Manual annotation
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Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge.
12p vibransone 28-03-2024 1 1 Download
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The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge.
18p vicwell 29-02-2024 5 2 Download
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Continued part 1, part 2 of ebook "PHPUnit manual: Release latest" provides readers with contents including: logging; extending PHPUnit; assertions; annotations; the XML configuration file; write custom assertions;...
98p tieulangtran 28-09-2023 1 1 Download
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Scoring laboratory polysomnography (PSG) data remains a manual task of visually annotating 3 primary categories: sleep stages, sleep disordered breathing, and limb movements. Attempts to automate this process have been hampered by the complexity of PSG signals and physiological heterogeneity between patients.
8p visteverogers 24-06-2023 6 2 Download
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To automatically recognize self-acknowledged limitations in clinical research publications to support efforts in improving research transparency. To develop our recognition methods, we used a set of 8431 sentences from 1197 PubMed Central articles. A subset of these sentences was manually annotated for training/testing, and inter-annotator agreement was calculated.
7p visteverogers 24-06-2023 4 2 Download
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Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible
19p vielonmusk 30-01-2022 14 0 Download
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Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Manual annotation efforts are time-consuming and complex; however, software can help reduce these drawbacks.
14p vilarryellison 29-10-2021 11 0 Download
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Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models.
19p vibeauty 23-10-2021 8 1 Download
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The quality of microbial genome sequences has been a concern ever since the emergence of genome sequencing. The quality of the genome assemblies is dependent on the sequencing technology used and the aims for which the sequence was generated.
4p visilicon2711 20-08-2021 12 1 Download
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The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution.
12p visilicon2711 20-08-2021 8 1 Download
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Traditional anthropometric studies of human face rely on manual measurements of simple features, which are labor intensive and lack of full comprehensive inference. Dense surface registration of three-dimensional (3D) human facial images holds great potential for high throughput quantitative analyses of complex facial traits.
12p viwyoming2711 16-12-2020 14 1 Download
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Cilia are hairlike structures protruding from nearly every cell in the body. Diseases known as ciliopathies where cilia function is disrupted can result in a wide spectrum of diseases. However, most techniques for assessing ciliary motion rely on manual identification and tracking of cilia. This annotation is tedious and error-prone and more analytical techniques impose strong assumptions such as periodic motion of beating cilia.
8p vigeorgia2711 01-12-2020 9 1 Download
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The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data.
11p vikentucky2711 26-11-2020 11 1 Download
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Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task.
6p vikentucky2711 26-11-2020 16 2 Download
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Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes by using published literature.
13p vioklahoma2711 19-11-2020 9 1 Download
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Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred.
13p viflorida2711 30-10-2020 9 2 Download
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Named Entity Recognition (NER) is a key task in biomedical text mining. Accurate NER systems require task-specific, manually-annotated datasets, which are expensive to develop and thus limited in size. Since such datasets contain related but different information, an interesting question is whether it might be possible to use them together to improve NER performance.
14p viflorida2711 30-10-2020 9 2 Download
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Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With deep learning, cells can be detected with high accuracy, but manually annotated training data is required.
10p vicoachella2711 27-10-2020 11 0 Download
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Fast and accurate automatic segmentation of skeletal muscle cell image is crucial for the diagnosis of muscle related diseases, which extremely reduces the labor-intensive manual annotation. Recently, several methods have been presented for automatic muscle cell segmentation.
9p vicoachella2711 27-10-2020 26 0 Download
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Automatically understanding chemical-disease relations (CDRs) is crucial in various areas of biomedical research and health care. Supervised machine learning provides a feasible solution to automatically extract relations between biomedical entities from scientific literature, its success, however, heavily depends on large-scale biomedical corpora manually annotated with intensive labor and tremendous investment.
14p vijisoo2711 27-10-2020 16 1 Download