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OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
BackgroundMajor advances in sequencing technologies and the sharing of data and metadata in science have resulted in a wealth of publicly available...
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Novel and improved Caenorhabditis briggsae gene models generated by community curation
BackgroundThe nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their...
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RelCurator: a text mining-based curation system for extracting gene–phenotype relationships specific to neurodegenerative disorders
BackgroundThe identification of gene–phenotype relationships is important in medical genetics as it serves as a basis for precision medicine....
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MetaPro: a web-based metabolomics application for LC-MS data batch inspection and library curation
IntroductionMetabolomics analysis based on liquid chromatography-mass spectrometry (LC-MS) has been a prevalent method in the metabolic field....
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Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus
BackgroundApproximately 4–8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved...
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Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation
BackgroundBiomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from...
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Approaching Mass Cytometry Translational Studies by Experimental and Data Curation Settings
Clinical studies are conducted to better understand the pathological mechanism of diseases and to find biomarkers associated with disease activity,...
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Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes
BackgroundFunctional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can...
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Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application
Virtual screening (VS) is an important approach in drug discovery and relies on the availability of a virtual library of synthetically tractable...
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Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN
Over the last 15 years, the costs of DNA sequencing have sharply fallen, effectively shifting the costs of DNA analysis from sequencing to...
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Avant-garde: an automated data-driven DIA data curation tool
Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration...
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Manual correction of genome annotation improved alternative splicing identification of Artemisia annua
Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic...
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Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
BackgroundThe DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples...
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Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
BackgroundNematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene...
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Functional annotation of a divergent genome using sequence and structure-based similarity
BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high...
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Genomic variant benchmark: if you cannot measure it, you cannot improve it
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of...
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Development, Preparation, and Curation of High-Throughput Phenotypic Data for Genome-Wide Association Studies: A Sample Pipeline in R
Genome-wide association studies (GWAS) have benefited from the advances of sequencing methods for the generation of high-density genomic data. By...
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Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine
BackgroundHigh tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an...
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Using Natural Language Processing for Context Identification in COVID-19 Literature
The COVID-19 pandemic led to an unprecedented volume of articles published in scientific journals with possible strategies and technologies to...
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Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
BackgroundKnowledge graphs support biomedical research efforts by providing contextual information for biomedical entities, constructing networks,...
