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BioPath specifications

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Unique identifier OMICS_02679
Name BioPath
Restrictions to use None
Maintained Yes

Publication for BioPath

BioPath citations

 (6)
library_books

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

2017
J Cheminform
PMCID: 5471289
DOI: 10.1186/s13321-017-0223-1

[…] o have reliable algorithms to predict atom mappings, especially for large sets of reactions found in metabolic databases and genome-scale metabolic network reconstructions. To our knowledge, only the BioPath [] and KEGG RPAIR [] databases disseminate manually curated atom mappings. Other metabolic databases such as EC-BLAST [] MetaCyc [] and MetRxn [] include predicted atom mappings.A genome-scale […]

library_books

Reconstruction and analysis of a genome scale metabolic model of the oleaginous fungus Mortierella alpina

2015
BMC Syst Biol
PMCID: 4301621
PMID: 25582171
DOI: 10.1186/s12918-014-0137-8

[…] tated by submitting ORFs to the KAAS online annotation server []. Metabolic reactions absent from the draft model were added from the KEGG database [] based on KAAS annotation results. MetaCyc [] and BioPath [] databases were used to judge reaction reversibility. Compartmentalization information assigned to reactions was determined by subcellular localization prediction tools CELLO [] and WoLF PSO […]

library_books

Inference of phenotype defining functional modules of protein families for microbial plant biomass degraders

2014
Biotechnol Biofuels
PMCID: 4189754
PMID: 25342967
DOI: 10.1186/s13068-014-0124-8

[…] f functionally coupled protein families related to a specific phenotype. These methods use prior information about pathways from, for example, the Kyoto Encyclopedia of Genes and Genomes (KEGG) [] or BioPath [] databases in the form of organism-specific enzyme reaction networks based on enzyme classification (EC) numbers. The Network Instance-Based Biased Subgraph Search (NIBBS) searches for pheno […]

library_books

Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

2009
Genome Biol
PMCID: 2690999
PMID: 19284550
DOI: 10.1186/gb-2009-10-3-r28

[…] omes, we applied our metabolic reconstruction method to each genome using the automatic genome annotation provided by PEDANT and the (organism unspecific) metabolic reaction and pathway data given by BioPath (for details see Materials and methods). The reconstruction results in a 290-dimensional pathway profile for each genome. Each dimension corresponds to the weighted completeness of a reference […]

library_books

An extensive (co )expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

2008
BMC Plant Biol
PMCID: 2383897
PMID: 18433503
DOI: 10.1186/1471-2229-8-47

[…] One of the most striking features revealed by the co-expression analysis is an unexpectedly large subset of P450 genes being mapped to pathways identified as 'plastidial isoprenoids' (BioPath), 'photosystems' (BioPath), 'photosynthesis' (KEGG or FunCat), and 'biogenesis of the chloroplast' (FunCat). At the 'CYPedia' homepage follow the link 'browse pathways' and 'CYP => pathway' to […]

library_books

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

2007
BMC Syst Biol
PMCID: 1934383
PMID: 17608928
DOI: 10.1186/1752-0509-1-29

[…] iner uses a hierarchical drawing algorithm which embeds nodes on regular horizontal layers []. Others propose adapted versions of classical hierarchical drawing algorithms, like in [] (implemented in BIOPATH []) or in [] (implemented in Wilmascope).However, these algorithms do not emphasize cyclic patterns which are also relevant (see for instance the TCA cycle). Thus, other methods were designed […]

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BioPath institution(s)
Fakultüt für Mathematik und Informatik, Universität Passau, Passau, Germany

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