1-20 of 8844
Journal Article
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress
Database, Volume 2025, 2025, baaf015, https://doi.org/10.1093/database/baaf015
Published: 22 February 2025
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Characterization of potato lncRNAs. (a) Percentage of lncRNAs and mRNAs wit...
Published: 22 February 2025
Figure 2.
Characterization of potato lncRNAs. (a) Percentage of lncRNAs and mRNAs with different lengths. (b) Percentage of lncRNAs and mRNAs with different numbers of exons.
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The user interface of the “Browse” and “Expression” contents in PotatoBSLnc...
Published: 22 February 2025
Figure 4.
The user interface of the “Browse” and “Expression” contents in PotatoBSLnc. (a) The data displayed after clicking the “Samples,” “Information,” “Sequence” sub-menus in the “Browse” menu. (b) The “Expression” dropdown options. (c) The figure displayed after clicking the StLNC15667 corresponding ro
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Overview of the potato lncRNA annotation and sample information. (a) The pi...
Published: 22 February 2025
Figure 1.
Overview of the potato lncRNA annotation and sample information. (a) The pipeline for the identification of lncRNAs. (b) The number of RNA-seq data at different disease/biotic stresses. (c) The number of RNA-seq data at different organ types.
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Analysis of lncRNAs from R. solanacearum-infected and -related con...
Published: 22 February 2025
Figure 3.
Analysis of lncRNAs from R. solanacearum -infected and -related control RNA-seq data. (a) Volcano map of DElncRNAs between the infected and noninfected groups of R. solanacearum . (b) Heat map of DElncRNAs. (c, d) The top 10 GO terms and KEGG pathways based on the cis / trans targets of DElncRNA
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The user interface of the “Biotic stress” content in PotatoBSLnc. (a) The “...
Published: 22 February 2025
Figure 5.
The user interface of the “Biotic stress” content in PotatoBSLnc. (a) The “Biotic stress” dropdown options. (b) The entries displayed after clicking each of the 12 biotic stress-lncRNA sub-menu. (c) The data displayed after clicking some entries in (b).
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The architecture of MANUDB with the process of creating MANUDB’s data (a) (...
Published: 21 February 2025
Figure 1.
The architecture of MANUDB with the process of creating MANUDB’s data (a) (nDNA means nuclear DNA, while mtDNA means mitochondrial DNA); frontend and backend layers and detailed SQL schema with datatypes where arrows mean that the connected tables can be joined by the indicated fields.
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The taxonomical structure of MANUDB with order, family, and genus informati...
Published: 21 February 2025
Figure 2.
The taxonomical structure of MANUDB with order, family, and genus information where orders are represented by blue color, families are represented by green color and genera are represented by yellow color and numbers in the brackets display the sizes of the corresponding taxonomical units.
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Plots of the comparative use case using the human and rat NUMTs as examples...
Published: 21 February 2025
Figure 4.
Plots of the comparative use case using the human and rat NUMTs as examples with distribution of NUMT sizes (a); distribution of sequence identities of NUMTs and their corresponding mitochondrial regions (b); regression plots of selected species’ genomic parts (chromosomes and scaffolds) and their c
Journal Article
MANUDB: database and application to retrieve and visualize mammalian NUMTs
Database, Volume 2025, 2025, baaf009, https://doi.org/10.1093/database/baaf009
Published: 21 February 2025
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Circos plot of the Visualize functionality, single species use case using N...
Published: 21 February 2025
Figure 3.
Circos plot of the Visualize functionality, single species use case using NUMTs of the rat genome where teal-colored outer track represents the different chromosomes and scaffolds; middle track shows a heatmap representation of cumulative NUMT sizes (in bp) of a given chromosome’s part while the inn
Journal Article
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database
Database, Volume 2025, 2025, baaf013, https://doi.org/10.1093/database/baaf013
Published: 20 February 2025
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Term normalization during CTD curation application interaction entry. CTD b...
Published: 20 February 2025
Figure 2.
Term normalization during CTD curation application interaction entry. CTD biocurators use a structured notation as shorthand to capture an interaction (circle 1), in this case requiring the entry of two genes (G1 and G2), three chemicals (C1-C3), and one phenotype (P1). Once the notation is entered,
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CTD/PubTator engineering architecture and workflow. In most cases, CTD iden...
Published: 20 February 2025
Figure 3.
CTD/PubTator engineering architecture and workflow. In most cases, CTD identifies articles for curation by either targeting specific chemicals or chemical sets from a “Chemical Priority Matrix,” or curating articles from 19 important toxicological journals on an ongoing basis. CTD’s Biocuration Mana
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Text mining summary report. The CTD CAPP’s PubMed Curation Activity page pr...
Published: 20 February 2025
Figure 4.
Text mining summary report. The CTD CAPP’s PubMed Curation Activity page provides links to both PubMed and PubTator; the green check mark (circle 1) indicates that the paper has undergone NLP-based preprocessing (conversely, a red “X” would indicate that the paper has not been preprocessed). The use
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CTD/pubtator integration. CTD biocurators typically curate the literature u...
Published: 20 February 2025
Figure 5.
CTD/pubtator integration. CTD biocurators typically curate the literature using PubTator’s online interface (circle 1). An excerpt is provided of the Text Mining Summary Report (circle 2), which summarizes the chemicals identified by PubTator that are relevant to CTD. The fully normalized MeSH chemi
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CTD Curation Overview. CTD biocurators review the literature (circle 1), tr...
Published: 20 February 2025
Figure 1.
CTD Curation Overview. CTD biocurators review the literature (circle 1), transforming authors’ free text using a specific methodology to make it informative and computational. Well-defined controlled vocabularies are used for every biological aspect of CTD, including chemicals, genes, phenotypes, di
Journal Article
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design
Database, Volume 2025, 2025, baaf001, https://doi.org/10.1093/database/baaf001
Published: 18 February 2025
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An overview of the LICEDB interface. (a) The homepage of the database, (b) ...
Published: 18 February 2025
Figure 1.
An overview of the LICEDB interface. (a) The homepage of the database, (b) the search interface of the database, (c) the batch data upload interface of the database, (d) the single data upload form interface, (e) BLAST similarity analysis tool, and (f) Clustal Omega similarity analysis tool.
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LICEDB search case. (a) Use the quick search feature to find information re...
Published: 18 February 2025
Figure 2.
LICEDB search case. (a) Use the quick search feature to find information related to pullulanase and (b) use the advanced search feature to query for enzymes with the English name “pullulanase” and Gene Bank number “AZP53538.1” for related information.
