2,995 research outputs found
phenoscape/phenoscape-kb-services: Release 2.0
No full textWhat's Changed
Enables Docker build for this application by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/52
Query by publications by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/54
Restore TSV output for taxon list output by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/60
Implement preliminary service providing Jaccard similarity score for a pair of character states by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/61
Add missing import. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/62
Correct services to ignore limit if <1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/65
Update from swagger hub to fix study query doc. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/66
Service for pairwise similarity of list of ontology classes by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/67
Include entity in OntoTrace query including its parts. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/71
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/72
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/74
Created service for computing ancestor matrix by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/75
Issue 77 by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/78
Document subsumer matrix service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/79
Make sort case-insensitive by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/80
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/84
Update matrix service to take JSON array of IRIs. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/85
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/86
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/88
Support POST for OntoTrace. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/87
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/96
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/97
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/99
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/100
Make ic_disparity query parameter names consistent. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/101
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/102
Return matrix for study as application/xml. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/103
Added method for executing SPARQL ASK queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/105
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/107
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/108
Implement services to handle queries for inferred presence/absence. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/110
New presence absence matrix branch by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/111
Generalize term search. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/115
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/117
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/118
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/120
Accept JSON array for definedBy. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/119
Add ui button to get dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/114
Merge master by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/123
Fix query parameter name by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/124
Fix space in sample data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/125
Update media type to text/csv. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/126
Boost match rank of terms with text exactly equal to search text. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/131
Return only one label for ancestor and descendant queries. Fixes #129. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/132
Add newline in results EOF by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/133
Provide option to make use of part_of for ancestor and descendant queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/134
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/135
Fixes typos in /similarity/matrix documentation by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/140
Use correct media type for ancestor matrix service by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/142
Add POST to /term/labels and /entity/dependency services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/143
Implement service providing frequency information for an ontology term according to some identified corpus by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/151
Allow caching of POST requests. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/152
Preserve user specified order of iris in dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/150
Support streaming response for TaxonPhenotypeAnnotations TSV (and more) by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/153
Add documentation for taxon annotations query and annotation sources query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/155
Document publication parameter. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/158
Return character id and label in the results of the study/phenotype kb-service by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/156
Accept JSON arrays for all IRI lists. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/159
Enable content negotiation with streaming annotations response. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/160
Migrate matrix renderer test to utest by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/164
Fix #26: Annotate ontotrace matrix with variable status by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/166
Order text search results consistently for different values of limit by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/168
Document acceptance of json array of IRIs for kb services by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/169
Make character IRI and label available where needed. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/178
Combine character id and label into a single json object by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/180
Issue 139 - merge term labels by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/170
Add 'phenotype' parameter to query endpoints. For issue #148. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/181
Implement phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/185
Refinements to phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/186
Document phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/187
Retrieve dependency matrix with a single query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/204
Fixes #167: Adds missing author to ontotrace matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/205
Add implementation for similarity/frequency for genes corpus by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/206
Return null if label doesn't exist by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/209
Only show states that are linked to taxon in /phenotype/info. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/208
Update sparql-interpolator. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/213
Return only one label for a term. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/211
Convert None responses for Option values into 404. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/212
Change MinimalTerm label to Option[String]. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/214
Fix null pointer exception in query result. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/215
Update sbt to 1.3.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/235
Update scalaz-core to 7.2.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/236
Update scowl to 1.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/234
Update phenoscape-kb-ingest to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/233
Update groovy-all to 2.4.19 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/231
Update apache-jena-libs to 3.14.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/230
Update owlapi-distribution to 4.2.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/229
Update sbt-native-packager to 1.3.25 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/226
Update utest to 0.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/223
Update scala. Remove guava. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/237
Update sbt-native-packager to 1.7.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/238
Update groovy-all to 2.5.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/240
Update owlapi-distribution to 4.5.15 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/239
Update commons-io to 2.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/227
Update to JavaConverters, remove warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/241
Update akka-stream-alpakka-xml to 1.1.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/222
Update owlet to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/232
Update akka-actor, akka-slf4j, akka-stream to 2.5.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/224
Update spray-json to 1.3.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/228
Update akka-http-cors to 0.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/219
Update logback-classic to 1.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/220
Update results json in api docs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/248
Update akka-actor, akka-slf4j, akka-stream to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/246
Update akka-http-cors to 0.4.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/244
Update logback-classic to 1.2.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/245
Update akka-http, akka-http-caching, ... to 10.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/225
Update owlet to 1.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/247
Fix missing results in ancestors & descendants services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/218
Return 0 count for frequency query when term is not matched in SPARQL query by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/216
Include character, state, and cell IRIs in matrix output. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/217
