Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms .The metabolome is the global collection of all low molecular weight metabolites that are produced by cells during metabolism, and provides a direct functional readout of cellular activity and physiological status. In this presentation i have given the list of various Metabolomic databases and metabolite databases. In addition to this there is a brief description about SMPDB and HMDB and BioTransformer

1. BIG
DATA
IN
METABOLISM
Presented By:
Alichy Sowmya
Chintala Chaitanya
Gundaboina Shalini
Gudea Jaya Krishna

2. • Metabolism is the set of life-sustaining chemical transformations
within the cells of living organisms
• These enzyme-catalyzed reactions allow organisms to grow and
reproduce, maintain their structures, and respond to their
environments
• The word metabolism can also refer to all chemical reactions that
occur in living organisms, including digestion and the transport of
substances into and between different cells, in which case the set of
reactions within the cells is called intermediary metabolism or
intermediate metabolism
Metabolism:

3. • The metabolome is the global collection of all low molecular
weight metabolites that are produced by cells during metabolism,
and provides a direct functional readout of cellular activity and
physiological status
Metabolome:

4. • Metabolites are the intermediates and products of metabolism.
Within the context of metabolomics, a metabolite is usually defined
as any molecule less than 1 kDa in size
• In human-based metabolomics, it is common to describe
metabolites as being either endogenous (produced by the host
organism) or exogenous. Metabolites of foreign substances such as
drugs are termed Xeno-metabolites
Metabolites:

5. • A metabolic pathway is a set of biochemical reactions by which a
substrate gets converted to other compounds
• It governs the flow of energy and matter in biological organisms
• Up to 10% genes in any species code proteins that works on the
operation and regulation of metabolic pathways
Metabolic pathway:

6. • ~1400 enzyme commission (EC) numbers are mapped to the
human genome. (source NCBI) . An EC number represents a
catalytic activity
• ~6500 EC numbers are known so far. (source expasy)
• Many enzymes are promiscuous. They can work on several
substrates. For example - alcohol dehydrogenase
• ~25000 reactions are known so far. (source Brenda)
• And there are many pathways and reactions which are yet to be
mapped
• There is a lot more yet to come
Why is it a big data?

7. Metabolomic databases:
Database Name Comments
BioMagResBank (BMRB – Metabolimics) -Emphasis on NMR data, no biological or biochemical data
-Specific to plants (Arabadopsis)
Chemicals Entities of Biological Interest (ChEBI) -Covers metabolites and drugs of biological interest
-Focus on ontology and nomenclature not biology
ChemSpider -Meta-database containing chemical data from 100+ other
databases
-20+ million compounds
-Good search utilities
Golm Metabolome Database -Emphasis on MS or GC-MS data only -No biological data
-Few data fields
-Specific to plants
Human Metabolome Database -Largest and most completely annotated metabolomic database
-Specific to humans only
KNApSAcK -A phytochemical database containing data for 50,000
compounds
LipidMaps -Contains 22,500 different lipids found in plants & animals
-Nomenclature standard
METLIN Metabolite Database -Human specific metabolite database
-Name, structure, ID only
PubChem -Database containing 27 million unique chemicals with links to
Bioassays and PubMed abstracts

8. Metabolic pathway databases:
Database Name Comments
HumanCyc (Encylopedia of Human Metabolic
Pathways)
-MetaCyc adopted to human metabolism
-No disease or drug pathways
KEGG (Kyoto Encyclopedia of Genes and
Genomes)
-Best known and among the most complete metabolic pathway databases
-Covers many organisms
-A Few disease and drug pathways
The Medical Biochemistry Page -Simple metabolic pathway diagrams with extensive explanations
-A few drug and disease pathways
MetaCyc (Encyclopedia of Metabolic
Pathways)
-Similar to KEGG in coverage, but different emphasis
-Well referenced
-No disease or drug pathways
Reactome (A Curated Knowledgebase of
Pathways)
-Pathway database with more advanced query features
-Not as complete as KEGG or MetaCyc
Roche Applied Sciences Biochemical
Pathways Chart
-The old metabolism standard (on line)
-Describes most human metabolism
Small Molecule Pathway Database (SMPDB) -Pathway database with disease, drug and metabolic pathways for
humans
-Extensive search, analysis and visualization tools
Wikipathways -Community annotated pathway database for 19 model organisms -
Contains 175 human pathways
-Few drug or disease pathways

