sources (civic.MolecularProfile property) evidence_type (civic.Evidence attribute) exon (civic.ExonCoordinate attribute) exon_offset (civic.ExonCoordinate attribute) exon_offset_direction (civic.ExonCoordinate attribute) ExonCoordinate (class in civic) exports module

F

factor (civic.FactorVariant property) Factor (class in civic) factors (civic.Source property) FactorVariant (class in civic) fda_companion_test (civic.Assertion attribute) fda_regulatory_approval (civic.Assertion attribute) feature (civic.FactorVariant property) (civic.FusionVariant property) (civic.GeneVariant property) (civic.RegionVariant property)

feature_id (civic.Variant attribute) five_prime_coordinates (civic.FusionVariant attribute) five_prime_gene (civic.Fusion property) five_prime_gene_id (civic.Fusion attribute) five_prime_partner_status (civic.Fusion attribute) full_journal_title (civic.Source attribute) full_name (civic.Factor attribute) fusion (civic.FusionVariant property) Fusion (class in civic) fusions (civic.Source property) FusionVariant (class in civic)

G

gene (civic.GeneVariant property) Gene (class in civic) genes (civic.Source property) GeneVariant (class in civic) get_all_approvals() (in module civic) get_all_approvals_ready_for_clinvar_submission_for_org() (in module civic) get_all_assertions() (in module civic) get_all_assertions_ready_for_clinvar_submission_for_org() (in module civic) get_all_diseases() (in module civic) get_all_evidence() (in module civic) get_all_factor_variants() (in module civic) get_all_factors() (in module civic) get_all_features() (in module civic) get_all_fusion_variants() (in module civic) get_all_fusions() (in module civic) get_all_gene_variants() (in module civic) get_all_genes() (in module civic) get_all_molecular_profiles() (in module civic) get_all_organizations() (in module civic) get_all_phenotypes() (in module civic) get_all_region_variants() (in module civic) get_all_regions() (in module civic) get_all_sources() (in module civic) get_all_therapies() (in module civic) get_all_variant_groups() (in module civic) get_all_variants() (in module civic) get_approval_by_id() (in module civic) get_approvals_by_ids() (in module civic) get_asco_source_by_id() (in module civic) get_ash_source_by_doi() (in module civic) get_assertion_by_id() (in module civic) get_assertions_by_ids() (in module civic) get_classification_and_strength() (civicpy.exports.civic_gks_record._CivicGksAssertionRecord method) get_contributions() (civicpy.exports.civic_gks_record._CivicGksAssertionRecord static method) get_disease_by_doid() (in module civic) get_disease_by_id() (in module civic) get_disease_by_name() (in module civic) get_diseases_by_ids() (in module civic)

get_evidence_by_id() (in module civic) get_evidence_by_ids() (in module civic) get_evidence_lines() (civicpy.exports.civic_gks_record._CivicGksAssertionRecord method) get_factor_by_id() (in module civic) get_factor_by_name() (in module civic) get_factor_by_ncit_id() (in module civic) get_factors_by_ids() (in module civic) get_feature_by_id() (in module civic) get_features_by_ids() (in module civic) get_fusion_by_id() (in module civic) get_fusion_by_name() (in module civic) get_fusions_by_ids() (in module civic) get_gene_by_entrez_id() (in module civic) get_gene_by_id() (in module civic) get_gene_by_name() (in module civic) get_genes_by_ids() (in module civic) get_molecular_profile_by_id() (in module civic) get_molecular_profiles_by_ids() (in module civic) get_organization_by_id() (in module civic) get_organizations_by_ids() (in module civic) get_phenotype_by_hpo_id() (in module civic) get_phenotype_by_id() (in module civic) get_phenotype_by_name() (in module civic) get_phenotypes_by_ids() (in module civic) get_pubmed_source_by_id() (in module civic) get_region_by_id() (in module civic) get_region_by_name() (in module civic) get_regions_by_ids() (in module civic) get_source_by_id() (in module civic) get_sources_by_ids() (in module civic) get_therapies_by_ids() (in module civic) get_therapy_by_id() (in module civic) get_therapy_by_name() (in module civic) get_therapy_by_ncit_id() (in module civic) get_variant_by_id() (in module civic) get_variant_group_by_id() (in module civic) get_variant_groups_by_ids() (in module civic) get_variants_by_ids() (in module civic) groups (civic.Variant property)

H

hgvs_expressions (civic.GeneVariant attribute)

hpo_id (civic.Phenotype attribute) hpo_ids (civic.Assertion property)

I

id (civic.CivicRecord attribute) is_deletion (civic.GeneVariant property) is_insertion (civic.GeneVariant property)

is_valid_for_gks_json() (civic.Assertion method) (civic.Evidence method) iscn_name (civic.RegionVariant attribute)

