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Human Metabolome Database Version 2.5

 

Data Sources

Metabolite Field Sources

Accession No Automatically determined, internal program
Creation Date Automatically determined, internal program
Last Update Automatically determined, internal program
Common Name PubChem, KEGG, PubMed, Merck Manual, ChEBI, SciFinder, MetaCyc, OMMBID, Manual Search
Description Wikipedia, PubChem, KEGG, PubMed, Merck Manual, SciFinder, Manual Search
Synonyms PubChem, KEGG, PubMed, Merck Manual, ChEBI, SciFinder, LipidMaps, OMMBID, Manual Search
Chemical IUPAC Name PubChem, ChEBI, SciFinder, Manual Search, ChemDraw, ACD
Chemical Formula PubChem, KEGG, PubMed, Merck Manual, ChEBI, SciFinder, MetaCyc, Manual Search
Chemical Structure PubChem, KEGG, Merck Manual, ChEBI, SciFinder, LipidMaps, MetaCyc, ChemDraw, ACD, Manual Search
Chemical Taxonomy Internal program, CheckMol, NuGO, Manual annotations
Molecular Weight Internal program
Smiles (Isomeric) PubChem, KEGG, MolConverter, ACD, OpenBabel
Smiles (Canonical) PubChem, KEGG, MolConverter, ACD, OpenBabel
KEGG Compound ID KEGG
BioCyc ID BioCyc
PubChem Compound ID PubChem
PubChem Substance ID's PubChem
ChEBI ID ChEBI
CAS Registry Number SciFinder, KEGG, ChEBI
InCHI Identifier PubChem, SciFinder,
Synthesis Reference PubChem, Merck Manual, PubMed, Manual Search
Melting Point Manual Search, PhysProp, MSDS data, Wikipedia
H2O Solubility Experimental Manual Search, PhysProp, MSDS data, Wikipedia
H2O Solubility Predicted Local Program, ACD
State Local Program, MSDS data, Wikipedia
LogP/Hphobicity PubChem, PhysProp, ALOGPS
Material Safety Data Sheet (MSDS) Various sources (Sigma, Aldrich, online references)
MOL File Image Molconverter, KEGG, PubChem, ChemDraw, ChemSketch
MOL File Text Molconverter, KEGG, PubChem, ChemDraw, ChemSketch
SDF File [Text] Molconverter, KEGG, PubChem, ChemDraw, ChemSketch
PDB File Calculated Image CORINA, Molconverter, ChemDraw, ChemSketch
PDB File Calculated Text CORINA, Molconverter, ChemDraw, ChemSketch
PDB ID PDB
PDB File Experimental Text PDB
PDB File Experimental Image Image
Experimental 1H NMR Spectrum Local data collection
Experimental 13C NMR Spectrum Local data collection
Predicted 1H NMR Spectrum ACD
Experimental 13C NMR Spectrum ACD
Mass Spectrum Local data collection
Cellular Location PubMed, Manual Search, Local program
Biofluid Location PubMed, Local data collection, MetaGene, OMIM
Tissue Location PubMed, SwissProt, MetaGene, OMIM
Concentration [Normal Urine] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Normal Plasma] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Normal CSF] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Normal Cellular] PubMed, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Normal Other Biofluids] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Associated Disorders OMIM, PubMed, OMMBID, Teitz, Clinical textbooks, Merck Manual
OMIM ID OMIM
MetaGene ID MetaGene
Concentration [Abnormal Urine] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Abnormal Plasma] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Abnormal CSF] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Abnormal Cellular] PubMed, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration [Normal Other Biofluids] PubMed, Local data collection, Teitz, Clinical textbooks, Merck Manual, OMMBID
Concentration References PubMed, Teitz, Clinical textbooks, Merck Manual, OMMBID
Pathway Names KEGG, MetaCyc
KEGG Images KEGG
SimCell Pathway Images SimCell, Manual
SimCell Pathway Graphs SimCell
SimCell Pathway SBMLs SimCell
Metabolite's Protein Targets KEGG, MetaCyc, SwissProt

Metabolizing Enzyme/Cofactor Field Sources

Name Manual Search, Local program, PubMed, SwissProt, KEGG, MetaCyc
Gene Name SwissProt
Synonyms SwissProt
Protein Sequence SwissProt, GenBank
Number of Residues Internal program
Molecular Weight Internal program
Theoretical pI Internal program
GO Classification Gene Ontology, internal program
General function SwissProt, ProtFun, internal program, manual search and entry
Specific Function SwissProt
Pathway KEGG, SwissProt
Reaction SwissProt
Pfam Domain Function SwissProt
Signals SwissProt, internal program
Transmembrane Regions SwissProt, TMHMM
Metabolic Importance Manual search
EC Link SwissProt
GenBank ID Protein GenBank, GeneCards
SwissProt ID SwissProt
PDB ID PDB
3D Structure Image PDB
3D Structure Text PDB
Cellular Location SwissProt
Gene Sequence GeneCards
GenBank ID Gene GenBank, GeneCards
Chromosome Location GeneCards
Locus GeneCards
SNPs RefSNP, internal program
References PubMed, internal program, manual search

Source Links

PubChem http://pubchem.ncbi.nlm.nih.gov/
KEGG http://www.genome.jp/kegg/
BioCyc http://www.biocyc.org/
SwissProt http://us.expasy.org/sprot/
GenBank http://www.ncbi.nlm.nih.gov/
ChEBI http://www.ebi.ac.uk/chebi/
BRENDA http://www.brenda-enzymes.info/
PDB http://www.rcsb.org/pdb/
Pubmed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
PhysProp http://www.syrres.com/esc/physdemo.htm
MolConverter http://www.chemaxon.com/marvin/doc/user/molconvert.html
Gene Ontology http://www.geneontology.org/
Pfam http://www.sanger.ac.uk/Software/Pfam/
Open Babel http://openbabel.sourceforge.net/
Corina http://openbabel.sourceforge.net/
Ligand Depot http://ligand-depot.rutgers.edu/
GeneCards http://www.genecards.org/
TMHMM TMHMM
MetaCyc http://metacyc.org/
OMIM http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
OMMBID http://genetics.accessmedicine.com/
SciFinder http://www.cas.org/SCIFINDER/
ACD http://www.acdlabs.com/products/
ChemDraw http://www.cambridgesoft.com/
Wikipedia http://en.wikipedia.org/wiki/Main_Page
Google Scholar http://scholar.google.com/
SDBS http://www.aist.go.jp/RIODB/SDBS/cgi-bin/direct_frame_top.cgi?lang=eng
METLIN http://metlin.scripps.edu/
BMRB http://www.bmrb.wisc.edu/metabolomics/
NuGO http://www.ifr.bbsrc.ac.uk/Science/ScienceBriefs/nugo.html
SIGMA http://www.sigmaaldrich.com/
LIPID MAPS http://www.lipidmaps.org/