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

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")

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")

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")