ライフサイエンスコーパス: curated

1 In total 20 models were manually curated.

2 All data are manually curated.

3 -consumingly visually inspected and manually curated.

4 d peptide ligands is annotated with manually curated 2D chemical structures or amino acid sequences,

5 delineate genome-wide lncRNA expression, we curated 7,256 RNA sequencing (RNA-seq) libraries from tu

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

7 0), which greatly expands the number of both curated (968) and automatically annotated catalytic site

8 We manually curated a gold standard set of 132 crosstalking pathway

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

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

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

12 , 36 compounds of 3925 unique chemicals with curated activity in the HTS data using high-quality dose

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

14 ged the way many specimens are collected and curated, advances in technology have shown promise for e

15 5% of relevant published literature manually curated amounting to more than 15,000 journal articles a

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

17 As a proof-of-concept, we have curated and analyzed control and case breast cancer data

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

19 Here, we performed, curated and analyzed nearly 300 RNA-Seq libraries coveri

20 We classified, curated and annotated predicted kinases, and assessed th

21 Our goal was to provide an accurately curated and annotated Reference Sequence (RefSeq) data s

22 intrinsic value, have never been collected, curated and classified.

23 Using the merged collection of curated and converted Reactome pathways, we demonstrate

24 These datasets were manually curated and hierarchically organized based on Experiment

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

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

27 han a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be di

28 nkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely ca

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

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

31 All the data have been carefully curated and processed with a streamlined analysis pipeli

32 izing ageing resources, providing a manually-curated and readily accessible source of age-related cha

33 tic suppression, we examined both literature-curated and unbiased experimental data, involving system

34 We assembled, curated, and integrated genetic, genomic, transcriptomic

35 from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high

36 Existing ontology tools provide functional, curated annotations for many genes and can be used to de

37 tems when tested on prokaryotic genomes with curated annotations of IS elements.

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

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

40 proteins are functionally connected, we also curated antizyme inhibitor genes to more fully represent

41 We've developed a highly curated bacterial virulence factor (VF) library in PATRI

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

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

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

45 hensive and non-redundant resource of expert-curated biochemical reactions described using species fr

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

47 the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows.

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

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

50 The results show that curated biomedical databases can potentially be reused a

51 m where pathways are created and continually curated by any interested party.

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

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

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

55 more similar to a gold standard matrix hand-curated by the scientist co-authors.

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

57 omprehensive analysis of seven independently curated cancer gene sets as well as six disease or trait

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

59 Methods We curated candidate genetic variants from previously publi

60 ic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pa

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

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

63 to build tools that leverage this carefully curated chemical biology resource.

64 curacy studies performed using a panel of 80 curated clinical isolates, rates of essential and catego

65 from a chosen somatic CNV caller, such that curated CNV segments will be used for down-stream applic

66 Aging Chart is a new, community-curated collection of aging pathways and knowledge that

67 rom >46,000 publications, and is the largest curated collection of metabolic pathways.

68 However, extensive and well-curated collections of landraces, wild barley accessions

69 Expression Database is an extensive and well-curated community resource of mouse developmental expres

70 g/expression.shtml) is an extensive and well-curated community resource of mouse developmental expres

71 MaizeGDB is a highly curated, community-oriented database and informatics ser

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

73 RFAMILY has more than doubled its holding of curated complete proteomes over all cellular life, from

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

75 The manually curated condition annotation has been overhauled as well

76 the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species

77 resent Secmarker, a method based on manually curated covariance models capturing the specific tRNASec

78 tudies, MGD maintains a core of high-quality curated data and integrates experimentally and computati

79 ittee of weak classifiers that consider both curated data and the text.

80 ral approach to information extraction using curated data as training examples.

81 The curated data can be useful as training examples for info

82 the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed an

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

84 inical data are needed in a standardized and curated data platform.

85 oster the creation and dissemination of well-curated data repositories.

86 tudies and data collection and analysis, and curated data sets have .

87 s and community researchers provide manually curated data to PomBase.

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

89 ing examples for information extraction, but curated data usually lack the exact mentions and their l

90 Using the curated data, BIO_CYCLE is compared to other approaches

91 growth in recent years in terms of new data curated, data downloads and new functions and tools.

92 our approach with entries in a popular human-curated database (UniProt) for each of the previously me

93 The CCGD is a manually curated database containing a unified description of all

94 We provide a curated database of 746 currently known genes, mutations

95 REBASE is a comprehensive and fully curated database of information about the components of

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

97 A curated database of rodent uterotrophic bioactivity.

98 s, using a benchmark data set extracted from curated database records.

99 ease associations when benchmarking based on curated database records.

100 ing protein mutation disease associations in curated database records.

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

102 We previously developed a manually curated database, DBSecSys, of bacterial secretion syste

103 After adjusting for the defects in the curated database, the revised F-measure of MutD in assoc

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

105 It is a curated database; each glycan-protein binding pair is as

106 ranscriptomes was examined by BLASTx against curated databases of genes intimately and exclusively in

107 SeqSero is based on curated databases of Salmonella serotype determinants (r

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

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

110 rate relationships mined from literature and curated databases, to first generate biologically meanin

111 This extensive, well-curated dataset should provide a basis for developing ne

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

113 uthoritative and timely research resource of curated descriptions of human genes and phenotypes and t

114 We integrate curated, directly submitted, and collaboratively generat

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

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

117 ng of the Ebola literature and creation of a curated Ebola database.

