Function reference • massdatabase

Request information Request information from the website of database
`request_bigg_model_info()`	Request BIGG model information
`request_bigg_universal_metabolite_info()`	Request BIGG universal metabolite information
`request_bigg_universal_metabolite()`	Request BIGG metabolite
`request_bigg_universal_reaction_info()`	Request BIGG universal reaction information
`request_bigg_universal_reaction()`	Request BIGG reaction
`request_bigg_version()`	Request BIGG version
`request_chebi_compound()`	Request CHEBI compound
`request_foodb_compound_info()`	Request all the food information in FoodB
`request_foodb_compound_ms2()`	Request MS2 spectra of one compound in FoodB
`request_foodb_compound()`	Request one specific the compound information in FoodB
`request_hmdb_metabolite()`	Request one specific the metabolite information in HMDB
`request_kegg_compound_info()`	Request all compound information in KEGG
`request_kegg_compound()`	Request one specific compound information in KEGG
`request_kegg_drug_info()`	Request all drug information in KEGG
`request_kegg_drug()`	Request one specific drug information in KEGG
`request_kegg_rclass_info()`	Request all reaction class information in KEGG
`request_kegg_reaction_info()`	Request all reaction information in KEGG
`request_kegg_rclass()`	Request one specific reaction class information in KEGG
`request_kegg_reaction()`	Request one specific reaction information in KEGG
`request_lipidbank_lipid_class()`	Request Lipidbank database
`request_lipidmaps_lipid()`	Request one lipid information in LIPIDMAPS
`request_wikipedia_compound()`	Request the information of one compound
`request_wikipedia_scientific_classification()`	Request the scientific classification of one species from wikipedia
`request_kegg_pathway_info()`	Request all pathway information in KEGG
`request_kegg_pathway()`	Request one specific pathway information in KEGG
`request_hmdb_reaction()`	Request one specific reaction information in HMDB
`request_bigg_reaction_info()`	Request BIGG reaction information for specific species (model)
`request_foodb_compound_info_crawler()`	Request all the compound information in FooDB based on web crawler
`request_pubchem_compound()`	Request the information of one compound from PubChem
`request_reactome_reaction()`	Request one specific reaction information in Reactome
Download database Download databases
`download_bigg_model()`	Download BIGG model data
`download_bigg_universal_metabolite()`	Download BIGG universal metabolites
`download_chebi_compound()`	Download the CHEBI compound database
`download_foodb_compound()`	Download FOODB compound data
`download_gnps_spectral_library()`	Download GNPS MS2 database (msp)
`download_kegg_compound()`	Download KEGG compound data
`download_kegg_drug()`	Download KEGG drug data
`download_lipidbank_lipid_class()`	Download lIPIDBANK database
`download_lipidmaps_lipid()`	Download LIPIDMAPS data
`download_massbank_compound()`	Download the MassBank compound database
`download_kegg_pathway()`	Download KEGG pathway data
`download_kegg_rclass()`	Download KEGG reaction class database
`download_kegg_reaction()`	Download KEGG reaction database
`download_smpdb_pathway()`	Download SMPDB pathway data
`download_pubchem_compound()`	Request the information of one compound from PubChem
Read downloaded database Read downloaded database
`read_bigg_universal_metabolite()`	Read the BIGG universal metabolite database from download_bigg_universal_metabolite function
`read_chebi_compound()`	Read the CHEBI compound database from download_chebi_compound function
`read_foodb_compound()`	Read the FOODB compound database from download_foodb_compound function
`read_kegg_compound()`	Read the KEGG compound database from download_kegg_compound function
`read_kegg_drug()`	Read the KEGG drug database from download_kegg_drug function
`read_msp_data_gnps()`	read_msp_data_gnps
`read_msp_data_massbank()`	read_msp_data_massbank
`read_msp_data_mona()`	read_msp_data_mona
`read_msp_data_nist()`	read_msp_data_nist
`read_msp_data()`	read_msp_data
`read_sdf_data_lipidmaps()`	Read the sdf database from download_lipidmaps_lipid function
`read_xml_data_hmdb()`	read_xml_data_hmdb
`read_xml_data()`	read_xml_data
`read_kegg_pathway()`	Read the KEGG pathway database from download_kegg_pathway function
`read_smpdb_pathway()`	Read the SMPDB pathway database from download_smpdb_pathway function
`read_bigg_model()`	Read the BIGG model from download_bigg_model function
Convert database to specific format Convert database to specific format
`convert_bigg_universal2metid()`	Convert BIGG universal metabolites (data.frame, from read_bigg_universal_metabolite) to metID format database
`convert_chebi2metid()`	Convert BIGG universal metabolites (data.frame, from read_chebi_metabolite) to metID format database
`convert_foodb2metid()`	Convert FOODB compound data (list, from download_foodb_compound function) to metID format database
`convert_gnps2metid()`	Convert GNPS data (list) to metID format database
`convert_hmdb2metid()`	Convert HMDB data (MS1 or MS2) to metID format database
`convert_kegg2metid()`	Convert KEGG compound/drug data (data.frame, from read_kegg_compound or read_kegg_drug function) to metID format database
`convert_lipidbank2metid()`	Convert lipid bank data (data.frame) to metID format database
`convert_lipidmaps2metid()`	Convert LIPIDMAPS compound data (list, from read_sdf_data_lipidmaps function) to metID format database
`convert_massbank2metid_nist()`	Convert MassBank data (list, from NIST) to metID format database
`convert_massbank2metid_riken()`	Convert MassBank data (list, from RIKEN) to metID format database
`convert_massbank2metid()`	Convert MassBank data (list) to metID format database
`convert_mona2metid()`	Convert MoNA data (list) to metID format database
`convert_nist2metid()`	Convert GNPS data (list) to metID format database
`convert_kegg2metpath()`	Convert KEGG pathway data (list, from read_kegg_pathway function) to metpath format database
`convert_smpdb2metpath()`	Convert smpdb pathway data (list, from read_smpdb_pathway function) to metpath format database
Data Some data embed in massdatabase
`match_table`	match_table
`smpdb_primary_pathway_id`	smpdb_primary_pathway_id
Other functions Other usefull functions in massdatabase
`get_words_similarity()`	Get the similarity between two words
`convert_species2source()`	Convert species to source
`massdatabase_logo()`	Show the base information of massdatabase pacakge
`search_hmdb_database()`	Search metabolite in HMDB
`show_progresser()`	show_progresser
`parse_pubchem_compound()`	Parse the json or xml compound data from PubChem
`read_gpml()`	Read GPML format data from wikipathway database
`massdatabase_packages()` `massdatabase_packages()`	List all packages in the massdatabase
`parse_reactome_reaction()`	Parse the sbml reaction data from Reactome

Reference

Request information

Download database

Read downloaded database

Convert database to specific format

Data

Other functions