The civic module

CIViCpy is primarily designed to enable exploration of the content of CIViC through Python CivicRecord objects. While these record objects can be initialized independently, the civic module also provides several routines for getting records directly from CIViC. Use of these routines is recommended.

The civic module may be imported from civicpy at the top level:

>>>from civicpy import civic

CIViC records

class civic.CivicRecord(partial=False, **kwargs)

As a base class, CivicRecord is used to define the characteristic of all records in CIViC. This class is not intended to be invoked directly by the end user, but provided for documentation of shared methods and variables in child classes.

__init__(partial=False, **kwargs)

The record object may be initialized by the user, though the practice is discouraged. To do so, values for each of the object attributes (except type) must be specified as keyword arguments, or the partial parameter must be set to True. If partial is set to True, the id keyword argument is still required.

Users are encouraged to use the functions for getting records in lieu of directly initializing record objects.

Parameters

partial (bool) – Indicates whether the the set of object attributes passed is incomplete. If set to True the id keyword is required.

type

The type of record. This field is set automatically by child classes and should not be changed.

id

The record ID. This is set on initialization using the id keyword argument, and reflects the primary ID for the record as stored in CIViC.

property site_link

Returns a URL to the record on the CIViC web application.

update(allow_partial=True, force=False, **kwargs)

Updates the record object from the cache or the server. Keyword arguments may be passed to kwargs, which will update the corresponding attributes of the CivicRecord instance.

Parameters

• allow_partial (bool) – Flag to indicate whether the record will be updated according to the contents of CACHe, without requiring all attributes to be assigned.

• force (bool) – Flag to indicate whether to force an update fromt he server, even if a full record ecists in the cache.

Returns

True if record is complete after update, else False.

CIViC record types

The primary CIViC records are found on the CIViC advanced search page, and are fully-formed

class civic.Gene(**kwargs)

description

A curated summary of the clinical significance of this gene.

entrez_id

The Entrez ID associated with this gene.

name

The HGNC Gene Symbol associated with this gene.

aliases

A list of alternate gene symbols by which this gene is referenced.

variants

A list of Variant records associated with this gene.

class civic.Variant(**kwargs)

allele_registry_id

The allele registry id associated with this variant.

civic_actionability_score

The CIViC actionability score associated with this variant.

description

A curated summary of the clinical significance of this variant.

entrez_id

The Entrez ID of the gene this variant belongs to.

entrez_name

The HGNC Gene Symbol of the gene this variant belongs to.

gene

The Gene this variant belongs to.

gene_id

The CivicRecord.id of the gene this variant belongs to.

name

The curated name given to this variant.

assertions

A list of Assertion records associated with this variant.

clinvar_entries

A list of clinvar ids associated with this variant.

coordinates

A CivicAttribute object describing CIViC coordinates.

evidence_items

evidence

A list of Evidence associated with this variant.

evidence_sources

A list of sources associated with the evidence from this variant.

hgvs_expressions

Curated HGVS expressions describing this variant.

sources

A list of sources objects associated with the variant description.

variant_aliases

aliases

A curated list of aliases by which this variant is referenced.

variant_groups

groups

A list of variant groups to which this variant belongs.

variant_types

types

A list of CivicAttribute objects describing variant types from the Sequence Ontology.

class civic.Evidence(**kwargs)

class civic.Assertion(partial=False, **kwargs)

CIViC attributes

The CivicAttribute class is a special type of CivicRecord that is not indexed, and is used as a base container class for additional complex records beyond those mentioned above (e.g. diseases, drugs). CivicAttributes are not cached except as attached objects to non-CivicAttribute CivicRecord objects, and cannot be retrieved independently.

class CivicAttribute

Getting records

Records can be obtained by ID through a collection of functions provided in the civic module. Gene objects can be queried by the following methods:

civic.get_gene_by_id(gene_id)

Parameters

gene_id (int) – A single CIViC gene ID.

Returns

A Gene object.

civic.get_genes_by_ids(gene_id_list)

Parameters

gene_id_list (list) – A list of CIViC gene IDs to query against to cache and (as needed) CIViC.

Returns

A list of Gene objects.

civic.get_all_genes(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True)

Queries CIViC for all genes. The cache is not considered by this function.

Parameters

• include_status (list) – A list of statuses. Only genes and their associated entities matching the given statuses will be returned.

• allow_cached (bool) – Indicates whether or not object retrieval from CACHE is allowed. If False it will query the CIViC database directly.

Returns

A list of Gene objects.

civic.get_all_gene_ids()

Queries CIViC for a list of all gene IDs. Useful for passing to get_genes_by_ids() to first check cache for any previously queried genes.

Returns

A list of all CIViC gene IDs.

Analogous methods exist for Variant, Assertion, and Evidence:

civic.get_variants_by_ids(variant_id_list)

civic.get_variant_by_id(variant_id)

civic.get_all_variants(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True)

civic.get_all_variant_ids()

civic.get_assertions_by_ids(assertion_id_list=[], get_all=False)

civic.get_assertion_by_id(assertion_id)

civic.get_all_assertions(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True)

civic.get_all_assertion_ids()

civic.get_all_evidence(include_status=['accepted', 'submitted', 'rejected'], allow_cached=True)

civic.get_all_evidence_ids()