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BioCyc Database Collection

The BioCyc database collection contains over 17,800 organism-specific databases that provide reference to genome and metabolic pathway information. It is maintained by SRI International and divided into three tiers based on manual curation. Tier 1 databases receive the most curation, Tier 2 receive moderate curation, and Tier 3 are computationally predicted without curation. The BioCyc website provides tools for analyzing and visualizing data within the databases and for integrating omics data. Researchers have used BioCyc databases at both the genome scale and pathway level, such as in constructing a genome-scale model of algae metabolism and identifying SNPs associated with congenital heart defects.

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24 views

BioCyc Database Collection

The BioCyc database collection contains over 17,800 organism-specific databases that provide reference to genome and metabolic pathway information. It is maintained by SRI International and divided into three tiers based on manual curation. Tier 1 databases receive the most curation, Tier 2 receive moderate curation, and Tier 3 are computationally predicted without curation. The BioCyc website provides tools for analyzing and visualizing data within the databases and for integrating omics data. Researchers have used BioCyc databases at both the genome scale and pathway level, such as in constructing a genome-scale model of algae metabolism and identifying SNPs associated with congenital heart defects.

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noah676
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
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BioCyc database collection

The BioCyc database collection is an assortment of organism


specific Pathway/Genome Databases (PGDBs) that provide
BioCyc
reference to genome and metabolic pathway information for
thousands of organisms.[1] As of June 2021, there were over Content
17,800 databases within BioCyc. SRI International,[2] based in
Description Tools for
Menlo Park, California, maintains the BioCyc database family.
navigating,
visualizing, and
Categories of Databases analyzing the
underlying
Based on the manual curation done, BioCyc database family is
databases, and
divided into 3 tiers:
for analyzing
Tier 1: Databases which have received at least one year of omics data
literature based manual curation. Currently there are seven Contact
databases in Tier 1. Out of the seven, MetaCyc is a major database
Research center SRI International
that contains almost 2500 metabolic pathways from many
organisms.[1][3] The other important Tier 1 database is HumanCyc Authors Peter Karp et al
which contains around 300 metabolic pathways found in Release date 1997
humans.[4] The remaining five databases include, EcoCyc (E.
Access
coli),[5] AraCyc (Arabidopsis thaliana), YeastCyc (Saccharomyces
cerevisiae), LeishCyc (Leishmania major Friedlin) and Website biocyc.org (htt
TrypanoCyc (Trypanosoma brucei). p://biocyc.org)

Tier 2: Databases that were computationally predicted but have received moderate manual curation (most
with 1–4 months curation). Tier 2 Databases are available for manual curation by scientists who are
interested in any particular organism. Tier 2 databases currently contain 43 different organism databases.

Tier 3: Databases that were computationally predicted by PathoLogic and received no manual curation. As
with Tier 2, Tier 3 databases are also available for curation for interested scientists.

Software tools
The BioCyc website contains a variety of software tools for searching, visualizing, comparing, and
analyzing genome and pathway information. It includes a genome browser, and browsers for metabolic and
regulatory networks. The website also includes tools for painting large-scale ("omics") datasets onto
metabolic and regulatory networks, and onto the genome.

Use in Research
Since BioCyc Database family comprises a long list of organism specific databases and also data at
different systems level in a living system, the usage in research has been in a wide variety of context. Here,
two studies are highlighted which show two different varieties of uses, one on a genome scale and other on
identifying specific SNPs (Single Nucleotide Polymorphisms) within a genome.

AlgaGEM
AlgaGEM is a genome scale metabolic network model for a compartmentalized algae cell developed by
Gomes de Oliveira Dal’Molin et al.[6] based on the Chlamydomonas reinhardtii genome. It has 866 unique
ORFs, 1862 metabolites, 2499 gene-enzyme-reaction-association entries, and 1725 unique reactions. One
of the Pathway databases used for reconstruction is MetaCyc.

SNPs

The study by Shimul Chowdhury et al.[7] showed association differed between maternal SNPs and
metabolites involved in homocysteine, folate, and transsulfuration pathways in cases with Congenital Heart
Defects (CHDs) as opposed to controls. The study used HumanCyc to select candidate genes and SNPs.

