paxtoolsr

paxtoolsr accesses BioPAX OWL files and queries the Pathway Commons molecular interaction database to extract, merge, validate, and integrate pathway data for pathway analysis and systems biology workflows in R.

Key Features:

• BioPAX Format Interaction: Extracts, merges, and validates pathway data encoded in BioPAX and BioPAX OWL files.
• Pathway Commons Integration: Queries the Pathway Commons webservice to retrieve molecular interaction data aggregated from BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, and TRANSFAC.
• Novel Pathway Datasets: Accesses novel and updated pathway datasets available via Pathway Commons queries.
• Advanced Querying Features: Supports extraction of specific data elements from Pathway Commons responses and integration of those results with local BioPAX datasets.

Scientific Applications:

• Data Integration: Combines molecular interaction data from multiple databases and local BioPAX files into unified pathway representations.
• Pathway Analysis: Enables analysis of molecular interactions and pathway structures represented in BioPAX.
• Gene Set Enrichment Analysis: Facilitates generation of gene sets from pathway data for gene set enrichment analysis.

Methodology:

Extraction, merging, and validation of BioPAX OWL files; querying the Pathway Commons webservice to retrieve molecular interaction data from the listed databases; and integration of retrieved data with local BioPAX datasets.