2017
DOI: 10.1093/bib/bbx085
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The BioCyc collection of microbial genomes and metabolic pathways

Abstract: BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion… Show more

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Cited by 717 publications
(560 citation statements)
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“…EV is wild type with pAH9 (EBT169) and GFP is wild type with pAH13 (UM20). Streptavidin IR680LT was used to detect HD73_4231 (PycA homolog) which served as a loading control (63, 64). The color blot showing both anti-GFP and Streptavidin on a single gel is Fig.…”
Section: Resultsmentioning
confidence: 99%
“…EV is wild type with pAH9 (EBT169) and GFP is wild type with pAH13 (UM20). Streptavidin IR680LT was used to detect HD73_4231 (PycA homolog) which served as a loading control (63, 64). The color blot showing both anti-GFP and Streptavidin on a single gel is Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Subsequent to merging the existing S. coelicolor GEMs, we performed a number of further curations of the model: including improvement of annotations, both in terms of coverage and number of different databases, e.g. KEGG (Kanehisa, 2000;Kanehisa et al, 2019), BioCyC (Karp et al, 2017), ChEBI (Hastings et al, 2016) and MetaNetX (Moretti et al, 2016). All reactions and metabolites have been given identifiers according to the BiGG namespace (King et al, 2016), and all reactions are categorized into 15 different subsystems, covering 128 different pathways.…”
Section: Reproducible Reconstruction Of Sco-gemmentioning
confidence: 99%
“…Illustrating a more serious error, a 2013 paper claimed that Rv1749c is part of a VapBC toxin-antitoxin system in M. bovis 125 , but their cited source 126 mentioned Rv1749c neither in the paper nor in the supplementary material. The same paper claims Rv0988 is a hydrolase, but provides no citation for this claim 125 , and no major database supports this claim 2,5,17,[34][35][36]38 . These examples underscore the need for skepticism and caution when evaluating evidence for functional annotation in literature.…”
Section: Manual Annotationmentioning
confidence: 99%
“…To assess the novelty of manual product annotations, we compared each to their counterparts on UniProt 17 , Mtb Network Portal 5 (which included annotations from TBDB 1 ), PATRIC 2 , RefSeq 34 , BioCyc 35 , and KEGG 36 . We obtained the UniProt, Mtb Network Portal, and RefSeq annotations for each of our genes with new product annotation programmatically.…”
Section: Comparison To Existing Databasesmentioning
confidence: 99%