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1.
Nucleic Acids Res ; 52(D1): D891-D899, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-37953337

RESUMO

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.


Assuntos
Bases de Dados Genéticas , Genômica , Animais , Genoma , Anotação de Sequência Molecular , Filogenia , Software , Humanos
2.
Nucleic Acids Res ; 50(D1): D837-D847, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34788826

RESUMO

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.


Assuntos
Bases de Dados Factuais , Interações Hospedeiro-Patógeno/genética , Fenótipo , Interface Usuário-Computador , Animais , Apicomplexa/classificação , Apicomplexa/genética , Apicomplexa/patogenicidade , Bactérias/classificação , Bactérias/genética , Bactérias/patogenicidade , Diplomonadida/classificação , Diplomonadida/genética , Diplomonadida/patogenicidade , Fungos/classificação , Fungos/genética , Fungos/patogenicidade , Insetos/classificação , Insetos/genética , Insetos/patogenicidade , Internet , Nematoides/classificação , Nematoides/genética , Nematoides/patogenicidade , Filogenia , Plantas/microbiologia , Plantas/parasitologia , Virulência
3.
Nucleic Acids Res ; 48(D1): D613-D620, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31733065

RESUMO

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.


Assuntos
Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/parasitologia , Biologia Computacional/métodos , Bases de Dados Factuais , Interações Hospedeiro-Patógeno/genética , Algoritmos , Animais , Antifúngicos , Bioensaio , Produtos Agrícolas , Gerenciamento de Dados , Genoma de Planta , Humanos , Internet , Fenótipo , Plantas , Ferramenta de Busca
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