List of BioCyc Pathway/Genome Databases

The 14558 databases within the BioCyc collection as of Dec 12, 2018 (version 22.6) are as follows:

Tier 1 Databases

PGDBs in Tier 1 have received at least one year of literature-based curation by scientists. For example, the EcoCyc DB is the result of more than 20 person-years of effort to enter information from the E. coli literature about the metabolism, transport, and genetic regulatory processes of this organism, and to update the genome annotation to reflect newly characterized E. coli genes.

Database	Contents	Organization
EcoCyc	Escherichia coli K-12 substr.MG1655	SRI International
MetaCyc	Metabolic pathways and enzymes from over 2063 organisms	SRI International
HumanCyc	250 metabolic pathways	SRI International
AraCyc	Arabidopsis thaliana	S. Rhee, Department of Plant Biology, Carnegie Institution, USA
YeastCyc	Saccharomyces cerevisiae	SGD Curators, Stanford U., USA and SRI International
LeishCyc	Leishmania major Friedlin	Bio21 Molecular Science and Biotechnology Institute, University of Melbourne
TrypanoCyc	Trypanosoma brucei	French National Institute of Agricultural Reasearch (INRA) , University of Glasgow (UoG)

Tier 2 Databases

PGDBs in Tier 2 were generated by the PathoLogic program, which was used to predict their metabolic pathways, their operons (for bacteria only), and their pathway hole fillers (for many of the PGDBs). The resulting PGDBs underwent manual review by a person to remove false-positive pathway predictions that they could detect, and to perform other manual polishing steps such as defining protein complexes. The resulting PGDBs also underwent less than one year of literature-based curation, such as to enter metabolic pathways that had been experimentally elucidated in the organism but that were not inferred by PathoLogic. Most Tier 2 PGDBs have undergone 1-4 months of curation.

Many of the Tier 2 DBs are available for adoption [more] for curation and updating by interested scientists.

Click on the name of a database to navigate to the home page for that database for more information, such as the database authors, and statistics on the database content.

Database	Organization
Agrobacterium fabrum C58	SRI International
Anopheles gambiae	Ezekiel Adebiyi, Olubanke Ogunlana, Covenant University
Aurantimonas manganoxydans SI85-9A1	SRI International
Bacillus anthracis Ames	SRI International
Bacillus subtilis 168	SRI International
Bacteroides thetaiotaomicron VPI-5482	SRI International
Candidatus Cardinium hertigii	Cavanilles Institute
Collinsella aerofaciens ATCC 25986	SRI International
Candidatus Evansia muelleri	Cavanilles Institute
Candidatus Portiera aleyrodidarum BT-QVLC	Cavanilles Institute
Caulobacter crescentus CB15	SRI International
Caulobacter crescentus NA1000	SRI International
Clostridium saccharoperbutylacetonicum ATCC 27021	Biswarup Sen, Feng Chia University, Taiwan
Clostridium symbiosum WAL-14163	SRI International
Corynebacterium glutamicum ATCC 13032	SRI International
Desulfovibrio piger ATCC 29098	SRI International
Faecalibacterium prausnitzii A2-165	SRI International
Drosophila melanogaster	Kenneth L Wiley, Harvard University
Escherichia coli B str. REL606	SRI International
Escherichia coli CFT073	SRI International
Escherichia coli K-12 substr. W3110	SRI International
Escherichia coli O157:H7 str. EDL933	SRI International
Eubacterium rectale ATCC 33656	SRI International
Helicobacter pylori 26695	SRI International
Lactobacillus rhamnosus GG	SRI International
Listeria monocytogenes 10403S	Renato H. Orsi, Department of Food Science - Cornell University
Methanobrevibacter smithiiATCC 35061	SRI International
Methylosinus trichosporium OB3b	Katherine Rostkowski, Stanford University
Mus musculus	Carol J. Bult, The Jackson Laboratory
Mycobacterium tuberculosis CDC1551	SRI International
Mycobacterium tuberculosis H37Rv	SRI International
Penicillium chrysogenum Wisconsin 54-1255	Zheng Zhao, Delft University of Technology
Peptoclostridium difficile 630	SRI International
Plasmodium falciparum 3D7	SRI International
Prevotella copri DSM 18205	SRI International
Salmonella enterica enterica serovar Typhimurium str. 14028S	SRI International
Schistosoma mansoni	Adhemar Zerlotini Neto, FIOCRUZ
Shigella flexneri 2a str. 2457T	SRI International
Staphylococcus subsp. aureus str. NCTC 8325	SRI International
Streptomyces coelicolor A3(2)	University of Warwick
Synechococcus elongatus PCC 7942	SRI International
Thalassiosira pseudonana CCMP1335	Karen Parker, Moss Landing Marine Labs
Vibrio cholerae O1 biovar El Tor str. N16961	SRI International

Tier 3 Databases

The 14489 PGDBs in Tier 3 were generated by the PathoLogic program, which was used to predict their metabolic pathways and their operons (for bacteria only). The resulting PGDBs did not undergo manual review of the pathway predictions, nor subsequent literature curation. Therefore, the pathway predictions should be treated with due caution. PathoLogic is tuned to err on the side of over-predicting pathways to bring them to scientists' attention, rather than under-predicting pathways. PGDBs in Tier 3 were produced as a collaboration between the group of Peter D. Karp at SRI International and the group of Christos Ouzounis at the European Bioinformatics Institute. Click here to request the addition of a Tier 3 PGDB for a new genome to BioCyc.

The Tier 3 DBs are available for adoption [more] by interested scientists, to undergo curation and updating.

Click on the name of a database to navigate to the home page for that database for more information, such as the database authors, and statistics on the database content.

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List of BioCyc Pathway/Genome Databases

Tier 1 Databases

Tier 2 Databases

Tier 3 Databases