| Title: | Lipid Maps Rest Service |
|---|---|
| Description: | Lipid Maps Rest service. Researchers can access the Lipid Maps Rest service programmatically and conveniently integrate it into the current workflow or packages. |
| Authors: | Mingzhuo Tian [aut, cre], Yaoxiang Li [ctb], Amrita Cheema [ctb] |
| Maintainer: | Mingzhuo Tian <[email protected]> |
| License: | GPL-3 |
| Version: | 1.0.4 |
| Built: | 2025-03-13 03:00:15 UTC |
| Source: | https://github.com/cran/lipidmapsR |
A function for compound search
compound_search( input_item = "lm_id", input_value, output_item, output_format = "" )compound_search( input_item = "lm_id", input_value, output_item, output_format = "" )
input_item |
choose input item from the following options: "lm_id", "formula","inchi_key","pubchem_cid","hmdb_id","kegg_id","chebi_id","smiles","abbrev","abbrev_chains" |
input_value |
input the value you want to search |
output_item |
select your output from following options:"all","classification","lm_id","name","sys_name","synonyms","core","main_class","sub_class","class_level4","exactmass","formula","inchi","inchi_key","kegg_id","hmdb_id","chebi_id","lipidbank_id","pubchem_cid","smiles","molfile","structure","physchem" |
output_format |
select your output format from following options: "json (default)","text" |
The search results
Mingzhuo Tian [email protected] License: GPL (>= 3)
# Fetch compound name from LM_ID compound_search("lm_id", "LMFA01010001", "name") # Fetch all compound fields from LM_ID compound_search("lm_id", "LMFA01010001", "all") # Fetch all compound fields as text from LM_ID compound_search("lm_id", "LMFA01010001", "all", "txt") # Fetch compound smiles from PubChem CID compound_search("pubchem_cid", "985", "smiles") # Fetch compound sytematic name from inchi key compound_search("inchi_key", "IPCSVZSSVZVIGE-UHFFFAOYSA-N", "sys_name") # Fetch compound physicochemical properties from inchi key compound_search("inchi_key", "IPCSVZSSVZVIGE-UHFFFAOYSA-N", "physchem") # Fetch all compound fields from formula (multiple records) compound_search("formula", "C20H34O", "all") # Fetch compound classification hierarchy from PubChem CID compound_search("pubchem_cid", "985", "classification") # Fetch all compound fields from bulk abbreviation compound_search("abbrev", "PA(38:0)", "all") # Fetch all compound fields from chain abbreviation compound_search("abbrev_chains", "PC(16:0_18:0)", "all")# Fetch compound name from LM_ID compound_search("lm_id", "LMFA01010001", "name") # Fetch all compound fields from LM_ID compound_search("lm_id", "LMFA01010001", "all") # Fetch all compound fields as text from LM_ID compound_search("lm_id", "LMFA01010001", "all", "txt") # Fetch compound smiles from PubChem CID compound_search("pubchem_cid", "985", "smiles") # Fetch compound sytematic name from inchi key compound_search("inchi_key", "IPCSVZSSVZVIGE-UHFFFAOYSA-N", "sys_name") # Fetch compound physicochemical properties from inchi key compound_search("inchi_key", "IPCSVZSSVZVIGE-UHFFFAOYSA-N", "physchem") # Fetch all compound fields from formula (multiple records) compound_search("formula", "C20H34O", "all") # Fetch compound classification hierarchy from PubChem CID compound_search("pubchem_cid", "985", "classification") # Fetch all compound fields from bulk abbreviation compound_search("abbrev", "PA(38:0)", "all") # Fetch all compound fields from chain abbreviation compound_search("abbrev_chains", "PC(16:0_18:0)", "all")
A function for Gene search
gene_search( input_item = "lmp_id", input_value, output_item, output_format = "" )gene_search( input_item = "lmp_id", input_value, output_item, output_format = "" )
input_item |
choose input item from the following options: "lm_id", "formula","inchi_key","pubchem_cid","hmdb_id","kegg_id","chebi_id","smiles","abbrev","abbrev_chains" |
input_value |
input the value you want to search |
output_item |
select your output from following options:"all","classification","lm_id","name","sys_name","synonyms","core","main_class","sub_class","class_level4","exactmass","formula","inchi","inchi_key","kegg_id","hmdb_id","chebi_id","lipidbank_id","pubchem_cid","smiles","molfile","structure","physchem" |
output_format |
select your output format from following options: "json (default)","text" |
The search results
Mingzhuo Tian [email protected] License: GPL (>= 3)
# Fetch all gene fields from gene symbol gene_search("gene_symbol", "acaca", "all") # Fetch gene name from Entrez gene id gene_search("gene_id", "31", "gene_name")# Fetch all gene fields from gene symbol gene_search("gene_symbol", "acaca", "all") # Fetch gene name from Entrez gene id gene_search("gene_id", "31", "gene_name")
A function for Protein search
protein_search(input_item, input_value, output_item, output_format = "")protein_search(input_item, input_value, output_item, output_format = "")
input_item |
choose input item from the following options: "lm_id", "formula","inchi_key","pubchem_cid","hmdb_id","kegg_id","chebi_id","smiles","abbrev","abbrev_chains" |
input_value |
input the value you want to search |
output_item |
select your output from following options:"all","classification","lm_id","name","sys_name","synonyms","core","main_class","sub_class","class_level4","exactmass","formula","inchi","inchi_key","kegg_id","hmdb_id","chebi_id","lipidbank_id","pubchem_cid","smiles","molfile","structure","physchem" |
output_format |
select your output format from following options: "json (default)","text" |
The search results
Mingzhuo Tian [email protected] License: GPL (>= 3)
# Fetch all protein fields from UniProt id protein_search("uniprot_id", "Q13085", "all") # Fetch all protein fields from Entrez gene id protein_search("gene_id", "19", "all") # Fetch mRNA id from protein Refseq id protein_search("refseq_id", "NP_005493", "mrna_id")# Fetch all protein fields from UniProt id protein_search("uniprot_id", "Q13085", "all") # Fetch all protein fields from Entrez gene id protein_search("gene_id", "19", "all") # Fetch mRNA id from protein Refseq id protein_search("refseq_id", "NP_005493", "mrna_id")