Command Line Access to Structure Database (LMSD)

Programmatic Access

We provide support for command line data retrieval as CSV, TSV, and SDF files for any search type that can be performed via a web browser. Options are available to control display of column headers, types of delimiters for CSV files (comma or semicolon), and double quoting of values.

Two command line scripts are available to search and retrieve LMSD data: LMSDRecord.php and LMSDSearch.php

The LMSDRecord.php script supports retrieval of detailed information for a specific lipid with a valid LMID as CSV/TSV or SD file. The LMSDSearch.php is provided to search LMSD using a variety of parameters specified in a user query and retrieve the data for those LMSD records which match the query. The usage details and examples for these two scripts are provided in the following two sections.

LMSDRecord.php script

Available parameters

All parameters are case sensitive.

Common parameters to control CSV, TSV, SDF, and MDLMOL output

Parameter	Possible values	Default	Comments
Mode	File or Download	File	Must be set to eliminate html
OutputType	TSV, CSV, SDF, MDLMOL	MDLMOL	TSV=tab separated values CSV=comma or semicolon separated values SDF=Structure Data File MDLMOL=Mol Structure Data File
OutputDelimiter	For TSV: Tab For CSV: Comma or Semicolon	Comma
OutputQuote	Yes,No	No
OutputColumnHeader	Yes,No	Yes

Examples

Note: Updated URLs October 2021

Please note that the following examples are meant to be typed on one line.

wget -O "LMFA08040013.mol" "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=mdlmol"
returns a MDLMOL file for LMID LMFA08040013

wget -O "LMFA08040013.sdf" "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=sdf"
returns a SDF file for LMID LMFA08040013

wget -O "LMFA08040013.csv" "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=csv"
returns a CSV file for LMID LMFA08040013 with double quotes around column values

wget -O "LMFA08040013.tsv" "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv"
returns a TSV file for LMID LMFA08040013

LMSDSearch.php script

Available parameters

All parameters are case sensitive.

Common parameters to control CSV, TSV, and SDF output

Parameter	Possible values	Default	Comments
OutputMode	File	File	Must be set to eliminate html
OutputType	TSV, CSV, SDF	TSV	TSV=tab separated values CSV=comma or semicolon separated values SDF=Structure Data File
OutputDelimiter	For TSV: Tab For CSV: Comma or Semicolon	Comma
OutputQuote	Yes,No	No
OutputColumnHeader	Yes,No	Yes

Mode parameter

For command-line data retrieveal, the Mode parameter must be set to one of:

  Mode=ProcessStrSearch
  Mode=ProcessTextSearch
  Mode=ProcessTextOntologySearch

When used with no other parameters, the following will all return the entire LMSD:

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File"

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=SDF"

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=CSV&OutputColumnHeader=Yes"

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File"

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextOntologySearch&OutputMode=File"

Optional Parameters for `mode=ProcessStrSearch`

(Structure-based search)

Parameter	Possible values	Example	Default
LMID	any	LMSL02000001	none
Name	any	acetic	none
Formula	any	C110H202N2O39P2	none
SearchType	SubStructure,ExactMatch	ExactMatch	SubStructure
SMILESString	aNY VAlid SMILES string	c1ccccc1	none

Examples:

Please note that the following examples are meant to be typed on one line and that results for these examples may change as more records are added to the database, or if any changes are made to the existing records.

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001"

wget -O "Test.tsv" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&SearchType=SubStructure&SMILESString=c1ccccc1"

Web interfaces for Structure-based searches can be found at:
http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=SetupStrSearch

Optional Parameters for `Mode=ProcessTextSearch` or `mode=ProcessTextOntologySearch`

(Text-based or Text/ontology -based searches)

Parameter	Possible values	Example	Default
LMID	any LM_ID	LMSL02000001	none
Name	any part of any common name	fat	none
Formula	any formula	CHO2	none
ExactMass	any positive number	45	none
ExactMassOffSet	any positive number	5	none
CoreClass	1=Fatty Acyls [FA] 2=Glycerolipids [GL] 3=Glycerophospholipids [GP] 4=Sphingolipids [SP] 5=Sterol Lipids [ST] 6=Prenol Lipids [PR] 7=Saccharolipids [SL] 8=Polyketides [PK]	1	none
MainClass	e.g.: FA10=101 FA11=111 ST05=505	101	none
SubClass	e.g.: ST0402=50402	50402	none

Examples:

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&CoreClass=1"

returns all Fatty acids

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&CoreClass=1&MainClass=101&SubClass=10101"

returns all Straight chain fatty acids [FA0101]

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextOntologySearch&OutputMode=File&CoreClass=1&MainClass=101&SubClass=10101"

returns all Straight chain fatty acids [FA0101]

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&SubClass=10101"

returns all Straight chain fatty acids [FA0101]

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&CoreClass=2&MainClass=202&SubClass=20201&ExactMass=594&ExactMassOffSet=10"

returns all Diacylglycerols [GL0201] with mass between 584.00 and 604.00

wget -O "Test.tsv" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&OutputType=TSV&OutputQuote=Yes&Name=acetic"

"
returns all lipids whose common name contains 'acetic', tab-delimited with values quoted

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputMode=File&CoreClass=1&MainClass=101&SubClass=10101&ExactMass=45&ExactMassOffSet=1&Name=fat"

returns one record: LM_ID=LMFA01010000, Common Name=fatty acid

Additional parameters for ProcessTextOntologySearch mode

Up to four set of triplets - OntologyParamName, OntologyParamModifier, and OntologyParamValue - to control the ontology search. The name of the parameters are generated by appended a integer value from 1 to 4 to each set of the four set of names triplets. For example:

Parameter	Possible values	Example	Default
OntologyParamName1	carbons, doublebonds, triplebonds, rings, OH, NH2, OOH, ketones, epoxides, COOH, methyls, SH, Br, Cl, F, Methylenes, CHO, OMe, OAc, COOMe, Ester, Ether	carbons	none
OntologyParamModifier1	eq, ge, le	le	none
OntologyParamValue1	any valid number	20	none
OntologyParamName2	carbons, doublebonds, triplebonds, rings, OH, NH2, OOH, ketones, epoxides, COOH, methyls, SH, Br, Cl, F, Methylenes, CHO, OMe, OAc, COOMe, Ester, Ether	carbons	none
OntologyParamModifier2	eq, ge, le	le	none
OntologyParamValue2	any valid number	20	none
OntologyParamName3	carbons, doublebonds, triplebonds, rings, OH, NH2, OOH, ketones, epoxides, COOH, methyls, SH, Br, Cl, F, Methylenes, CHO, OMe, OAc, COOMe, Ester, Ether	carbons	none
OntologyParamModifier3	eq, ge, le	le	none
OntologyParamValue3	any valid number	20	none
OntologyParamName4	carbons, doublebonds, triplebonds, rings, OH, NH2, OOH, ketones, epoxides, COOH, methyls, SH, Br, Cl, F, Methylenes, CHO, OMe, OAc, COOMe, Ester, Ether	carbons	none
OntologyParamModifier4	eq, ge, le	le	none
OntologyParamValue4	any valid number	20	none

Examples:

wget -O "Test" "http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextOntologySearch&OutputMode=File&OntologyParamName1=carbons&OntologyParamModifier1=eq&OntologyParamValue1=20&OntologyParamName2=doublebonds&OntologyParamModifier2=eq&OntologyParamValue2=1"

returns a list of mostly fatty acids, with some glycerophospholipids

Web interfaces for Text-based and Text/ontology -based searches can be found at:
http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=SetupTextSearch
http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=SetupTextOntologySearch