Open Source
Collections:
- Stanford Biomedical Network Dataset Collection [link]
- List of biological databases (WiKi)
- Reactome: human molecular pathways: metabolism, signaling, regulation.
- Recon3D: protein, gene, metabolite, reaction
- Pubchem: chemical information: name, molecular formula, structure, and other identifiers (CID, SMILES, InChi)
- BioPortal: the world’s most comprehensive repository of biomedical ontologies: interaction ontology
- CTD: chemicals, diseases, genes and their interactions and associations
- DrugBank: drug data with comprehensive drug target information
- STITCH: chemical-chemical and chemical-protein networks
- STRING: protein/gene interaction network search and virtualisation
- KEGG: for understanding high-level functions and utilities of the biological system (cell, organism and ecosystem) from molecular-level information.
- CMAP: A Next Generation Connectivity Map: L1000
Python Packages:
- pubchempy: PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
- goatools: Tools for gene ontology
Software:
