vignettes/download_functions.Rmd
download_functions.Rmd“Download functions” is series functions that could be used to download online databases.
BIGG modelis a knowledge base of genome-scale metabolic network reconstructions.
Download the BIGG model data
download_bigg_model(model_id = "iND750")Download the BIGG universal metabolite database
download_bigg_universal_metabolite(path = ".", sleep = 1)Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
Download ChEBI compound database
download_chebi_compound(path = ".")FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology.
Download the FooDB compound database
download_foodb_compound(compound_id = "all", path = ".")The GNPS GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.
Download one GNPS compound database
download_gnps_spectral_library(gnps_library = "HMDB", path = ".")KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
Download KEGG compound database
download_kegg_compound(path = ".")Download KEGG pathway database
download_kegg_pathway(path = ".", organism = "hsa")Download KEGG reaction class database
Download KEGG drug database
download_kegg_drug(path = ".")The official database of Japanese Conference on the Biochemistry of Lipids (JCBL). Link
Download the LipidBank lipid class database.
download_lipidbank_lipid_class(lipid_class = "Acylglycerol", path = ".")LIPID MAPS Lipidomics Gateway was created in 2003 via an NIH “Glue Grant” to provide access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community.
Download lipidmaps database
download_lipidmaps_lipid(path = ".")MassBank is a community effort and you are invited to contribute. Please refer to our contributor documentation and get in touch via github or email.
Download MassBnak compound database.
download_massbank_compound(source = "nist")SMPDB is an interactive, visual database containing more than 30000 small molecule pathways found in humans only.
Download SMPDB pathway database.
download_smpdb_pathway(path = ".")
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