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Journal Article
Leho Tedersoo and others
Database, Volume 2024, 2024, baae043, https://doi.org/10.1093/database/baae043
Published: 12 June 2024
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Published: 12 June 2024
Figure 1. Relative contribution of read sources ( A ) and taxonomic assignment sources ( B ) in the EUKARYOME dataset. GSMc, Global Soil Mycobiome consortium dataset ( 41 ; V. Mikryukov et al ., unpublished results). This image shows that 1) roughly one third of data are derived from metabarcoding studies
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Published: 12 June 2024
Figure 5. Relative richness and overlap of valid Glomeromycota genus names based on three marker genes in EUKARYOME, GlobalAMFungi and MaarjAM. Figure 5 shows that for the arbuscular mycorrhizal Glomeromycota genera, EUKARYOME has nearly twice higher taxonomic coverage compared with previous Glomeromycot
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Published: 12 June 2024
Figure 1. The architecture and content of IPAD-DB. In the major fields’ module, the black font is the information listed for all five inhibitors. The blue font is information unique to natural compounds, synthetic compounds and drugs.
Journal Article
Chong Peng and others
Database, Volume 2024, 2024, baae048, https://doi.org/10.1093/database/baae048
Published: 12 June 2024
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Published: 12 June 2024
Figure 2. Comparison of kingdom-level taxonomic composition in data subsets of EUKARYOME: SSU, ITS, LSU and long-read SSU-ITS-LSU. Figure 2 shows that fungi prevail in the ITS and LSU data subsets, animals are overrepresented in the SSU subset, and various organism kingdoms are more evenly distributed in t
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Published: 12 June 2024
Figure 4. Relative richness of eukaryote species names ( A ) and kingdom names ( B ) in EUKARYOME and three other major reference sequence databases, SILVA (SSU and LSU), PR2 (SSU) and UNITE (ITS). Note that besides species names, UNITE harbors 793 114 species hypotheses. Figure 4 indicates that EUKARYOME
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Published: 12 June 2024
Figure 3. Comparison of kingdom-level taxonomic composition in the EUKARYOME core database and three other major reference sequence databases, SILVA v138.1 (46 577 SSU reads and 16 152 LSU reads), PR2 v4.14.1 (162 563 SSU reads) and UNITE v9.0 (Sanger sequence data subset; 2 367 811 ITS reads). Figure 3 in
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Published: 10 June 2024
Figure 1. Overview of the methodology for developing ImPO, their methods and participants in each step. Full lines represent input from one step to another. Dashed lines represent feedback iteration cycles.
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Published: 10 June 2024
Figure 6. Diagram of the representation of the process of peptide identification through MS in ImPO. Purple rectangles represent classes, blue ellipses represent individuals, and yellow circles represent data values; black arrows represent subclass axioms; purple arrows represent rdf:type assertions of indivi
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Published: 10 June 2024
Figure 3. ER model representing the data from the immunopeptidomics domain.
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Published: 10 June 2024
Figure 8. Example displaying the modeling difference between ImPO and NCIt. ImPO and NCIt model the biological entities relevant to immunopeptidomics in a strikingly different manner. ImPO and NCIt can both classify (most of) the data objects but only ImPO contains the properties and restrictions to interconn
Journal Article
Daniel Faria and others
Database, Volume 2024, 2024, baae014, https://doi.org/10.1093/database/baae014
Published: 10 June 2024
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Published: 10 June 2024
Figure 2. Overview of the data collected in the Knowledge At the Tip of Your (KATY) project. Distribution and percentage breakdown of datasets by year (left), disease condition (center) and data source (right). Total number of datasets collected ( n ) = 75.
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Published: 10 June 2024
Figure 4. Excerpt of the ImPO visualized in GraphDB ( 78 ). The classes are represented as red circles and object property assertions between instances of the represented classes as directed arrows. Elements are labeled.
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Published: 10 June 2024
Figure 5. Diagram of the representation of a gene in ImPO. Purple rectangles represent classes, blue ellipses represent individuals, and yellow circles represent data values; black arrows represent subclass axioms; purple arrows represent rdf:type assertions of individuals or object property restrictions rela
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Published: 10 June 2024
Figure 7. Diagram of the representation of the concept of epitope contig in ImPO. Purple rectangles represent classes, blue ellipses represent individuals, and yellow circles represent data values; black arrows represent subclass axioms; purple arrows represent rdf:type assertions of individuals or object pro
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Published: 06 June 2024
Figure 3. Sankey figure of specialties distribution of low predictability for costs/ALOS, low quality of care or insufficient access to medical resources, insufficient consideration about complexity classification and inadequate reimbursement, respectively.
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Published: 06 June 2024
Figure 1. Work flow of the study and the website interfaces of DRGKB (A) Flowchart of the search strategy (B) Entity-relation diagram of DRGKB, where the red parts represent the classifications of indicators; the interface of DRGKB (C) Home, (D) Information page, (E) Search page and (F) Search results page.
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Published: 06 June 2024
Figure 4. DRGs evolution model and related core concepts.