ライフサイエンスコーパス: curate

1 In total 20 models were manually curated.

2 All data are manually curated.

3 -consumingly visually inspected and manually curated.

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

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

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

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

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

9 otechnology Information (NCBI) maintains and curates a publicly available database of annotated genom

10 As the process of curating a published phylogenetic estimate is not error-

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

16 re, offers a computational workflow that can curate and evaluate BP-related genetic data.

17 We import, analyse, curate and integrate a diverse collection of large-scale

18 ing results and enables analysts to manually curate and refine cluster assignments.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

35 Xenbase imports, indexes, curates and manages data from both species; all of which

36 MGD curates and provides functional and phenotype annotation

37 The ChEMBL database curates and stores standardized bioactivity, molecule, t

38 a publically available resource for storing, curating and analyzing sets of genes from heterogeneous

39 By curating and annotating data from the literature and maj

40 read and evaluate many more papers than they curate, and that measuring the number of curated publica

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

65 Methods We curated candidate genetic variants from previously publi

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

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

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

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

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

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

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

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

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

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

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

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

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

79 The manually curated condition annotation has been overhauled as well

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

101 A curated database of rodent uterotrophic bioactivity.

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

103 ease associations when benchmarking based on curated database records.

104 ing protein mutation disease associations in curated database records.

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

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

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

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

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

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

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

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

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

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

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

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

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

118 We integrate curated, directly submitted, and collaboratively generat

119 to a multi-editor model utilizing Protege to curate DO in web ontology language.

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

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

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

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

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

125 of Interacting Proteins and against randomly curated extractions.

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

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

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

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

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

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

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

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

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

135 018 protein-coding and 199 non-coding genes) curated from over 9000 articles.

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

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

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

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

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

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

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

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

144 vailable biomedical databases derive data by curating from literatures.

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

146 eb Apollo software for groups that choose to curate gene models.

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

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

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

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

151 addition to naming genomic loci we manually curate genes into family sets based on shared characteri

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

167 This curated information on virulence has been integrated wit

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

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

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

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

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

173 dden Markov models constructed from manually curated IS elements.

174 formance against a gold standard of manually curated labels.

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

176 GEneSTATION contains curated life history information on pregnancy and reprod

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

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

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

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 Importantly, it curates model organism-specific databases to concurrentl

190 These curated models comprehensively capture metabolic feature

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

192 % differences in growth yields for 12 of the curated models.

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

194 We manually curate molecular details of pathways in these domains fo

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

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

197 nces and filters for predefined biologically curated motif compositions.

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

199 We obtained curated N-terminally acetylated and unacetylated sequenc

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

218 We used curated phosphoproteomic experiments and a gold standard

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

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

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

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

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

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

225 s via sequence comparisons with reference or curated proteins.

226 We used curated proteomic data from endogenous kinase substrates

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

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

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

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

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

232 nt containing information from 2219 manually curated references.

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

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

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

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

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

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

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

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

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

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

243 model organisms and those without extensive curated resources available.

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

245 observations from the literature and highly curated resources.

246 curacy in many organisms without extensively curated resources.

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

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

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

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

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

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

253 Curated sequence assemblies belonging to five genera wer

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

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

256 D-MHC Database project collects and expertly curates sequences of the major histocompatibility comple

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

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

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

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

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

262 We first curate several large synthetic and biological time serie

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

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

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

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

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

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

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

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

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

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

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

274 levant features allowing user to examine and curate the CNV calls.

275 Our annual updates curate the data using a semi-automated literature search

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

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

278 BioGRID curates the biomedical literature for major model organi

279 ch into Candida pathogenesis and biology, by curating the scientific literature in real time, and con

280 to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base.

281 nces of toxicologically significant genes by curating these sequences and electronically annotating t

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

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

284 The metadata were manually curated to ensure annotation consistency.

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.