Utils

Utility functions for Reactome data-fetch, mappings, and overlay networks in human.

reactome2py.utils.drug_data_source(release='2019', source='drugcentral')

Query a list of drug-target interactions from targetome or drugcentral

Parameters

  • release -- release year for Functional Interactions (FI) data

  • source -- drugcentral or targetome

Returns

json dictionary object

reactome2py.utils.drug_targets(release='2019', drug='Gefitinib', source='drugcentral')

Query known/available drug-target interactions for a drug

Parameters

  • release -- release year for Functional Interactions (FI) data

  • ids -- String of comma separated Gene names (HGNC)

  • source -- drugcentral or targetome

Returns

json dictionary object

reactome2py.utils.ehld_stids()

Retrieves a list of high-level hierarchy pathway with Enhanced High Level Diagrams (EHLD) https://reactome.org/icon-info/ehld-specs-guideline

Returns

list of pathway stIds

reactome2py.utils.gene_mappings()

Maps reactome pathway stId and name to it's associated gene list (HGNC)

Returns

dictionary of reactome pathways and HGNC gene mappings to the pathway.

reactome2py.utils.genelist_drug_target(release='2019', ids='EGFR,ESR1,BRAF', source='drugcentral')

Query drug-target interactions for a gene list from targetome or drugcentral

Parameters

  • release -- release year for Functional Interactions (FI) data

  • ids -- String of comma separated Gene names (HGNC)

  • source -- drugcentral or targetome

Returns

json dictionary object

reactome2py.utils.genelist_fi(release='2019', ids='EGF,EGFR')

Fetch Pathway's genelist Functional Interactions (FI) https://www.ncbi.nlm.nih.gov/pubmed/20482850

Parameters

  • release -- release year for Functional Interactions (FI) data

  • ids -- String of comma separated Gene names (HGNC)

Returns

json dictionary object

reactome2py.utils.pathway_boolean_network(release='2019', stId='R-HSA-177929', pattern='R-HSA-')

Fetch Pathway as a boolean network

Parameters

  • release -- release year for Functional Interactions (FI) data

  • stId -- stable Identifier (stID) of a pathway

  • pattern -- reactome's stable Identifier (stID) string tag for Human "R-HSA-"

Returns

json dictionary object

reactome2py.utils.pathway_drug_target(release='2019', source='drugcentral', pdId='507988', pattern='R-HSA-')

Query drug-target interactions for a PhysicalEntity

Parameters

  • release -- release year for Functional Interactions (FI) data

  • source -- drugcentral or targetome

  • pdId -- stable Identifier (stID) of a pathway

Returns

json dictionary object

reactome2py.utils.pathway_factor_graph(release='2019', stId='R-HSA-177929', pattern='R-HSA-')

Fetch Pathway as a factor graph

Parameters

  • release -- release year for Functional Interactions (FI) data

  • stId -- stable Identifier (stID) of a pathway

  • pattern -- reactome's stable Identifier (stID) string tag for Human "R-HSA-"

Returns

json dictionary object

reactome2py.utils.pathway_fi(release='2019', stId='R-HSA-177929', pattern='R-HSA-')

Fetch Pathway's Functional Interactions (FI) https://www.ncbi.nlm.nih.gov/pubmed/20482850

Parameters

  • release -- release year for Functional Interactions (FI) data

  • stId -- stable Identifier (stID) of a pathway

  • pattern -- reactome's stable Identifier (stID) string tag for Human "R-HSA-"

Returns

json dictionary object

reactome2py.utils.pathway_pe_drug_target(release='2019', source='drugcentral', pdId='507988', peId='1220578', pattern='R-HSA-')

Query drug-target interactions for a Physical Entity ex a complex within a pathway

Parameters

  • release -- release year for Functional Interactions (FI) data

  • source -- drugcentral or targetome

  • pdId -- stable Identifier (stID) of a pathway

  • peId -- stable Identifier (stID) of a PhysicalEntity ex. EGF:Ligand-responsive R-HSA-1220578' within human context

Returns

json dictionary object

reactome2py.utils.sbgn_stids()

Retieves a list of lower-level (with hierarchy) pathways that have SBGNs https://reactome.org/about/news/110-sbgn-files-revamp

Returns

list of pathway stIds