2019
DOI: 10.1101/788521
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Pathway Commons: 2019 Update

Abstract: Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative M… Show more

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Cited by 7 publications
(8 citation statements)
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“…Finally, our comparative analysis also includes GeneMANIA 24 (http://genemania.org), as it can perform functional annotation and prediction from a flat list of protein genes, by integrating data from PPIs databases, such as BioGRID (https://thebiogrid.org/) 25 or PathwayCommons (https://www.pathwaycommons.org/). 26 Interestingly, Gene-MANIA is able to predict ortholog PPIs (interologs) through the integration of data from other species. However, it is currently limited to only nine organisms.…”
Section: Introductionmentioning
confidence: 99%
“…Finally, our comparative analysis also includes GeneMANIA 24 (http://genemania.org), as it can perform functional annotation and prediction from a flat list of protein genes, by integrating data from PPIs databases, such as BioGRID (https://thebiogrid.org/) 25 or PathwayCommons (https://www.pathwaycommons.org/). 26 Interestingly, Gene-MANIA is able to predict ortholog PPIs (interologs) through the integration of data from other species. However, it is currently limited to only nine organisms.…”
Section: Introductionmentioning
confidence: 99%
“…Maps generated ad-hoc by our workflow can be further refined using available diagram editors, CellDesigner in particular. Such on-the-fly query for diagram components is similar to the functionality of Newt editor (Balci et al, 2021) querying of PathwayCommons resources (Rodchenkov et al, 2019). Our workflow preserves the layout of the original components, which may result in a patchwork of styles.…”
Section: Discussionmentioning
confidence: 99%
“…To this end we consider 11,582 proteins from H. sapiens associated to BP-GO:0030154 listed at QuickGo database [18], which include 87 child BP terms, these proteins constitute the nodes of the network. Further, we also consider the biochemical interactions listed in Pathways Commons (version 12), that integrate 2,424,055 interactions from 22 databases [19]. From this set of interactions we select the 191,072 interactions that involve only human proteins associated with BP-GO:0030154, we do not take into account interactions involving chemical compounds nor other not-protein molecules.…”
Section: Methods Detailsmentioning
confidence: 99%