| Type: | Package |
| Title: | Lipid Maps Rest Service |
| Version: | 1.0.4 |
| Date: | 2022-06-17 |
| Depends: | R (≥ 4.2.0) |
| Imports: | httr (≥ 1.3.1), RJSONIO (≥ 1.3-0) |
| Description: | Lipid Maps Rest service. Researchers can access the Lipid Maps Rest service programmatically and conveniently integrate it into the current workflow or packages. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.0 |
| NeedsCompilation: | no |
| Packaged: | 2022-06-24 23:22:21 UTC; liyao |
| Author: | Mingzhuo Tian [aut, cre], Yaoxiang Li [ctb], Amrita Cheema [ctb] |
| Maintainer: | Mingzhuo Tian <tianmingzhuo@outlook.com> |
| Repository: | CRAN |
| Date/Publication: | 2022-06-27 07:30:02 UTC |
A function for compound search
Description
A function for compound search
Usage
compound_search(
input_item = "lm_id",
input_value,
output_item,
output_format = ""
)
Arguments
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" |
Value
The search results
Author(s)
Mingzhuo Tian tianmingzhuo@outlook.com License: GPL (>= 3)
Examples
# 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
Description
A function for Gene search
Usage
gene_search(
input_item = "lmp_id",
input_value,
output_item,
output_format = ""
)
Arguments
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" |
Value
The search results
Author(s)
Mingzhuo Tian tianmingzhuo@outlook.com License: GPL (>= 3)
Examples
# 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
Description
A function for Protein search
Usage
protein_search(input_item, input_value, output_item, output_format = "")
Arguments
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" |
Value
The search results
Author(s)
Mingzhuo Tian tianmingzhuo@outlook.com License: GPL (>= 3)
Examples
# 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")