9. • Special emphasis on clinical biochemistry and clinical
pharmacology
• Currently consist of more then 450 highly detailed pathways, of
which >100 metabolic disease pathways and >200 drug pathways
• Text querying
• Chemical structure querying
• Sequence querying
• Pathway mapping
Small Molecule Pathway Database(SMPDB):

10. Small Molecule Pathway Database(SMPDB):

11. Small Molecule Pathway Database(SMPDB):

12. • Contains comprehensive spectroscopic, quantitative, analytic &
physiological information about human metabolites and their
associated enzymes, tranporters, their abundancies and their disease
related properties
• Each metabolite in HMDB is linked to a “Metabocard”
• Every Metabocard has 114 data fields in which 2/3rd are chemical
and physico chemical and 1/3rd are biochemical
• Each Metabocard contains hyperlinks to many other databases
Human Metabolome Database (HMBD):

13. Human Metabolome Database (HMBD):

14. Human Metabolome Database (HMBD):

15. Category HMDB 1.0 HMDB 2.0 HMDB 3.0 HMDB 4.0
Total number of metabolites 2180 6408 40 153 114 100
Number of detected & quantified metabolites 883 4413 16 714 18 557
Number of detected, not quantified metabolites 1297 1995 2798 3271
Number of expected metabolites 0 0 20 641 82 274
Number of predicted metabolites* 0 0 0 9548
Number of unique synonyms 27 700 43 882 199 668 1 231 398
Number of cmpds with expt. MS/MS spectra 390 799 1249 2265
Number of cmpds with expt. GC/MS spectra 0 279 1220 2544
Number of cmpds with expt. NMR spectra 385 792 1054 1494
Number of cmpds with pred. MS/MS spectra* 0 0 0 98 601
Number of cmpds with pred. GC/MS spectra* 0 0 0 26 880
Number of experimental NMR spectra 765 1580 2032 3840
Number of experimental MS/MS spectra 1180 2397 5776 22 198
Number of experimental GC/MS spectra 0 279 1763 7418
Number of predicted MS/MS spectra* 0 0 0 279 972
Number of predicted GC/MS spectra* 0 0 0 38 277
Number of metabolic pathway maps 26 58 442 25 570
Number of compounds with disease links 862 1002 3105 5498
Number of compounds with concentration data 883 4413 5027 7552
Number of predicted molecular properties 2 2 10 24
Number of metabolite-SNP interactions* 0 0 0 6777
Number of metabolite-drug interactions* 0 0 0 2497
No. of metabolites w. sex/diurnal/age variation* 0 0 0 2901
Number of metabolic reactions* 0 0 0 18,192
Number of defined ontology terms* 0 0 0 3150
Number of HMDB data fields 91 102 114 130
Comparison between the coverage in HMDB
1.0, 2.0, 3.0 and HMDB 4.0
* New for HMDB 4.0

16. Metabocard:

17. Metabocard:

18. Metabocard:

19. Metabocard:

20. Metabocard:

21. • In silico metabolite prediction is a well-developed field of
chemoinformatics that has been central to advancing drug research
and development for more than three decades
• In silico metabolite modeling has been extended to the prediction of
environmental degradation products through the EWAG-BBD
System
• Building from these well-developed ideas and precedents, the
HMDB curation team has developed an in silico, open access
metabolite prediction system called BioTransformer (Djoumbou Feunang, Y.
(2017) Cheminformatics tools for enabling metabolomics. PhD Thesis, University of Alberta, Edmonton,
AB, Canada)
BioTransformer:

22. • Given an input structure, BioTransformer predicts the site of
metabolism, the reacting enzyme, and the resulting product
structure(s) for single-step, multi-step more or multi-compartmental
phase I, phase II, microbial and promiscuous enzymatic reactions
• The input may be given in form of valid smiles string
• Extensive testing indicates that BioTransformer is able to predict
biotransformation products with a precision of 46%, and a recall of
66%
BioTransformer:

23. • It is also very good at identifying which compounds are NOT
biotransformed (unlike most other in silico predictors). While still
imperfect, BioTransformer's performance is 20–30% better than any
other system (commercial or non-commercial)
• BioTransformer has been applied to a selected set of ‘Detected’
compounds in the HMDB. As a result, there are now 9548
‘Predicted’ metabolites in HMDB 4.0, which represents about 8%
of the current collection of metabolites in the HMDB
BioTransformer:

24. BioTransformer:

25. What can we do?

26. THANK YOU