- Pathway and Compound Databases
- Metabolic pathways from a large number of plants are comprehensively cataloged in PMN's PlantCyc database. PlantCyc includes experimentally supported,computationally predicted, and hypothetical pathways and enzymes. PMN is also a gateway to species-specific pathway databases for several plants, including Arabidopsis, rice, tomato, medicago, and poplar.
- A universal metabolic pathway database for all organisms. MetaCyc only includes experimentally supported pathways and enzymes.
- Catalogs all kinds of pathways, including metabolic pathways.
- Provides information for a large number of Arabidopsis genes involved in acyl-lipid metabolism pathways in conjunction with chapters from The Arabidopsis Book.
- Includes information on manually curated Arabidopsis isoprenoid pathways and genes and allows to user to visualize pathway topology.
- A searchable, digitized version of the Roche Applied Science "Biochemical Pathways" wall chart.
- A compound database that also provides tools for compound clustering and other types of analysis.
- A compound database.
- A compound database.
- A compound database. The compounds are classified by an ontological classification system. ChEBI uses nomenclature, symbolism and terminology endorsed by IUPAC and IUBMB.
- A compound database that links metabolites to species, focusing specifically on plants.
- A database that provides useful biological numbers. Some are related to metabolism and energy capture, such as the percent of total soluble protein in C3 plants that is Rubisco.
- 2. Metabolite Profiling Data
MetabolomeExpress
Provides a public metabolomics data repository and processing pipeline enabling web-based processing, analysis and transparent dissemination of metabolite profiling datasets from all organisms, including Arabidopsis. Available data include metabolite response statistics, raw and processed GC/MS data, data matrices, mass-spectrum and retention-index libraries and standards-compliant metadata in systematic text file formats. Data may be analysed online using a wide variety of built-in analysis tools or downloaded for offline analysis. .
NSF2010 Metabolomics
Allows access to Arabidopsis metabolite profiling data.
The Golm Metabolome Database
Allows access to mass spectra and retention time index libraries, and metabolite profiling experiments.
SpinAssign
Performs batch-assignments of NMR peaks.
Standard Spectrum
Allows access to mass spectra data for compounds measured through mass spectrometry or NMR.
3. Data Analysis Tools
- This "Batch-learning self-organizing map" allows integrated analysis of a range of "omics" data. Two-dimensional feature maps can be generated linking genes and metabolites.
- An open source software platform for visualizing molecular interaction networks.
- A user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other cellular processes.
- A public metabolomics data repository and processing pipeline enabling web-based processing, analysis and transparent dissemination of metabolite profiling datasets from all organisms, including Arabidopsis. The GC/MS data processing pipeline includes peak integration, library matching, data matrix construction and normalisation, univariate statistics, multivariate analysis (PCA and HCA), correlation analysis and export of metabolite response data to popular metabolic pathway visualisation tools such as MapMan and Cytoscape. A database of pre-calculated metabolite response statistics may be interrogated using simple search, cross-experiment meta-analysis or a novel pattern-matching ‘phenocopy search’ that uses a metabolic phenotype of interest as bait to retrieve similar phenotypes from the database.
- An integrated software for visualization and analysis of the metabolomic, proteomic and transcriptomic networks of Arabidopsis.
- Using a species-specific pathway database such as those listed on PMN, the software overlays data values from the user's high-throughput experiments (e.g. metabolite profiling, microarray, or proteome profiling) onto the metabolic network of an organism.
- The Platform for RIKEN Metabolomics provides a number of web-based tools for integrated analysis of metabolomic, transcriptomic, and other data.
- A variety of tools for peak alignment of MS and NMR data.
- This tool, provided by PRIMe, performs batch-assignments of NMR peaks.
- 4. Services and Facilities
- Performs qualitative analysis of any biological samples.
- Provides general metabolite profiling service for plants and microbes.
- Provides metabolite profiling service for Arabidopsis.
- 5. Metabolomics Standards
- A forum for establishing metabolomics standards.
- An initiative for creating standards used in describing plant metabolomics experiments and results that has produced a Core Specification document.
- An effort to develop a common exchange format for biological pathway data.
- 6. Chemical Structure Tools
- Marvin Sketch allows users to draw compounds, import existing compounds, edit their structures, depict reactions, and perform many other tasks. It is a Java-based program provided by ChemAxon.
- MarvinSpace allows high-powered visualization of chemical structures in 3D. It can be used on a range of platforms including Windows, Linux, Mac OS X, and Solaris
- Marvin View provides a large set of visualization tools to allow the viewing of one or more compounds or reactions. It is a Java-based program provided by ChemAxon.
- In addition to MarvinSketch, MarvinSpace, and MarvinView, ChemAxon provides several additional tools such as the Reactor and Fragmenter tools that could be useful to biochemists.
- Jmol is a java-based open-source tool for viewing chemical structurs in 3D.
- The DS Visualizer enables users to view molecules and to generate high quality graphics files.
Pilot and Feasibility projects
Software tool to display biochemical and chemical relationships of metabolomic data
CTS (Chemical translation service)
Software tool to convert metabolite identifiers between different databases (HMDB, PubChem and others)
Software tool and database to process, store and compare GC-TOF MS metabolomic data (LECO formats only)
Gert Wohlgemuth, DB team leader
Software tool and database to define study design parameters
that enables managing metabolomic data files for different platforms
MZmine Lipid Parameters, database and instructions
Parameters for processing lipid data including a csv database for automated peak list generation and annotation presented at Metabolomics Society conference, Glasgow 2013
Links to External Downloads
NIH Metabolomics Data repository
Prof. Shankar Subramaniam at UC San Diego will develop a public data repository for all NIH-funded regional metabolomics resource cores. The Fiehn laboratory is partnering in this effort.
Software tool to process and compare LC-MS metabolomic data files
Software tool to process and compare LC-MS metabolomic data files
Resources for analyzing lipid metabolism data
- Metscape 2.0 (http://metscape.ncibi.org/) allows users to upload a list of metabolites with experimentally determined concentrations and significance values, and identify reactions, genes and pathways that are associated, and analyze them in the context of relevant metabolic networks.
- Metab2MeSH (http://metab2mesh.ncibi.org/) uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings (MeSH), the National Library of Medicine’s (NLM) controlled vocabulary for biomedical concepts and provide links from compounds to biomedical literature, thus complementing existing resources such as PubChem and the Human Metabolome Database
