ライフサイエンスコーパス: curated

1 inical data were standardized and rigorously curated.

2 ated inversion recovery [FLAIR] images) were curated.

3 In total 20 models were manually curated.

4 ancer metastasis using a clinical dataset we curated.

5 for modeling studies due to the way they are curated.

6 Here, we manually curated 112 datasets of phospho-enriched proteins, gener

7 LnCeVar curated 119 501 variation-ceRNA events from thousands of

8 In this study, we manually curated 1235 SVs, which can ultimately be used to evalua

9 We curated 610 pncA mutations with high confidence experime

10 When manually curated, 87% of these additional flagged features were v

11 mation from publicly available databases, we curated 883 FDA approved or investigational stage small

12 Here, we curated a comprehensive, searchable database that docume

13 To overcome this gap, we have curated a dataset of 242 experimentally determined chang

14 We have generated and curated a genome-scale metabolic model (iTgo) for the fa

15 g of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phyloge

16 its performance in the clinical setting, we curated a large representative dataset from the UK and a

17 Here, we curated a library of short hairpin RNAs for targeted sil

18 We curated a list (>2,500 ligand-receptor pairs) and identi

19 and peptide evidence from proteomic data, we curated a list of 254 PSGs with different levels of prot

20 For this, we curated a list of metabolic tasks and developed a framew

21 om the National Lung Screening Trial (NLST), curated a subset of 479 participants (244 for training a

22 etween neuropeptides and cancer, we manually curated a total of 127 human neuropeptide genes by integ

23 Study data provided to CEBS are manually curated, accessioned and subject to quality assurance re

24 sis that the expression of genes in a set of curated ADHD candidate genes and five a priori selected,

25 online content, spread via social media and curated algorithmically.

26 Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed

27 In addition, we curated an extensive set of ADAR1 and ADAR2 targets and

28 Data was curated and analyzed in a linked workflow involving non-

29 Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR

30 search engine employing in-house customized, curated and computationally generated databases and mult

31 Expert-curated and computer readable, disease maps may serve as

32 ng those identified from 13 registries, were curated and harmonized into a minimum set of 21 measures

33 LP, RNN, BiRNN) when compared on hundreds of curated and inferred transcription modules.

34 These sequences are expertly curated and made publicly available through an open acce

35 As this information is curated and made widely available to all stakeholders, i

36 Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular

37 Manually curated and predicted scaffold protein data will be a fo

38 package compendium, which includes manually-curated and standardized clinical, pathological, surviva

39 The project aims for an integrated, highly curated and user-friendly platform for disease-related k

40 include availability of sufficiently large, curated, and representative training data that includes

41 The available CDB was properly curated, and the pesticides were represented by conforma

42 ources and must be gathered, reconciled, and curated; and computational infrastructure is only now ga

43 We evaluated MirCure on a set of manually curated animal and plant miRNAs and demonstrated great a

44 it this feature to showcase integration with curated annotations from high-precision assays.

45 negative annotations are derived from expert-curated annotations of protein families on phylogenetic

46 we combine information mined from text with curated annotations stored in ChEMBL to investigate the

47 hese limitations, we present MEGARes, a hand-curated antimicrobial resistance database and annotation

48 Only 3 genes (KCNQ1, KCNH2, SCN5A) were curated as definitive genes for typical LQTS.

49 gy terms as our previous GO-slim, as well as curated associations of genes to these terms.

50 cal reaction relationships from two corpora: curated bacteria-related abstracts from the MetaCyc data

51 ur results emphasize the importance of using curated barcode libraries to obtain interpretable quanti

52 arious components of the database, visualize curated baseline expression of pathway-associated genes

53 We further provide a manually curated benchmark dataset that can be used for further m

54 This version now contains manually curated binding data for 7085 mutations, an increase of

55 rawn from the DrugBank database and manually curated bioactive compounds reported in the literature.

56 hensive and non-redundant resource of expert-curated biochemical reactions designed for the functiona

57 Finally, we curated biological data from the literature to show that

58 ces such as protein-protein interactions and curated biological pathways.

