ChEBI in 2016: Improved services and an expanding collection of metabolites

Hastings, Janna; Owen, Gareth; Dekker, Adriano; Ennis, Marcus; Kale, Namrata; Muthukrishnan, Venkatesh; Turner, Steve; Swainston, Neil; Mendes, Pedro; Steinbeck, Christoph

doi:10.1093/nar/gkv1031

Cited by 901 publications

(681 citation statements)

References 20 publications

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“…The ontologies associated with chemical compounds may be found in special databases, such as ChEBI (European Institute of Bioinformatics, Hinxton, UK) [22] and OlsVis (Norwegian University of Science and Technology, Trondheim, Norway) [38]. The National Center for Biotechnology Information (NCBI) (Bethesda, MD, USA) has developed the Medical Subject Headings (MeSH) database [36] which is used in other databases, including PubChem [43].…”

Section: Text-based Database Screeningmentioning

confidence: 99%

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

Minkiewicz

Darewicz

Iwaniak

et al. 2016

IJMS

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Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

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Section: Text-based Database Screeningmentioning

confidence: 99%

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

Minkiewicz

Darewicz

Iwaniak

et al. 2016

IJMS

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“…To consistently identify all ncRNAs, the RNAcentral platform was developed (http://rnacentral.org/), with the aim of incorporating and combining the numerous ncRNA databases to create a unified reference resource that allows the search or comparison of any ncRNA of interest (The RNAcentral Consortium 2015. RNAcentral is now available and acts as an external reference resource for all ncRNA molecules, as UniProtKB (The UniProt Consortium 2015) does for proteins and ChEBI (Hastings et al 2016) for small molecules. The linking of identifier to sequence enables the precise mapping of point mutation data, which researchers generate to experimentally demonstrate the effect of these mutants on the interactions of ncRNA with other molecules.…”

Section: Introductionmentioning

confidence: 99%

The yeast noncoding RNA interaction network

Panni

Prakash

Bateman

et al. 2017

RNA

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This article describes the creation of the first expert manually curated noncoding RNA interaction networks for S. cerevisiae. The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains. We also see an enrichment of WD40 domains suggesting their direct involvement in ncRNA interactions. We discuss the challenges in collecting noncoding RNA interaction data and the opportunities for worldwide collaboration to fill the unmet need for this data.

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“…Services such as identifiers.org and the IMS itself provide routes to convert between alphanumeric identifiers (e.g. CHEBI:33128) and IRI-based identifiers (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33128) as defined in the ChEBI ontology (Hastings et al, 2015b). …”

Section: Data Integration Approachesmentioning

confidence: 99%

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

et al. 2018

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Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

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ChEBI in 2016: Improved services and an expanding collection of metabolites

Cited by 901 publications

References 20 publications

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

The yeast noncoding RNA interaction network

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

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