Index

_

__init__() (civic.CivicRecord method)

A

abstract (civic.Source attribute) acmg_codes (civic.Assertion attribute) addrecord() (exports.VCFWriter method) addrecords() (exports.VCFWriter method) aliases (civic.Disease attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile attribute) (civic.Therapy attribute) (civic.Variant property) allele_registry_id (civic.GeneVariant attribute)

amp_level (civic.Assertion attribute) asco_abstract_id (civic.Source attribute) Assertion (class in civic) assertion_direction (civic.Assertion 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

citation (civic.Source attribute) citation_id (civic.Source attribute) civic module CivicAttribute (class in civic)

CivicRecord (class in civic) clingen_codes (civic.Assertion attribute) clinical_trials (civic.Source attribute) clinvar_entries (civic.GeneVariant attribute) CoordinateQuery (class in civic) coordinates (civic.GeneVariant attribute)

D

description (civic.Assertion attribute) (civic.Evidence attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile 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

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) 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) 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_assertions() (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_phenotypes() (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_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_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_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_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_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)

J

journal (civic.Source attribute)

M

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.Disease attribute) (civic.Evidence attribute) (civic.Factor attribute) (civic.Fusion attribute) (civic.Gene attribute) (civic.MolecularProfile attribute) (civic.Phenotype attribute) (civic.Therapy attribute) (civic.Variant attribute)

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

S

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) 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) statement (civic.Evidence property) status (civic.Assertion attribute) (civic.Evidence 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)

V

Variant (class in civic) variant_aliases (civic.Variant attribute) variant_groups (civic.Variant property) variant_ids (civic.MolecularProfile attribute) variant_origin (civic.Assertion attribute) variant_types (civic.Variant attribute)

variants (civic.Factor property) (civic.Fusion property) (civic.Gene property) (civic.MolecularProfile property) VCFWriter (class in exports) vicc_compliant_name (civic.FusionVariant attribute)

W

writeheader() (exports.VCFWriter method)

writerecords() (exports.VCFWriter method)