Downloads

Databases

LIPID MAPS Structure Database (LMSD)

Exports of structures and annotations, updated December 06, 2016

Annotations include:
LM_ID, COMMON_NAME, CATEGORY, MAIN_CLASS, SUB_CLASS, CHEBI_ID, INCHI_KEY,LIPID_MAPS_CMPD_URL,
PUBCHEM_SUBSTANCE_URL, SYSTEMATIC_NAME, SYNONYMS,EXACT_MASS, FORMULA, LIPIDBANK_ID,
PUBCHEM_SID, KEGG_ID, HMDBID, INCHI KEY, INCHI STRING, STATUS
LMSD Structure-data file (SDF)
LMSDFDownload6Dec16.tar.gz (44MB)
LMSDFDownload6Dec16.zip (44MB)

LIPID MAPS Proteome Database (LMPD)

Exports of structures and annotations, updated April 2, 2015

Annotations include:
 LMP ID, ENTREZ GENE ID, GENE NAME, GENE SYMBOL, REFSEQ ID, MRNA ID, GENBANK PROTEIN GI, SEQUENCE,
SEQUENCE LENGTH,UNIPROT ID, PROTEIN ENTRY, PROTEIN NAME, TAXONOMY ID, SPECIES.
LMPD tab-delimited text file
LMPD_040215.zip (3.4MB)

Pathways

Pathway Editor

Arachidonic AcidMetabolism

Pathway maps drawn using Pathway Editor software, plus
.path files for editing pathways using Pathway Editor

The Pathway Editor is a program for managing, visualizing, and editing signaling and metabolic pathways. Pathways may be created from scratch or accessed by opening a .path file. Time course graphs for both lipids and genes, and data for technical and biological replicates for lipids can be displayed within the Pathway Editor.

Please see our Pathway Editor tutorial for an overview of Pathway Editor features, including how to start the Pathway Editor, display user-provided experimental data, create pathways from scratch, and edit and save pathway files and images. Instructions for working with SBML and BioPAX formats are also provided.


Download and launch Pathway Editor Web Start version (no database connection; separate Java Runtime Environment required)

Download Pathway Editor installer program (includes Java Runtime Environment):

Windows (no database connection)
Mac (64 bit Mac OS X version) (no database connection)

Download BioPAX Level 3 files of 25 LIPID MAPS Pathways

- created using the Pathway Editor acting on downloaded path files from our Pathway database


Pathway Editor System requirements:

PC with Windows XP
1GHz or better Intel or AMD processor
512Mbytes of memory or more
3D graphics accelerator
Fast network connection

Mac with MacOSX 10.4 or later
1GHz or better G4, G5, or Intel processor (universal binary)
512Mbytes of memory or more
3D graphics accelerator
Fast network connection

On Safari and Chrome browsers, the Pathway Editor does not automatically start up when the Pathway Editor is downloaded. In these cases, the Pathway Editor may be started by double-clicking the .jnlp file icon in a Finder window or typing the following in a terminal window:
javaws http://www.lipidmaps.org/pathways/PathwayEditor.jnlp

LINUX
The Web Start version has been tested on the following versions of LINUX:

  • LINUX Ubuntu release 12.04 64-bit virtual machine containing 3.9 GB memory and 4 Intel Xeon 2GHz CPU with a Java 6 version of Open JDK, and
  • LINUX CentOS (Red Hat) release 6.5 virtual machine with 65 GB memory and 22 Intel Xeon 2 GHz CPU, with Oracle Java 7.

An installed version of the Pathway Editor for LINUX is not available at this time.

On CentOS installations, the OpenJDK Java which is installed by default may not contain Java Web Start. Java 7, which contains Web Start, may be installed by following the directions on http://www.java.com/en/download/help/linux_install.xml.

The version of Java that is used to run the Web Start version may be set in the browser. However, given difficulties associated with finding Java settings in browser menus, the Web Start version may be downloaded and started from a terminal window by entering the text
javaws http://www.lipidmaps.org/pathways/PathwayEditor.jnlp

UNIX and other platforms
The Pathway Editor has not been tested on UNIX and other platforms.



Software requirements:

The Pathway Editor uses Java Web Start 1.6 or later version and JOGL(Java Open Graphics Language) (JOGL is downloaded as part of the Pathway Editor). If you use the Web Start version, please install a Java Runtime Environment.

Tools

LIPID MAPS Structure Drawing Tools Package - Command line Perl scripts to generate SD files containing structure and ontological data for various lipid categories.

LIPID MAPS Mass Spectrometry Combinatorial Expansion Package - A set of command line PHP scripts to generate tabular datasets contining species name, m/z and molecular formula for some of the main lipid categories. User-defined options include a range of chain-lengths and a choice of poitive and negative ion-types. The generated MS datasets may then be used as databases or references to aid in identification and assignment of ions in mass spectrometry experiments of lipids. The current version supports Glycerolipids (GL), Glycerophospholipids (GP), Cardiolipins (CL) and Sphingolipids (SP).

  • Download Mass Spectrometry Combinatorial Expansion package and documentation: Details

LIPID MAPS Ontology Tools Package. Command line Perl script to generate ontology data using structure data in SD file(s). The LIPID MAPS ontology script uses Perl modules from MayaChemTools package, an external open source Perl package, to generate ontology data and requires its local installation.

Protocols

Please see our Protocols page for protocol descriptions and links to download protocols in PDF format.

Posters

Download posters generated by LIPID MAPS consortium members.

logo LIPID MAPS® is funded by a grant from the Wellcome Trust.