Manual curation
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
... In the case of chemicals, they can also be identified by a specific structure representation such as a connection table, an InChI string or a simplified molecular input line entry specification (SMILES). To achieve this, ...
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Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)
... Genes were identified using Prodigal [47] as part of the DOE-JGI genome annotation pipeline [48], followed by a round of manual curation using the JGI GenePRIMP pipeline [49]. The predicted CDSs were ...
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Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
... of manual curation using the JGI GenePRIMP pipeline CDSs were translated and used to search the Na- tional Center for Biotechnology Information (NCBI) nonredundant database, UniProt, ...
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The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial–mesenchymal transition, and immune response
... Manual curation of the entire list of identified mutated genes also indicated that 10 of them belonged to the MErT/EMT pathway in keeping with our data concern- ing gene expression on the same DSRCT ...
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Complete genome sequence of Sulfurimonas autotrophica type strain (OK10T)
... Genes were identified using Prodigal [37] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [38]. The ...
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Complete genome sequence of Kribbella flavida type strain (IFO 14399T)
... of manual curation using the JGI GenePRIMP pipeline ...and manual functional annotation was per- formed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform ...
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Complete genome sequence of Cellulophaga algicola type strain (IC166T)
... Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [34]. The ...
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Complete genome sequence of Marivirga tractuosa type strain (H-43T)
... Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipe[r] ...
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Complete genome sequence of Ferrimonas balearica type strain (PATT)
... of manual curation using the JG CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonre- dundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and ...
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Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)
... Genes were identified using Prodigal [25] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [26]. The ...
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Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T)
... Genes were identified using Prodigal [31] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePrimp pipeline [32]. The ...
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Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T
... Genes were identified using Prodigal [32] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePrimp pipeline [33]. The ...
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Complete genome sequence of Desulfomicrobium baculatum type strain (XT)
... Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using JGI’ predicted CDSs we[r] ...
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Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent
... Genes were identified using Prodigal [41] as part of the Oak Ridge National Laboratory genome annota- tion pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [42]. The ...
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Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)
... Genes were identified using Prodigal [28] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipe[r] ...
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Complete genome sequence of Tolumonas auensis type strain (TA 4T)
... Genes were identified using Prodigal [28] as part of the Oak Ridge National Laboratory genome an- notation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [29]. The ...
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Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus
... The manual curation of data from the published literature provides a rich and valuable resource that combines sequences with gene names and functional information about proteins, such as pheno- types of ...
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Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033
... The genome sequence was annotated using a com- bination of several annotation tools via the Magni- fying Genome (MaGe) Annotation Platform [28]. Genes were identified using Prodigal [29] and AMIGene [30] as part of the ...
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Computer-assisted curation of a human regulatory core network from the biological literature
... Of all 1625 manually inspected sentences, 643 (39.6%) con- tained no evidence that the article contains any information about a regulatory relationship. Thus, the precision of our text mining pipe- line on the top-2500 ...
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Plagiarism in submitted manuscripts: incidence, characteristics and optimization of screening—case study in a major specialty medical journal
... As have others before us [11, 12], we find iThenticate to be a useful tool for alerting editors to possible plagiar- ism. However without manual curation, it is impossible to determine if text copying rises ...
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