59 ks with predictable trajectories, literature-curated Boolean models and diverse transcriptional regul

60 ions in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing

61 istics in a large databank of natural images curated by human observers for salient objects and show

62 inct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGA

63 reference cell lines profiled by ENCODE and curated by the ENCODE Project Consortium for the ENCODE-

64 ngs (MeSH), which is a controlled vocabulary curated by the NLM experts.

65 ali, Niger, Nigeria, and Togo) collected and curated by the WHO Inter-country Support Team between 20

66 probabilistically integrating expertly-hand-curated (by reading original publications) heterogeneous

67 2,671,908 somatic mutations from 2780 highly curated cancer genomes with whole genome sequencing (WGS

68 systems biology maps captures all literature-curated cancer pathways with significant enrichment, alt

69 It can be used for viewing pre-curated cancer pathways, or as a graphical editor for cr

70 tified feature sets with each other and with curated cancer signatures.

71 g simulations and case studies of literature-curated candidate causal genes for schizophrenia, low-de

72 Methods We curated candidate genetic variants from previously publi

73 ge, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human c

74 We establish a high-quality curated catalogue of SVs in the genomes of a worldwide l

75 ing of more than 150 clinical variables were curated centrally, including demographics, laboratory va

76 -state cellular abundance with a large, well-curated clinical cohort of PTEN-variant carriers.

77 Our model was tested against internationally curated clinical datasets, achieving up to 85% accuracy.

78 wledgebase of ophthalmic diseases containing curated clinical, treatment and imaging data of 581,466

79 Using a clinico-genomically curated cohort, together with breast cancer models, we f

80 The GWAS Catalog delivers a high-quality curated collection of all published genome-wide associat

81 n 60 000 publications, making it the largest curated collection of metabolic pathways.

82 Experiments on five manually curated collections of TRs have shown that Dot2dot is mo

83 tility of integrative analysis of a manually curated compendium of genome-wide protein binding profil

84 ssifier to map and interpret interactions, a curated compendium of immunological combination treatmen

85 Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of hum

86 nternational Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exo

87 e also report a 46% increase in CTD manually curated content, which when integrated with other datase

88 gs fell into realistic ranges, with manually curated data less likely to contain implausible results

89 Genomes Online Database (GOLD) is a manually curated data management system that catalogs sequencing

90 would accurately determine skeletal age in a curated data set of pediatric hand radiographs.

91 We train and evaluate ThermoNet with a curated data set that accounts for protein homology and

92 Gene expression patterns were compared with curated data sets to identify upstream regulators.

93 BDSS then queries a metadata repository for curated data transfer mechanisms and optimal path to mov

94 Gephebase is a manually-curated database compiling our accumulated knowledge of

95 pike sorting algorithms across an extensive, curated database of ground-truth electrophysiological re

96 L) and to provide a well-annotated, manually curated database of high-confidence somatic mutations to

97 PhenoScanner is a curated database of publicly available results from larg

98 database is to continue to provide a highly curated database of sequence variants, while supporting

99 Disease NcRNAome Atlas (NSDNA) is a manually curated database that provides comprehensive experimenta

100 The PhenoScanner curated database was used to identify disease associatio

101 s prediction accuracies of 90% on a manually curated database.

102 Curated databases of chemical reactions exist but these

103 Benchmarks against manually curated databases of TF-gene interactions show that our

104 lenge to answer this question is the lack of curated databases with a representative set of experimen

105 ssible by the emergence of large-scale, well curated databases, as well as the substantial improvemen

106 ng known pathways and protein complexes from curated databases, interaction predictions are derived f

107 r 2) coding sequence homology searches using curated databases.

108 ds calculated either from user-input data or curated databases.

109 ing models for glycans that are trained on a curated dataset of 19,299 unique glycans and can be used

110 It is based on a curated dataset of blood Pb records from 59,483 North Ca

111 site prediction algorithms to a meticulously curated dataset of ligand-bound and ligand-free crystal

112 ea under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating

113 e benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun s

114 We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, where we ide

115 known structures and sequences, and download curated datasets of structurally characterized TCR compl

116 ers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofac

117 ) mutants analyzed in my laboratory; provide curated datasets with key features and publication links

118 By exploiting a well-curated deafness phenotype-genotype database, we identif

119 The Passports database currently contains curated details and standardized annotation for >1200 ce

120 We integrate curated, directly submitted, and collaboratively generat

121 Yet, experimentally curated disorder information still does not currently sc

122 res and has built up a significant corpus of curated domain architectures in support of naming bacter

123 Here we report a curated draft genome for 'Candidatus Parcunitrobacter ni

124 erence genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to a

125 s information publicly available for all the curated drugs.

