Query¶

Examples¶

For most of the string parameters you can use % as wildcard (please check the documentation below). All methods have a parameter limit which allows to limit the number of results.

Methods¶

>>> import pyctd
>>> q = pyctd.query()
>>> q.get_diseases(disease_id='MESH:D000544', definition='%degenerative%')
>>> q.get_genes(gene_symbol='TSP_15922', uniprot_id='E5T972')
>>> q.get_pathways(pathway_name='%bla')
>>> q.get_chemicals(chemical_name='Alz%')
>>> q.get_chem_gene_interaction_action(organism_id='9606', gene_symbol='APP')
>>> q.get_gene__diseases(limit=10)

Properties¶

>>> import pyctd
>>> q = pyctd.query()
>>> q.gene_forms
>>> q.interaction_actions
>>> q.actions
>>> q.pathways

Query Manager Reference¶

class pyctd.manager.query.QueryManager(connection=None, echo=False)[source]¶

Query interface to database.

Parameters:	connection (str) – SQLAlchemy echo (bool) – True or False for SQL output of SQLAlchemy engine

actions¶

Gets the list of allowed actions

Return type:	list[str]

direct_evidences¶

Returns:	All available direct evidences for gene disease correlations
Return type:	list

gene_forms¶

Returns:	List of strings for all available gene forms
Return type:	list[str]

get_action(limit=None, as_df=False)[source]¶

Parameters:	limit – as_df –
Returns:

get_chem_gene_interaction_actions(gene_name=None, gene_symbol=None, gene_id=None, limit=None, cas_rn=None, chemical_id=None, chemical_name=None, organism_id=None, interaction_sentence=None, chemical_definition=None, gene_form=None, interaction_action=None, as_df=False)[source]¶

Get all interactions for chemicals on a gene or biological entity (linked to this gene).

Chemicals can interact on different types of biological entities linked to a gene. A list of allowed entities linked to a gene can be retrieved via the attribute gene_forms.

Interactions are classified by a combination of interaction (‘affects’, ‘decreases’, ‘increases’) and actions (‘activity’, ‘expression’, ... ). A complete list of all allowed interaction_actions can be retrieved via the attribute interaction_actions.

Parameters:

as_df (bool) – if set to True result returns as pandas.DataFrame
interaction_sentence (str) – sentence describing the interactions
organism_id (int) – NCBI TaxTree identifier. Example: 9606 for Human.
chemical_name (str) – chemical name
chemical_id (str) – chemical identifier
cas_rn (str) – CAS registry number
chemical_definition (str) –
gene_symbol (str) – HGNC gene symbol
gene_name (str) – gene name
gene_id (int) – NCBI Entrez Gene identifier
gene_form (str) – gene form
interaction_action (str) – combination of interaction and actions
limit (int) – maximum number of results

Return type:

list[models.ChemGeneIxn]

See also

pyctd.manager.models.ChemGeneIxn

which is linked to: pyctd.manager.models.Chemical pyctd.manager.models.Gene pyctd.manager.models.ChemGeneIxnPubmed

Available interaction_actions and gene_forms pyctd.manager.database.Query.interaction_actions() pyctd.manager.database.Query.gene_forms()

get_chemical(chemical_name=None, chemical_id=None, cas_rn=None, drugbank_id=None, parent_id=None, parent_tree_number=None, tree_number=None, synonym=None, limit=None, as_df=False)[source]¶

Get chemical

Parameters:

as_df (bool) – if set to True result returns as pandas.DataFrame
chemical_name (str) – chemical name
chemical_id (str) – cehmical identifier
cas_rn (str) – CAS registry number
drugbank_id (str) – DrugBank identifier
parent_id (str) – identifiers of the parent terms
parent_tree_number (str) – identifiers of the parent nodes
tree_number (str) – identifiers of the chemical’s nodes
synonym (str) – chemical synonym
limit (int) – maximum number of results

Returns:

list of pyctd.manager.models.Chemical objects

See also

pyctd.manager.models.Chemical

get_chemical__by__disease(disease_name, limit=None, as_df=False)[source]¶

Parameters:	disease_name – limit – as_df –
Returns:

get_chemical_diseases(direct_evidence=None, inference_gene_symbol=None, inference_score=None, inference_score_operator=None, cas_rn=None, chemical_name=None, chemical_id=None, chemical_definition=None, disease_definition=None, disease_id=None, disease_name=None, limit=None, as_df=False)[source]¶

Get chemical–disease associations with inference gene

Parameters:

direct_evidence – direct evidence
inference_gene_symbol – inference gene symbol
inference_score – inference score
inference_score_operator – inference score operator
cas_rn –
chemical_name – chemical name
chemical_id –
chemical_definition –
disease_definition –
disease_id –
disease_name – disease name
limit (int) – maximum number of results
as_df (bool) – if set to True result returns as pandas.DataFrame

Returns:

list of pyctd.manager.database.models.ChemicalDisease objects

See also

pyctd.manager.models.ChemicalDisease

which is linked to: pyctd.manager.models.Disease pyctd.manager.models.Chemical

get_disease(disease_name=None, disease_id=None, definition=None, parent_ids=None, tree_numbers=None, parent_tree_numbers=None, slim_mapping=None, synonym=None, alt_disease_id=None, limit=None, as_df=False)[source]¶

