Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

By Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, B. J. Bolt, D. Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller and 36 more. Nucleic Acids Res., 2017

439 citations recorded by the source corpus.

Abstract Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1efb30509d204b5ed08c7d82c3927bec655eb1ce

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Citations in the corpus

The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, methodology): “Examples of tools integration are the NCBI BLAST+ services integrated into the websites of UniProtKB (8), ENA (9) and Ensembl Genomes (10).”
Genenames.org: the HGNC and VGNC resources in 2019 (2018, background): “The addition of Schizosaccharomyces pombe has led to the inclusion of nomenclature and orthology data from PomBase (25) as well as orthology data from Ensembl Genomes (26).”
Ensembl 2019 (2018, background): “To advance analysis of non-coding genomic regions, we will be incorporating a broad collection of experiments across a wide number of cell types, cell lines, tissues and species into the En-sembl Regulatory Build through our participation in both the International Human Epigenome Consortium (IHEC) (”
Ensembl 2020 (2019, background): “This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. alongside our companion ”
HMMER web server: 2018 update (2018, methodology): “Ensembl Genomes has adopted the HMMER search engine into its own web-site, by providing a specific input form and wrapping the HMMER web result pages into its own website.”
PHI-base: the pathogen–host interactions database (2019, background): “Excellent tools for genome browsing and sequence investigations are provided for example by Ensembl Genomes, FungiDB and other genomic resource providers (33,37).”