126 The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site

127 e genome engineering in BioDesignER, we have curated eight context--neutral genomic loci, termed Safe

128 cids, as compared to more classical manually-curated encoding strategies, has not been systematically

129 COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data

130 s are exclusively based on published, expert-curated evidence.

131 ith a time-delayed analysis leveraging newly curated experimentally supported annotations.

132 f (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SL

133 s/cell types and sncRNA annotations and >800 curated experiments from ENCODE and GEO/SRA across multi

134 The dataset was curated expertly from the neuroanatomical literature usi

135 and contributions from Expert Panel members' curated files.

136 We present a new, curated flux balance analysis-based model of B. pertussi

137 functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq

138 Applying our curated framework to signaling and metabolic pathways, w

139 We train and test our method on the datasets curated from 16 species, yielding an average classificat

140 individual protein motif instances manually curated from 3467 scientific publications.

141 ons and genotypes provide routes to all data curated from a single source and to all phenotypes assoc

142 Here we use data curated from literature and online repositories to exami

143 human and yeast proteins that were manually curated from literature, including descriptions of moonl

144 ween 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles.

145 contains massive datasets that were manually curated from NCBI GEO and the exRNA Atlas, including 66

146 mutations across 1.4 million tumour samples, curated from over 26 000 publications.

147 t proteins localized in different organelles curated from published literature and database.

148 Molecular data, curated from published studies or from database submissi

149 METHODS AND In this study, we curated from the literature a high-quality set of 107 fu

150 sease and gene-disease interactions manually curated from the literature) are integrated with each ot

151 sted predictions from >107 million molecules curated from the ZINC15 database, our model identified e

152 FDA-ARGOS reference genomes compared to non-curated GenBank genomes.

153 emonstrated the utility of NetPAS in 50 well-curated gene sets and comparison of association studies

154 We tested this algorithm on curated gene sets from the Molecular Signatures Database

155 he agreement of identified feature sets with curated gene signatures relevant to the investigated dis

156 For 98% of these loci, the expert-curated gene was one of the candidate causal genes prior

157 ns 5,384 genes, 753 SCPs and 19,180 expertly curated gene-SCP associations.

158 Using our manually curated genes and miRNAs with evidence in CP in humans a

159 ruction of PCa Interactome network using the curated genes.

160 Of manually curated genomes, 22 (18 are complete), ranging from 159

161 ontinuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be f

162 In this article we provide a one-stop, curated graphical source for the key numbers (based most

163 Systematically curated HCM genes are essential to guide appropriate rep

164 sults are compared against lists of manually curated hinge residues, and the results suggest that PAC

165 test GLIDE on a collection of three recently curated human biological networks derived from the 2016

166 Gene annotations were curated in nine vertebrate model organisms and integrate

167 experimentally verified protein interactions curated in rich contextual detail to an internationally

168 le of published drug-gene interaction claims curated in the Comparative Toxicogenomics Database (for

169 ated by the fact that 8000-10 000 papers are curated in UniProt each year while curators evaluate 50

170 (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabol

171 trategy and better performance by literature-curated information followed by ChIP-seq data.

172 XTalkDB contains curated information for 650 pairs of pathways from over

173 rs, but grew to be the primary repository of curated information on both genes and genetic phenotypes

174 Where available, additional curated information on the binding affinity of the compl

175 such interactions as there are high-quality curated interactions from small-scale studies.

176 is we have developed ImmunoGlobe, a manually curated intercellular immune interaction network extract

177 Here we report a literature-curated interspecies network of the human gut microbiota

178 coding sequences (CDS), which were manually curated into 116 different protein families.

179 dden Markov models constructed from manually curated IS elements.

