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   Articles with "knowledgebase" as a keyword



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A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

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recommendations! Published in 2020 at "Nature Genetics"

DOI: 10.1038/s41588-020-0603-8

Abstract: Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting… read more here.

Keywords: genomic variants; meta knowledgebase; knowledgebase; harmonized meta ... See more keywords
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MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

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recommendations! Published in 2021 at "Nature Methods"

DOI: 10.1038/s41592-021-01291-4

Abstract: Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase… read more here.

Keywords: spheroid; mispheroid knowledgebase; tool; experimental parameters ... See more keywords
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The NISO KBART Automation Working Group: Modernizing Knowledgebase Communications

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recommendations! Published in 2018 at "Serials Review"

DOI: 10.1080/00987913.2018.1522200

Abstract: Abstract The NISO KBART Automation Recommended Practice supplies instructions to content providers for automatic, behind-the-scenes transfer of library-specific subscriptions from a content provider to a knowledgebase vendor. These extensions of the well-established KBART (Knowledge Bases… read more here.

Keywords: working group; niso kbart; knowledgebase; automation working ... See more keywords
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UniProt: the Universal Protein Knowledgebase in 2023

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recommendations! Published in 2022 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkac1052

Abstract: Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our… read more here.

Keywords: knowledgebase; knowledgebase 2023; universal protein; uniprot universal ... See more keywords
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CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

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recommendations! Published in 2022 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkac979

Abstract: Abstract CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management,… read more here.

Keywords: civicdb; variant interpretation; knowledgebase; interpretation ... See more keywords
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Expansion of the Gene Ontology knowledgebase and resources

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recommendations! Published in 2017 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkw1108

Abstract: The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics… read more here.

Keywords: ontology; expansion gene; knowledgebase; biology ... See more keywords
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The Reactome Pathway Knowledgebase

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recommendations! Published in 2018 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkx1132

Abstract: Abstract The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a… read more here.

Keywords: reactome pathway; knowledgebase; pathway knowledgebase;
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Plant Reactome: a knowledgebase and resource for comparative pathway analysis

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recommendations! Published in 2020 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkz996

Abstract: Abstract Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another… read more here.

Keywords: plant; knowledgebase; pathway; gene ... See more keywords

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

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recommendations! Published in 2018 at "BMC Evolutionary Biology"

DOI: 10.1186/s12862-018-1309-8

Abstract: BackgroundThe family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives… read more here.

Keywords: knowledgebase; hydroxyacid dehydrogenases; classification; substrate specificity ... See more keywords