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Published: 17 January 2025
Figure 1. Illustration of the eight LSF–disease relation types in LSD600.
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Published: 17 January 2025
Figure 2. LSD600 statistics for the eight distinct LSF–disease relation types.
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Published: 17 January 2025
Figure 3. LSD600 statistics for eight distinct LSF–disease relation types per disease category.
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Published: 17 January 2025
Figure 6. Performance plot for relation extraction across different relation types.
Journal Article
Esmaeil Nourani and others
Database, Volume 2025, 2025, baae129, https://doi.org/10.1093/database/baae129
Published: 17 January 2025
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Published: 17 January 2025
Figure 5. Distribution of disease and LSF mentions in LSD600 abstracts.
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Published: 17 January 2025
Figure 4. An overview of the distribution of relations in LSD600.
Journal Article
Database, Volume 2025, 2025, baae131, https://doi.org/10.1093/database/baae131
Published: 13 January 2025
Journal Article
Alexander B Rogers and others
Database, Volume 2025, 2025, baae112, https://doi.org/10.1093/database/baae112
Published: 11 January 2025
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Published: 11 January 2025
Figure 1. The schema used for HoloFood animals and samples registered in BioSamples [ 8 ]. Individual animals are accessed as BioSamples, with metadata sections as shown on the left. Most of these metadata sections are shared between the two systems. Extraction-level (derived) samples are registered separatel
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Published: 11 January 2025
Figure 3. Overview of the multiomic samples available in the HoloFood Data Portal for each system. Different multiomics sample sets were extracted from animals in multiple trials and time points. Each row shows how many individual animals are available covering that multi-omic combination. Combinations are sh
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Published: 11 January 2025
Figure 4. The primary dataset available in the data portal is a list of samples (registered in BioSamples). The sample list (in the background of this composite screenshot) can be partitioned along different axes: in this case by system, omic type, and treatment. It can also be partitioned by host, as shown b
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Published: 11 January 2025
Figure 5. Screenshot showing a sample detail page for a metagenomic sample (left). The analysis of metagenomic samples is performed by and stored in MGnify [ 9 ]. The data portal shows a summary of this MGnify data and links to MGnify where users can browse the analysis dataset (right).
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Published: 11 January 2025
Figure 2. The data collection process of DisGeNet: (a) the collection of node information and (b) the collection of link information.
Journal Article
Yaxuan Hu and others
Database, Volume 2025, 2025, baae122, https://doi.org/10.1093/database/baae122
Published: 11 January 2025
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Published: 11 January 2025
Figure 1. The statistics of DisGeNet: (a) six types of links network, (b) four types of nodes, (c) statistics of links, and (d) the top 50 diseases associated with genes.
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Published: 11 January 2025
Figure 3. Statistical comparison of data in DisGeNet: (a) node data and (b) link data.
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Published: 11 January 2025
Figure 5. A general use process of DisGeNet: (a) the interface of the search module with “AIDS” input as the retrieved disease in the “Search” page (disease name used as an example), (b) fuzzy search result page of “AIDS”, (c) filtering links by node types, (d) the search results shown in a list manner, and (
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Published: 11 January 2025
Figure 2. Genome catalogues were created for each system. HoloFood-derived metagenome-assembled genomes were combined with other publicly available chicken and fish data to produce genome catalogues for the MGnify Genomes resource [ 11 ]. In this example, the HoloFood genome clusters with three other genomes
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Published: 11 January 2025
Figure 4. Interface of DisGeNet: (a) search for all associations and interactions, and (b) browse all associations and interactions.