180 -94% (measured relative to existing manually curated knowledge bases).

181 egulated GPVI/ITAM targets out of context of curated knowledge were also illuminated, including a sys

182 formance against a gold standard of manually curated labels.

183 found a similar correlation with previously curated LADs and repressive histone modifications.

184 HCT-116 and observed overlap with previously curated LADs.

185 Several curated libraries for protists exists; none, however are

186 ering curves were fit to a thermodynamically curated library of assembly intermediates, using the pri

187 Here we present a freely available curated library of implanted electrocorticographic data

188 hmark existing programs based on a carefully curated library of rice TEs.

189 used an association study design based on a curated list of 3,295 single nucleotide polymorphisms ma

190 d that were filtered against expression in a curated list of survival-critical tissues.

191 Finally, using a manually curated list of viruses and natural and symptomatic host

192 The resulting models were evaluated using curated literature data extracted from different sources

193 ally relevant gene sets, which are currently curated manually, limiting their availability and accura

194 a second step, we selectively expanded this curated map with database knowledge.

195 The PheWAS paradigm takes advantage of a curated medical phenome, often derived from electronic h

196 Using curated metabolic characterization data from a large sam

197 kinetic models of metabolic networks using a curated metabolic model and available 13C-labeling distr

198 ion method to annotate unknown signals using curated metabolic pathways containing known metabolites.

199 t of 227 previously reported and extensively curated metabolite QTLs.

200 nnotated and publicly available genomes with curated metadata.

201 Indeed, curated microRNA complements of closely related organism

202 addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organ

203 Using 4,094 ClinVar-curated missense variants in clinically actionable genes

204 e(II)/(III)-5-LO or Cu(II)-tyrosinase from a curated mixture (1-17).

205 has become the world's largest repository of curated models and emerged as the third most used data r

206 These curated models comprehensively capture metabolic feature

207 access to reliable and semantically enriched curated models in standard formats that are easy to shar

208 With about 800 curated models, BioModels has become the world's largest

209 % differences in growth yields for 12 of the curated models.

210 PHI-base contains expertly curated molecular and biological information on genes pr

211 Then, curated molecular networks of MS/MS data were generated

212 mainBenchmark (MDB), a database suite of 412 curated multi-domain queries and 227,512 target sequence

213 Using a diverse curated multi-institutional, multi-modality, multi-organ

214 fication, using NMR in tandem with two newly curated NMR molecular structural motif metabolomics data

215 cer Genome Atlas into over 170,000 carefully curated nonredundant phosphorylation sites covering 18,6

216 ss database containing fully coordinated and curated 'omics' (genomics, transcriptomics, proteomics,

217 ly generated by a novel geometric method and curated opensource software EASAL (efficient atlasing an

218 uch as the gene-expression data, and overlay curated or experimental gene-gene interaction data to ex

219 gulator target gene lists frequently are not curated or have permissive inclusion criteria, impairing

220 Two curated oral 16S rRNA databases are available: HOMD and

221 using hyperimmune mouse serum samples and a curated panel of human serum.

222 nd increased interaction with the authors of curated papers.

223 illomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by

224 with decreasing technology costs, expanding curated pathogen sequence databases, and better data ana

225 c signals is an active area of research, and curated pathway databases describe these complex signali

226 ics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many

227 We identify more curated pathway gene sets significantly associated with

228 databases provide valuable information about curated pathways and other resources that can be used to

229 In addition, CancerGeneNet annotates curated pathways that are relevant to rationalize the pa

230 ach merges interactions extracted from human curated pathways with predicted interactions from machin

231 MPD houses rigorously curated per-animal data with detailed protocols.

232 We built a database of 538,213 manually curated phage protein sequences that we split into eleve

233 Plant Reactome is a free, open-source, curated plant pathway database portal, provided as part

234 We sought to do so using curated plant specimen data in the Botanical Information

235 d a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly e

236 We have re-curated previous entries to purge DisProt from conflicti

237 ference viruses, 12 498 previously published curated prophages derived from cultivated microbial isol

238 protein and associated genomics data such as curated protein sequence positional annotations from Uni

239 e of MatrisomeDB, a searchable collection of curated proteomic data from 17 studies on the ECM of 15

240 th state-of-the-art bioinformatics tools and curated public data.

