Rogers Alexander B, Kale Varsha, Baldi Germana, Alberdi Antton, Gilbert M Thomas P, Gupta Dipayan, Limborg Morten T, Li Sen, Payne Thomas, Petersen Bent, Rasmussen Jacob A, Richardson Lorna, Finn Robert D
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen 1353, Denmark.
Database (Oxford). 2025 Jan 11;2025. doi: 10.1093/database/baae112.
The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.
HoloFood项目采用了全基因组学方法，通过分析多组学数据、表型特征以及针对新型饲料的相关元数据，来了解宿主-微生物群相互作用对鲑鱼和鸡肉生产的影响。该项目的原始数据、衍生分析结果和元数据都存放在公共的开放档案库（生物样本库、欧洲核苷酸档案馆、代谢组学数据库和MGnify）中，因此利用这些不同的数据类型可能需要访问多个资源。在分析流程产生功能概况或基因组目录等衍生输出的情况下，这尤其复杂。HoloFood数据门户是一个网络资源，它简化了对项目数据集的访问。例如，用户可以方便地访问来自同一个体的多组学数据集，或通过关联的肠道微生物群样本检索宿主表型数据。还提供了特定于该项目的宏基因组组装基因组和病毒目录，并与MGnify中更广泛的数据集相链接。该门户仅存储提供这些关系所需的数据，并可能链接到基础存储库。该门户展示了一种未来多组学数据集如何可用的示范方法。数据库网址：https://www.holofooddata.org。