118 protein families, containing 14 831 manually curated entries in the current release, version 27.0.

119 Since extensive and manually curated experimental data about NR ligands and structure

120 seline and differential expression data from curated expression studies in plants.

121 For randomly curated extractions, the system achieved between 62% and

122 of Interacting Proteins and against randomly curated extractions.

123 es existing experimental data and literature-curated facts to identify genes involved in aging and li

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

125 itions and developmental stage were manually curated for each sample.

126 om 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets f

127 workflow currently possible and the manually curated fragmentation characteristics presented here wil

128 in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all seq

129 of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD.

130 mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies.

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

132 018 protein-coding and 199 non-coding genes) curated from over 9000 articles.

133 ctional annotations for genomic elements are curated from published literature, submitted by research

134 on factors, based on validated data manually curated from published literature.

135 ers, acquired through bulk data pipelines or curated from published literature.

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

137 ly, we used regulatory interactions manually curated from the literature to construct a regulatory ne

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

139 s were evaluated on a set of 7,522 chemicals curated from the literature.

140 ecular targets of adaptive immune responses--curated from the published literature and submitted by N

141 gene-disease interactions that are manually curated from the scientific literature by professional b

142 Independently, manually curated FS are provided to principle investigators for r

143 While the manually curated Gene Ontology (GO) is widely used, inferring a G

144 esearchers can use orthology to leverage the curated gene pathways of model organisms, such as human,

145 all, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates b

146 In contrast with methods that use curated gene sets, this approach uses signatures extract

147 analyzing coordinated targeting of different curated gene sets, we observe distinct evolutionary sign

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

149 contains more than 75 high-quality, manually-curated genome-scale metabolic models.

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

151 In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA

152 Seq were highly consistent with the manually curated glycan structures.

153 A customized database was curated (GO-Elite) and used to identify AR-specific dysr

154 A repository of curated HTS training materials would support trainers in

155 s an openly accessible database of carefully curated hydrogen/deuterium exchange (HDX) data extracted

156 The algorithm was validated against manually curated images of pavement cells of widely varying sizes

157 atabase alignments, which have been manually curated in the light of available crystal structures, an

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

159 ICE currently includes curated in vivo test data, reference chemical informatio

160 tations of selected domain families that are curated in-house and organized into hierarchical classif

161 The 'Regulatory sites' dataset includes curated information about modification sites that regula

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

163 MTB provides online access to expertly curated information on diverse mouse models for human ca

164 This curated information on virulence has been integrated wit

165 ents the current databases that focus on the curated interactions and the BioDrugScreen database that

166 Moreover, we also include experimentally curated interactions which are linked to their sources:

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

168 color and depth image data were recorded and curated into 109 segments, each containing 1,000 images,

169 CSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures

170 dden Markov models constructed from manually curated IS elements.

171 to referencing genes in probe sets and using curated knowledge bases.

172 formance against a gold standard of manually curated labels.

173 fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select a

174 GEneSTATION contains curated life history information on pregnancy and reprod

175 This is achieved by combining a manually curated list of bacterial genomes from human faecal samp

176 Furthermore, after establishing a curated list of genes coding for products targeted to mi

177 Together, these results provide a curated list of genes required for VSV replication.

178 This manually curated, literature-derived database, comprising over 10

179 known cancer genes, mutation information is curated manually from the scientific literature, allowin

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

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

182 ystems biology requires extensive, carefully curated measurements of cellular components in response

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

184 ded in the HTML file connect the user to the curated metabolic databases housed in ProCyc, a Pathway

185 idual gene expression and on canonical human curated metabolic pathways.

186 uencing projects along with a broad array of curated metadata.

187 The highly curated model accurately predicts phenotypes under photo

188 The curated model of the metabolic network of Anabaena sp. P

189 These curated models comprehensively capture metabolic feature

190 We will continue documenting curated models of non-model microbial species and improv

191 % differences in growth yields for 12 of the curated models.

192 PubMed and other resources; (ii) We further curated moderate SNP-trait associations (P-value < 1.0 x

193 www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes pr

194 AR/BPS Guide to PHARMACOLOGY provides expert-curated molecular interactions between successful and po

195 nces and filters for predefined biologically curated motif compositions.

196 igital Development provides a comprehensive, curated, multidimensional database for developmental bio

197 We obtained curated N-terminally acetylated and unacetylated sequenc

198 Commercial tools based on large, manually curated networks of causal relationships offering such f

199 JASPAR is an open-access database storing curated, non-redundant transcription factor (TF) binding

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

201 capabilities of data mining approaches is a curated, open-access, up-to-date and comprehensive colle

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

203 cal molecules associated with all subsets of curated or user submitted groups of gene sets and gene n

204 SCOP is an expert-curated ordering of domains from the majority of protein

205 ling networks from BioModels with real-world curated outcomes.

