# BioCyc database collection
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{{infobox biodatabase
|title = BioCyc
|logo =File:Database.png
|description = Tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data
|scope =
|organism =
|center = [SRI International](/source/SRI_International)
|laboratory =
|author = [Peter Karp](/source/Peter_Karp_(scientist)) ''et al''
|citation =
|released = 1997
|standard =
|format =
|url = {{URL|biocyc.org}}
|download =
|webservice =
|sql =
|sparql =
|webapp =
|standalone =
|license =
|versioning =
|frequency =
|curation =
|bookmark =
|version=
}}
The BioCyc [database](/source/database) collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to [genome](/source/genome) and [metabolic pathway](/source/metabolic_pathway) information for thousands of organisms.[{{Cite journal|doi=10.1093/nar/gkr1014|pmid=22102576|pmc=3245006|title=The Meta ''Cyc'' database of metabolic pathways and enzymes and the Bio ''Cyc'' collection of pathway/genome databases|journal=Nucleic Acids Research|volume=40|issue=Database issue|pages=D742–53|year=2011|last1=Caspi|first1=R.|last2=Altman|first2=T.|last3=Dreher|first3=K.|last4=Fulcher|first4=C. A.|last5=Subhraveti|first5=P.|last6=Keseler|first6=I. M.|last7=Kothari|first7=A.|last8=Krummenacker|first8=M.|last9=Latendresse|first9=M.|last10=Mueller|first10=L. A.|last11=Ong|first11=Q.|last12=Paley|first12=S.|last13=Pujar|first13=A.|last14=Shearer|first14=A. G.|last15=Travers|first15=M.|last16=Weerasinghe|first16=D.|last17=Zhang|first17=P.|last18=Karp|first18=P. D.}}] As of July 2023, there were over 20,040 databases within BioCyc.[{{Cite web |title=BioCyc Pathway/Genome Database Collection |url=https://biocyc.org/ |access-date=2023-07-31 |website=biocyc.org |language=en}}] [SRI International](/source/SRI_International),[[http://www.sri.com/ Home page] of the [SRI International](/source/SRI_International)] based in [Menlo Park, California](/source/Menlo_Park%2C_California), maintains the BioCyc database family.
==Categories of Databases==
Based on the manual curation done, BioCyc database family is divided into 3 tiers:
'''Tier 1:''' Databases which have received at least one year of literature based manual curation. Currently there are seven databases in Tier 1. Out of the seven, [MetaCyc](/source/MetaCyc) is a major database that contains almost 2500 metabolic pathways from many organisms.[{{Cite journal|doi=10.1007/s00204-011-0705-2|pmid=21523460|title=A survey of metabolic databases emphasizing the Meta ''Cyc'' family|journal=Archives of Toxicology|volume=85|issue=9|pages=1015–33|year=2011|last1=Karp|first1=Peter D.|last2=Caspi|first2=Ron|pmc=3352032}}] The other important Tier 1 database is HumanCyc which contains around 300 metabolic pathways found in humans.[{{Cite journal|doi=10.1186/gb-2004-6-1-r2|pmid=15642094|pmc=549063|year=2004|last1=Romero|first1=Pedro|title=Computational prediction of human metabolic pathways from the complete human genome|journal=Genome Biology|volume=6|issue=1|pages=R2|last2=Wagg|first2=Jonathan|last3=Green|first3=Michelle L|last4=Kaiser|first4=Dale|last5=Krummenacker|first5=Markus|last6=Karp|first6=Peter D |doi-access=free }}] The remaining five databases include, EcoCyc (''E. coli''),[{{Cite journal|doi=10.1093/nar/gkq1143|pmid=21097882|pmc=3013716|title=Eco ''Cyc'': A comprehensive database of Escherichia coli biology|journal=Nucleic Acids Research|volume=39|issue=Database issue|pages=D583–90|year=2010|last1=Keseler|first1=I. M.|last2=Collado-Vides|first2=J.|last3=Santos-Zavaleta|first3=A.|last4=Peralta-Gil|first4=M.|last5=Gama-Castro|first5=S.|last6=Muniz-Rascado|first6=L.|last7=Bonavides-Martinez|first7=C.|last8=Paley|first8=S.|last9=Krummenacker|first9=M.|last10=Altman|first10=T.|last11=Kaipa|first11=P.|last12=Spaulding|first12=A.|last13=Pacheco|first13=J.|last14=Latendresse|first14=M.|last15=Fulcher|first15=C.|last16=Sarker|first16=M.|last17=Shearer|first17=A. G.|last18=MacKie|first18=A.|last19=Paulsen|first19=I.|last20=Gunsalus|first20=R. P.|last21=Karp|first21=P. D.}}] AraCyc (''Arabidopsis thaliana''), YeastCyc (''Saccharomyces cerevisiae''), LeishCyc (''Leishmania major Friedlin'') and TrypanoCyc (''Trypanosoma brucei'').
'''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 ontological resource 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](/source/Gene_regulatory_network). 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 Polymorphism](/source/Single_Nucleotide_Polymorphism)s) 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.[{{Cite journal|pmid=22369158|pmc=3287588|year=2011|last1=Dal'Molin|first1=C. G.|title=AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome|journal=BMC Genomics|volume=12|pages=S5|last2=Quek|first2=L. E.|last3=Palfreyman|first3=R. W.|last4=Nielsen|first4=L. K.|issue=Suppl 4 |doi=10.1186/1471-2164-12-S4-S5 |doi-access=free }}] 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.[{{cite journal|pmid=23059056|pmc=3523122|year=2012|last1=Chowdhury|first1=S|title=Associations between maternal genotypes and metabolites implicated in congenital heart defects|journal=Molecular Genetics and Metabolism|volume=107|issue=3|pages=596–604|last2=Hobbs|first2=C. A.|last3=MacLeod|first3=S. L.|last4=Cleves|first4=M. A.|last5=Melnyk|first5=S|last6=James|first6=S. J.|last7=Hu|first7=P|last8=Erickson|first8=S. W.|doi=10.1016/j.ymgme.2012.09.022}}] showed association differed between maternal SNPs and metabolites involved in [homocysteine](/source/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 ==
{{reflist}}
Category:Biochemistry databases
Category:Genome databases
Category:Biotechnology
Category:Metabolomic databases
Category:SRI International
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Adapted from the Wikipedia article [BioCyc database collection](https://en.wikipedia.org/wiki/BioCyc_database_collection) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/BioCyc_database_collection?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.