J

journal (civic.Source attribute)

L

last_reviewed (civic.Approval attribute)

M

model_config (civicpy.exports.civic_gks_record.CivicGksDiagnosticAssertion attribute) (civicpy.exports.civic_gks_record.CivicGksPredictiveAssertion attribute) (civicpy.exports.civic_gks_record.CivicGksPrognosticAssertion attribute) module civic exports molecular_profile (civic.Assertion property) (civic.Evidence property)

molecular_profile_id (civic.Assertion attribute) (civic.Evidence attribute) molecular_profile_score (civic.MolecularProfile attribute) molecular_profiles (civic.Source property) (civic.Variant property) MolecularProfile (class in civic)

N

name (civic.Assertion attribute) (civic.ClinicalTrial attribute) (civic.Disease attribute) (civic.Evidence attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile attribute) (civic.Organization attribute) (civic.Phenotype attribute) (civic.Region attribute) (civic.Therapy attribute) (civic.Variant attribute) (civic.VariantType attribute)

nccn_guideline (civic.Assertion attribute) nccn_guideline_version (civic.Assertion attribute) ncit_id (civic.Factor attribute) (civic.FactorVariant attribute) (civic.Therapy attribute) nct_id (civic.ClinicalTrial attribute)

O

organization (civic.Approval property)

Organization (class in civic) organization_id (civic.Approval attribute)

P

Phenotype (class in civic) phenotype_ids (civic.Assertion attribute) (civic.Evidence attribute) phenotype_url (civic.Phenotype attribute)

phenotypes (civic.Assertion property) (civic.Evidence property) pmc_id (civic.Source attribute) publication_date (civic.Source attribute)

R

rating (civic.Evidence attribute) ready_for_clinvar_submission (civic.Approval attribute) reference_bases (civic.Coordinate attribute) reference_build (civic.Coordinate attribute) (civic.ExonCoordinate attribute)

region (civic.RegionVariant property) Region (class in civic) regions (civic.Source property) RegionVariant (class in civic) representative_transcript (civic.Coordinate attribute) (civic.ExonCoordinate attribute)

S

search_approvals_by_assertion_id() (in module civic) search_approvals_by_organization_id() (in module civic) search_assertions_by_coordinates() (in module civic) search_evidence_by_coordinates() (in module civic) search_fusions_by_partner_gene_id() (in module civic) search_variants_by_allele_registry_id() (in module civic) search_variants_by_coordinates() (in module civic) search_variants_by_hgvs() (in module civic) search_variants_by_name() (in module civic) significance (civic.Assertion attribute) (civic.Evidence attribute) single_variant_molecular_profile (civic.Variant property) single_variant_molecular_profile_id (civic.Variant attribute) site_link (civic.CivicRecord property) so_id (civic.VariantType attribute) source (civic.Evidence property) Source (class in civic) source_id (civic.Evidence attribute) source_ids (civic.MolecularProfile attribute)

source_type (civic.Source attribute) source_url (civic.Source attribute) sources (civic.Factor property) (civic.Fusion property) (civic.Gene property) (civic.MolecularProfile property) (civic.Region property) start (civic.Coordinate attribute) (civic.ExonCoordinate attribute) statement (civic.Evidence property) status (civic.Approval attribute) (civic.Assertion attribute) (civic.Evidence attribute) stop (civic.Coordinate attribute) (civic.ExonCoordinate attribute) strand (civic.ExonCoordinate attribute) subtype (civic.Fusion attribute) (civic.Variant attribute) summary (civic.Assertion attribute) (civic.MolecularProfile property)

T

therapies (civic.Assertion property) (civic.Evidence property) Therapy (class in civic) therapy_ids (civic.Evidence attribute) therapy_interaction_type (civic.Assertion attribute) (civic.Evidence attribute) therapy_url (civic.Therapy attribute)

three_prime_coordinates (civic.FusionVariant attribute) three_prime_gene (civic.Fusion property) three_prime_gene_id (civic.Fusion attribute) three_prime_partner_status (civic.Fusion attribute) title (civic.Source attribute) type (civic.CivicRecord attribute) types (civic.Variant property)

U

update() (civic.CivicRecord method) url (civic.ClinicalTrial attribute) (civic.Organization attribute) (civic.VariantType attribute)

V

Variant (class in civic) variant_aliases (civic.Variant attribute) variant_bases (civic.Coordinate attribute) variant_groups (civic.Variant property) variant_ids (civic.MolecularProfile attribute) variant_origin (civic.Assertion attribute) variant_types (civic.Variant attribute) variants (civic.Assertion property) (civic.Evidence property) (civic.Factor property) (civic.Fusion property) (civic.Gene property) (civic.MolecularProfile property) (civic.Region property)

VariantType (class in civic) vicc_compliant_name (civic.FusionVariant attribute)