References
1. Caspi, R.; Altman, T.; Dreher, K.; Fulcher, C. A.; Subhraveti, P.; Keseler, I. M.; Kothari, A.;
Krummenacker, M.; Latendresse, M.; Mueller, L. A.; Ong, Q.; Paley, S.; Pujar, A.; Shearer, A.
G.; Travers, M.; Weerasinghe, D.; Zhang, P.; Karp, P. D. (2011). "The Meta Cyc database of
metabolic pathways and enzymes and the Bio Cyc collection of pathway/genome
databases" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245006). Nucleic Acids
Research. 40 (Database issue): D742–53. doi:10.1093/nar/gkr1014 (https://doi.org/10.109
3%2Fnar%2Fgkr1014). PMC 3245006 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245
006). PMID 22102576 (https://pubmed.ncbi.nlm.nih.gov/22102576).
2. Home page (http://www.sri.com/) of the SRI International
3. Karp, Peter D.; Caspi, Ron (2011). "A survey of metabolic databases emphasizing the Meta
Cyc family" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352032). Archives of
Toxicology. 85 (9): 1015–33. doi:10.1007/s00204-011-0705-2 (https://doi.org/10.1007%2Fs0
0204-011-0705-2). PMC 3352032 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352032).
PMID 21523460 (https://pubmed.ncbi.nlm.nih.gov/21523460).
4. Romero, Pedro; Wagg, Jonathan; Green, Michelle L; Kaiser, Dale; Krummenacker, Markus;
Karp, Peter D (2004). "Computational prediction of human metabolic pathways from the
complete human genome" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC549063).
Genome Biology. 6 (1): R2. doi:10.1186/gb-2004-6-1-r2 (https://doi.org/10.1186%2Fgb-2004
-6-1-r2). PMC 549063 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC549063).
PMID 15642094 (https://pubmed.ncbi.nlm.nih.gov/15642094).
5. Keseler, I. M.; Collado-Vides, J.; Santos-Zavaleta, A.; Peralta-Gil, M.; Gama-Castro, S.;
Muniz-Rascado, L.; Bonavides-Martinez, C.; Paley, S.; Krummenacker, M.; Altman, T.; Kaipa,
P.; Spaulding, A.; Pacheco, J.; Latendresse, M.; Fulcher, C.; Sarker, M.; Shearer, A. G.;
MacKie, A.; Paulsen, I.; Gunsalus, R. P.; Karp, P. D. (2010). "Eco Cyc: A comprehensive
database of Escherichia coli biology" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC30137
16). Nucleic Acids Research. 39 (Database issue): D583–90. doi:10.1093/nar/gkq1143 (http
s://doi.org/10.1093%2Fnar%2Fgkq1143). PMC 3013716 (https://www.ncbi.nlm.nih.gov/pmc/
articles/PMC3013716). PMID 21097882 (https://pubmed.ncbi.nlm.nih.gov/21097882).
6. Dal'Molin, C. G.; Quek, L. E.; Palfreyman, R. W.; Nielsen, L. K. (2011). "AlgaGEM--a
genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii
genome" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287588). BMC Genomics. 12
Suppl 4: S5. doi:10.1186/1471-2164-12-S4-S5 (https://doi.org/10.1186%2F1471-2164-12-S
4-S5). PMC 3287588 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287588).
PMID 22369158 (https://pubmed.ncbi.nlm.nih.gov/22369158).
7. Chowdhury, S; Hobbs, C. A.; MacLeod, S. L.; Cleves, M. A.; Melnyk, S; James, S. J.; Hu, P;
Erickson, S. W. (2012). "Associations between maternal genotypes and metabolites
implicated in congenital heart defects" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523
122). Molecular Genetics and Metabolism. 107 (3): 596–604.
doi:10.1016/j.ymgme.2012.09.022 (https://doi.org/10.1016%2Fj.ymgme.2012.09.022).
PMC 3523122 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523122). PMID 23059056
(https://pubmed.ncbi.nlm.nih.gov/23059056).

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