Get diseases

Parameters:

as_df (bool) – if set to True result returns as pandas.DataFrame
limit (int) – maximum number of results
disease_name (str) – disease name
disease_id (str) – disease identifier
definition (str) – definition of disease
parent_ids (str) – parent identifiers, delimiter |
tree_numbers (str) – tree numbers, delimiter |
parent_tree_numbers (str) – parent tree numbers, delimiter
slim_mapping (str) – term derived from the MeSH tree structure for the “Diseases” [C] branch, that classifies MEDIC diseases into high-level categories
synonym (str) – disease synonyms
alt_disease_id (str) – alternative disease identifiers

Returns:

list of pyctd.manager.models.Disease object

See also

pyctd.manager.models.Disease

Todo

normalize parent_ids, tree_numbers and parent_tree_numbers in pyctd.manager.models.Disease

get_disease_pathways(disease_id=None, disease_name=None, pathway_id=None, pathway_name=None, disease_definition=None, limit=None, as_df=False)[source]¶

Get disease pathway link

Parameters:	as_df (bool) – if set to True result returns as pandas.DataFrame disease_id – disease_name – pathway_id – pathway_name – disease_definition – limit (int) – maximum number of results
Returns:	list of `pyctd.manager.database.models.DiseasePathway` objects

See also

pyctd.manager.models.DiseasePathway

which is linked to: pyctd.manager.models.Disease pyctd.manager.models.Pathway

get_gene(gene_name=None, gene_symbol=None, gene_id=None, synonym=None, uniprot_id=None, pharmgkb_id=None, biogrid_id=None, alt_gene_id=None, limit=None, as_df=False)[source]¶

Get genes

Parameters:

as_df (bool) – if set to True result returns as pandas.DataFrame
alt_gene_id –
gene_name (str) – gene name
gene_symbol (str) – HGNC gene symbol
gene_id (int) – NCBI Entrez Gene identifier
synonym (str) – Synonym
uniprot_id (str) – UniProt primary accession number
pharmgkb_id (str) – PharmGKB identifier
biogrid_id (int) – BioGRID identifier
limit (int) – maximum of results

Return type:

list[models.Gene]

get_gene_disease(direct_evidence=None, inference_chemical_name=None, inference_score=None, gene_name=None, gene_symbol=None, gene_id=None, disease_name=None, disease_id=None, disease_definition=None, limit=None, as_df=False)[source]¶

Get gene–disease associations

Parameters:

as_df (bool) – if set to True result returns as pandas.DataFrame
gene_id (int) – gene identifier
gene_symbol (str) – gene symbol
gene_name (str) – gene name
direct_evidence (str) – direct evidence
inference_chemical_name (str) – inference_chemical_name
inference_score (float) – inference score
inference_chemical_name – chemical name
disease_name – disease name
disease_id – disease identifier
disease_definition – disease definition
limit (int) – maximum number of results

Returns:

list of pyctd.manager.database.models.GeneDisease objects

See also

pyctd.manager.models.GeneDisease

which is linked to: pyctd.manager.models.Chemical pyctd.manager.models.Gene

get_gene_pathways(gene_name=None, gene_symbol=None, gene_id=None, pathway_id=None, pathway_name=None, limit=None, as_df=False)[source]¶

Get gene pathway link

Parameters:	as_df (bool) – if set to True result returns as pandas.DataFrame gene_name (str) – gene name gene_symbol (str) – gene symbol gene_id (int) – NCBI Gene identifier pathway_id – pathway_name (str) – pathway name limit (int) – maximum number of results
Returns:	list of `pyctd.manager.database.models.GenePathway` objects

See also

pyctd.manager.models.GenePathway

which is linked to: pyctd.manager.models.Gene pyctd.manager.models.Pathway

get_go_enriched__by__chemical_name(chemical_name, limit=None, as_df=False)[source]¶

Parameters:	chemical_name – limit – as_df –
Returns:

get_marker_chemical__by__disease_name(disease_name, limit=None, as_df=False)[source]¶

Parameters:	disease_name – limit – as_df –
Returns:

get_pathway(pathway_name=None, pathway_id=None, limit=None, as_df=False)[source]¶

Get pathway

Note

Format of pathway_id is KEGG:X* or REACTOME:X* . X* stands for a sequence of digits

Parameters:	as_df (bool) – if set to True result returns as pandas.DataFrame pathway_name (str) – pathway name pathway_id (str) – KEGG or REACTOME identifier limit (int) – maximum number of results
Returns:	list of `pyctd.manager.models.Pathway` objects

See also

pyctd.manager.models.Pathway

get_pathway_enriched__by__chemical_name(chemical_name, limit=None, as_df=False)[source]¶

Parameters:	chemical_name – limit – as_df –
Returns:

get_therapeutic_chemical__by__disease_name(disease_name, limit=None, as_df=False)[source]¶

Get therapeutic chemical by disease name

Parameters:	as_df (bool) – if set to True result returns as pandas.DataFrame limit (int) – maximum number of results disease_name (str) – disease name
Returns:	therapeutic chemical
Return type:	list[models.ChemicalDisease]

interaction_actions¶

Returns:	List of strings for allowed interaction/actions combinations
Return type:	list[str]

pathways¶

Get all pathways

Return type:	list[models.Pathway]