1. S
Creating a Drosophila
Metabolomics
Database
Andrew Schwitzgebel and William Freeman
Dr. Laura Reed
Vishal Oza

2. S Metabolite : Metabolome :: Gene : Genome
S Metabolites are the intermediate products of metabolic
reactions catalyzed by various enzymes that naturally
occur within cells1
2
What is Metabolomics?
2/23/2016 Schwitzgebel & Freeman, CBH

3. Metabolic Syndrome
S MetS
S Suite of symptoms
S Obesity
S Elevated blood lipids
S Diabetes
S Complex interaction between
genetics and lifestyle
2/23/2016 3
Age-Adjusted Rate per 100 of Civilian, Noninstitutionalized Population with
Diagnosed Diabetes, by Race and Sex, United States, 1980–2011
Schwitzgebel & Freeman, CBH

4. Drosophila as a Human
Analog
S Complex genome
S Cryptic genetic variation8
S ~15,000 genes vs. ~23,000 in humans
S High throughput
S Fast results
S Observe population trends over time
S Accessibility to metabolic data
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5. Database Creation
S Goals for FlyMetLib
S Contain basic molecular data
S Reference other chemical identifiers
S HMDBID, DrugBank, ChemSpider, PubChem, etc.
S ~1,500 PubChem SIDs
S ~100 English synonyms
S Link to other bioinformatic databases
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6. 2/23/2016 6
Chemical IDs Example
Schwitzgebel & Freeman, CBH
PubChem SID 1
PubChem SID 2
PubChem SID 3
PubChem SID 4
SLING ID 1
SLING ID 2

7. Chemical ID Conversion
Procedure
InChiKey read from a .csv file
InChiKey translated into a URL of a chemical translation
service
Other identifiers retrieved using find and string methods
Identifiers stored in a list variable to be added to the
database
Sample (Ethanol)
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
http://cts.fiehnlab.ucdavis.edu/service/compound/LFQSCW
FLJHTTHZ-UHFFFAOYSA-N
“C2H6O”
MolFormList = [“C2H6O”]
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8. Structuring the Database
S Creating a unique ID
S FlyMetID
S 5 hexadecimal digits (Ex: FLY00001)
S Allows greater number of unique IDs with fewer digits
S InChiKey for ethanol:
S LFQSCWFLJHTTHZ-UHFFFAOYSA-N
S More human readable
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9. Structuring the Database
One to One
S Chemical data table (Master)
S Molecular weight
S Molecular formula
S Melting point
S Certain IDs
S Hotlinks
S Link to other databases
FlyMetID
Molecular
Weight
Molecular
Formula
FLY00001 16.042 CH4
FLY00002 30.068 C2H6
FLY00003 44.094 C3H8
FLY00004 58.120 C4H10
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10. Structuring the Database
One to Many
S Synonyms
S IUPAC names
S Certain IDs
S PubChem, CAS,
ChemSpider
S Citations
PubChem SIDs
FlyMetID SID 1 SID 2 SID 3
FLY00001 48416772
16385457
6
24112948
1
FLY00002
12728063
0
FLY00003
12885427
1
53776982
FLY00004
12729869
9
12729867
4
99205937
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11. Significance
S Researchers can access and contribute to the database
S Open source code
S One central place for data
S Analogous to the Human Metabolome Database (HMDB)
S Cuts down time cost for research
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12. Future Plans
S Making it publically accessible
S Creating a user interface
S Linking to FlyBase6
S Database for Drosophila genes
S and genomes
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13. Questions?
Andrew Schwitzgebel
Department of Biological Sciences
Computer Based Honors Program
ajschwitzgebel@crimson.ua.edu
William Freeman
Department of Chemical Engineering
Computer Based Honors Program
wjfreeman1@crimson.ua.edu
Dr. Laura Reed
Department of Biological Sciences
lreed1@ua.edu
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14. Proposed Metabolite
Identification Metrics
S Ex: Metabolite A
S Identified using: 1H 2D NMR,
Tandem Mass Spectrum, IR
Absorbance Spectrum
S Matched to an authentic reference
compound
S (3.0 + 1.5 + 0.5) (2) = 10
S Sumner suggests a minimum score of
59
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15. Works Cited
1. Meštrović, Tomislav. "What Are Metabolites?" News-Medical.net. N.p., 01 June 2010. Web. 06 Nov. 2015.
2. Glycolysis. Digital image. Northwest Metabolomics Research Center. University of Washington, n.d. Web. 6 Nov. 2015.
3. Zhang, Rong, Tong Zhang, Dominika Korzekwa, Shadi Al-Johani, Julian A.T. Dow, and David G. Watson. "A Comparison of the
Metabolome of Male and Female Drosophila Melanogaster.” ResearchGate. Strathclyde Institute of Pharmaceutical and Biomedical
Sciences,, 2014. Web. 06 Nov. 2015.
4. Pedrosa, Diego, Gert Wohlgemuth, Sajjan Mehta, and Oliver Fiehn. "Chemical Translation Service." Chemical Translation Service. U.C.
Davis, 2011. Web. 06 Nov. 2015.
5. "Age-Adjusted Rate per 100 of Civilian, Noninstitutionalized Population with Diagnosed Diabetes, by Race and Sex, United States, 1980–
2011." Centers for Disease Control and Prevention. Centers for Disease Control and Prevention, 05 Sept. 2014. Web. 08 Nov. 2015.
6. "A Database of Drosophila Genes and Genomes." FlyBase. N.p., n.d. Web. 08 Nov. 2015.
7. "What Is Metabolic Syndrome?" National Heart, Lung and Blood Institute. National Institutes of Health, 06 Nov. 2015. Web. 08 Nov. 2015.
8. Gibson, Greg, and Ian Dworkin. "Uncovering Cryptic Genetic Variation." Genetics. Nature.com, Sept. 2004. Web. 8 Nov. 2015.
9. Sumner, LW. "Proposed Quantitative and Alphanumeric Metabolite Identification Metrics." Springer (2014): n. pag. Web. 1 Dec. 2015.
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