241 hey curate, and that measuring the number of curated publications is insufficient to provide a comple

242 s compared to 548 healthy individuals, using curated publicly available microarray gene expression da

243 require tremendous amounts of data and well-curated reference data sets for algorithm training.

244 Leveraging a curated reference database of genes encoded by members o

245 vironmental sequences correctly, an expertly curated reference library is needed.

246 mic reads of known composition map onto well-curated reference protein sequences and thus, differs fr

247 e other available methods require a manually curated reference structure, ShaKer predicts reactivity

248 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 gen

249 nucleotide sequence using models built from curated RefSeqs.

250 mercial platforms provide large and manually curated regulatory networks and functionality to perform

251 ding standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phy

252 The most established ones are (1) manually curated repositories, (2) interactions derived from ChIP

253 Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modificat

254 Antibiotic Resistance Database is a manually curated resource containing high quality reference data

255 model organisms and those without extensive curated resources available.

256 curacy in many organisms without extensively curated resources.

257 ata in MetaCyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for

258 otation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBas

259 ndrome) and matched mouse models, using 2257 curated samples from the Inflammation and the Host Respo

260 ming to have the same accuracy as fully hand-curated SCOP releases.

261 coupling analysis strategy and apply it to a curated sequence database of hundreds of protein familie

262 entity and sequence coverage to the manually curated sequences than the original RepeatModeler.

263 near regression methodology using a manually curated set of 6,279 patients' longitudinal measurements

264 This paper presents a curated set of ethical dilemmas facing ophthalmologists

265 Using a manually-curated set of metabolic interactions between microbes,

266 We apply this index to a curated set of recurrent mutations identified within a d

267 Our approach relies on an expanded and curated set of viral protein families used as bait to id

268 Well-curated sets of pathology image features will be critica

269 ve extended the platform with a database for curated simulation experiments that can be accessed dire

270 ext, and to permit the downloading of highly curated, single- and multi-locus alignments for specific

271 although BIEN represents a comprehensive and curated source of point data, discrepancies in the appli

272 udy, we compile and evaluate a comprehensive curated stoichiometric model of this two-cell system, wi

273 tabase (MeLAD), which is designed to provide curated structural data and information exclusive to met

274 latform Bioconductor, to ensure that ImmPort curated study datasets are seamlessly accessible and rea

275 It provides a highly integrated and highly curated system offering a comprehensive view of current

276 Using other model species with curated TE libraries (maize and Drosophila), EDTA is sho

277 rse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly

278 We curated terms related to experimental conditions that af

279 We have manually curated the largest relational database of dendrimer pha

280 We curated the literature to keep RegulonDB up to date, and

281 We therefore integrated and extensively curated the most recent human metabolic models to constr

282 We curated the publicly available sequencing data for 3,393

283 images representing more than 200 syndromes, curated through a community-driven phenotyping platform.

284 Thirty-five genomes were manually curated to completion (circular and no gaps).

285 We manually curated to completion 15 distinct Lak phage genomes reco

286 d the first reported sequences were manually curated to completion.

287 ules and 256 literature references have been curated to date.

288 The captured data was manually curated to preserve data integrity and accuracy.

289 affect the disease interaction phenotype are curated to provide complete datasets for comparative pur

290 ivity that has to be actively maintained and curated to support its functional properties.

291 The models submitted to BioModels are curated to verify the computational representation of th

292 systematically analyzed over 10,000 manually curated toxin sequences using sequence clustering, netwo

293 est the underlying structure of data without curated training and specific problem definitions.

294 Instead of requiring highly curated training data, weak supervision relies on noisy

295 MetaGxData is the largest compendium of curated transcriptomic data for these cancer types to da

296 ge test data set, consisting of 200 manually curated US FDA drug labels.

297 odes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phe

298 o the use of AI, including the need for well-curated validation datasets, regulatory approval and fai

299 We further curated VIS-involved oncogenes and tumor suppressor gene

300 tly, such benchmarking features are manually curated with custom scripts in a non-standardized manner