206 pectral reference libraries, which have been curated over the last several decades, contain almost ex

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

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

209 ce methods in their capacity to retrieve the curated Pathway Commons interactions from RPPA data.

210 athVisio is also integrated in the community curated pathway database WikiPathways.

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

212 el of enrichment of somatic mutations within curated pathways, applying a novel approach that identif

213 nthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission

214 over the past 5 y has generated a rich, well-curated phantom dataset from which PET/CT make-and-model

215 atabase of cell lineage differentiation with curated phenotypes, cell-specific gene functions and a m

216 We used curated phosphoproteomic experiments and a gold standard

217 redicted in the FG proteome using a manually curated pipeline dedicated to the identification of GPCR

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

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

220 ed training which makes unnecessary manually curated preparation of training sets.

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

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

223 Significant genes are mapped to our manually curated protein-protein interaction database to construc

224 s via sequence comparisons with reference or curated proteins.

225 We used curated proteomic data from endogenous kinase substrates

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

227 n changes composition or size using a set of curated, publicly available breast cancer microarray exp

228 We curated qualitative Class I HLA-peptide binding data and

229 orldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse.

230 Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interaction

231 rovides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs tha

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

233 mation and included hundreds of new manually curated references to literature.

234 nt containing information from 2219 manually curated references.

235 tebrate organisms resulted in a total of 461 curated RefSeq records.

236 tation database (ORegAnno) is a resource for curated regulatory annotation.

237 ons into a single, high quality catalogue of curated regulatory information.

238 The Network of Cancer Genes is a manually curated repository of cancer genes derived from the scie

239 A provides manual and programmatic access to curated, representative ribosomal RNA sequence alignment

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

241 mber database (rrnDB), a publicly available, curated resource for copy number information for bacteri

242 ch aims to provide a comprehensive, manually curated resource for experimentally validated GPCR-ligan

243 These orthologous groups provide a curated resource for large-scale protein sequence annota

244 etabolism" seeks to provide a collective and curated resource on methods and models used to investiga

245 s created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/inta

246 model organisms and those without extensive curated resources available.

247 import of proteoform information from expert curated resources, and our ability to dynamically genera

248 observations from the literature and highly curated resources.

249 curacy in many organisms without extensively curated resources.

250 In addition to approximately 200 curated rice reference pathways, the portal hosts gene h

251 the exteriors of conventionally drilled and curated rocks of stratigraphic equivalence reach concent

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

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

254 munities (HPMC) database provides a manually curated, searchable, metagenomic resource to facilitate

255 It is expected that curated secondary databases will help organize some of t

256 We have collected manually curated sequence alignments for >3000 sequences, in vivo

257 Curated sequence assemblies belonging to five genera wer

258 Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene,

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

260 ian Inheritance in Animals), we introduced a curated set of 117 disease-causing SAVs in animals.

261 ata and detecting low quality cells, using a curated set of over 20 biological and technical features

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

263 validate EBC's performance against manually-curated sets of (1) pharmacogenomic relationships from P

264 among humans in Africa, here we examine well-curated sets of bat (Eidolon helvum, n = 44) and human (

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

266 Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide var

267 The manually curated signatures are used as a training set to develop

268 use of these types of statistics for highly curated signed networks in which ambiguities arise but a

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 ia, viruses, archaea and fungi with manually curated species classification and enhanced sample metad

272 As a resource for highly curated, standardized and accessible models of metabolis

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

274 protein function from multiple organisms and curated structural models for each variant from crystal

275 molecules (non-redundant) from 377 manually curated studies of 230 publications.

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

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

278 ving specific biochemical reactions from the curated systems biology markup language models contained

279 Consequently, we curated the data from 15 palmitoylation proteomics studi

280 predicted the putative causal genes; (iv) We curated the detailed sub-populations and related sample

281 of which are expressed in one or more of the curated tissues.

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

283 The metadata were manually curated to ensure annotation consistency.

284 The alignments were checked and curated to make them specific to the targeted KO.

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

286 SARG was curated to remove redundant sequences and optimized to f

287 nce of target gene inactivation, sgRNAs were curated to target both 5 constitutive exons and exons th

288 A large set of models is curated to verify both correspondence to the biological

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

290 ghput immuno-profiling study on all manually curated toxins from Dendroaspis species and selected Afr

291 piwi-interacting RNA clusters (3.6-fold) and curated transcription factors (4.1-fold), including zinc

292 In this study, we curated two datasets and conducted a comprehensive model

293 The system is largely un-curated, unstandardized, and lacks a method for linking

294 tion, and demonstrates the need for a better curated variant interpretation knowledge base.

295 We have manually curated VFs from six prioritized NIAID (National Institu

296 A curated Web-based user-friendly sequence typing tool bas

297 d for the construction and purification of a curated whole-genome collection of single-gene transposo

298 Rhea reactions are extensively curated with links to source literature and are mapped t

299 Reactome pathways are centrally curated with periodic input from selected domain experts

300 ly, it can be used to interrogate any genome curated within bioconductor.