Fixes #188: Return term source ontology by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/249
Update sbt to 1.3.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/250
Remove println by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/251
Update groovy-all to 2.5.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/253
Update sbt to 1.3.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/255
Update owlet to 1.8.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/259
Update akka-http-cors to 0.4.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/256
Update owlapi-distribution to 4.5.16 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/257
Issue 179 kb metadata by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/252
Update sbt-native-packager to 1.7.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/264
Update akka-actor, akka-slf4j, akka-stream to 2.6.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/263
Add synonym detail to taxon info by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/266
Fix some deprecation warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/265
Reformat with new scalafmt configs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/271
Update to new sparql-utils. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/276
Change scalafmt align setting by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/283
Update akka-http, akka-http-caching, ... to 10.1.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/269
Update apache-jena-libs to 3.15.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/273
Update groovy-all to 2.5.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/275
Update Scala version for Travis by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/285
Update sbt-native-packager to 1.7.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/270
Test automatic SPARQL result derivation. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/279
Update akka-actor, akka-slf4j, akka-stream to 2.6.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/291
Update akka-stream-alpakka-xml to 2.0.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/292
Update scalafmt-core to 2.5.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/278
Update sbt-native-packager to 1.7.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/289
Update sbt to 1.3.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/288
Update commons-io to 2.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/284
Update scalafmt-core to 2.6.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/293
Update akka-http-cors to 1.0.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/277
Make tests actually run. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/295
Update scalafmt-core to 2.6.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/296
Change phenotypic profiles method to work with the new monarch schema by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/183
Updates for new Gene model by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/297
Update owlapi-distribution to 4.5.17 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/301
Update sbt to 1.3.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/299
Update sbt-native-packager to 1.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/302
Update apache-jena-libs to 3.16.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/306
Update scalafmt-core to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/308
Update groovy-all to 2.5.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/309
Update akka-actor, akka-slf4j, akka-stream to 2.6.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/307
Update groovy-all to 3.0.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/311
Fixes #90 - add option to include subclasses, or not, for entity and … by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/290
Update sbt to 1.4.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/335
Update scalafmt-core to 2.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/341
Bug fix; rewrite query using sparql interpolator by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/344
Update sbt-native-packager to 1.7.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/340
Update owlapi-distribution to 4.5.18 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/345
Update sbt to 1.4.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/343
Update commons-io to 2.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/322
Update utest to 0.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/318
Update sbt to 1.4.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/356
Update utest to 0.7.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/375
Update scalaz-core to 7.2.31 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/373
Don't return owl:Thing in ancestor results. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/383
Update sbt to 1.4.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/381
Update sbt-native-packager to 1.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/369
Update akka-actor, akka-slf4j, akka-stream to 2.6.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/379
Update sparql-utils, sparql-utils-owlapi to 1.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/360
Update spray-json to 1.3.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/350
Roll back changes to taxon info return format. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/384
Create scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/385
Update scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/386
Services new data model by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/329
Update scala-library to 2.12.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/394
Allow return of all search results using limit < 1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/395
Update sparql-utils, sparql-utils-owlapi to 1.3.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/396
Update apache-jena-libs to 3.17.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/357
Update akka-http, akka-http-caching, ... to 10.1.14 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/392
Update akka-stream-alpakka-xml to 2.0.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/327
Support search and info for genes without phenotype annotations in switch to Monarch data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/399
Full Changelog: https://github.com/phenoscape/phenoscape-kb-services/compare/v0.5...v2.
TUMOR NECROSIS FACTOR BETA (TNF-P) INDUCES BINDING OF THE NF-KB TRANSCRIPTION FACTOR TO A HIGH-AFFINITY KB ELEMENT IN THE TNF-BETA PROMOTER
No full textPDBe-KB: collaboratively defining the biological context of structural data
No full textThe Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16_026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union's Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Foundation Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsråd) [288008]; E.D.L. acknowledges support from the European Union's Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z].Peer ReviewedCurrent PDBe-KB Consortium Members with Affiliations. (BSC author: Gonzalo Parra)
Mihaly Varadi1, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S Marks, Lennart Martens, Stuart A McGowan, Jake E McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe16, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J Rollins, Antonio Rosato, Paweł Rubach, Luis Serrano, Gulzar Singh,Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna I Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C.E. Tosatto, Wim Vranken, Mark N Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer VelankarPostprint (published version
Concatenated Low-Density Parity-Check and BCH Coding System for Magnetic Recording Read Channel With 4 kB Sector Format
No full textIn this paper, we examine the potential of applying concatenated low-density parity-check (LDPC) and Bose-Chaudhuri-Hocquenghem (BCH) coding for magnetic recording read channel with a 4 kB sector format. One key observation for such concatenated coding systems is that the overall error correction capability can be improved by exploiting the iteration-by-iteration bit error number oscillation behavior in case of inner LDPC code decoding failures. Moreover, assisted by field programmable gate array (FPGA)-based simulation platforms, empirical error-correcting performance analysis can reach a very low sector error rate (e.g., 10(-10) and below), which is almost infeasible for LDPC-only coding systems. Finally, concatenated coding can further reduce the silicon cost. By implementing a high-speed FPGA-based perpendicular recording read channel simulator, we investigate a 4 kB rate-15/16 concatenated coding system with a 512-byte rate-19/20 inner LDPC code and an outer 4 kB BCH code. We apply a decoding strategy that can fully utilize the bit error number oscillation behavior of inner LDPC code decoding, and show that its sector error rate drops down to 10(-11). For the purpose of comparison, we use the FPGA-based simulator to empirically observe the performance of 4 kB rate-15/16 LDPC and Reed-Solomon (RS) codes down to 10(-7)-10(-8). Finally, we estimate the silicon cost of this concatenated coding system at 65 nm node, and compare it with that of the RS-only and LDPC-only coding systems
Common polymorphisms in methylenetetrahydrofolate reductase gene are associated with risks of cervical intraepithelial neoplasia and cervical cancer in women with low serum folate and vitamin B12
No full textOBJECTIVE: We evaluated associations between folate, vitamin B12, and the methylenetetrahydrofolate reductase (MTHFR) gene, and risk of cervical intraepithelial neoplasia (CIN) and cervical cancer.
METHODS: This multicenter case-control study enrolled 927 Korean women (440 controls, 165 patients with CIN 1, 167 patients with CIN 2/3, and 155 patients with cervical cancer, aged 20-75 years).
RESULTS: Patients with cervical cancer had significantly lower median serum folate and vitamin B12 concentrations vs. controls. Higher serum folate was significantly associated with lower cervical cancer risk (p for linear trend = 0.0058) with a trend for a lower CIN risk after multivariate adjustment. Low folate and the MTHFR 677 C > T variant were associated with a higher risk for CIN2/3 and cervical cancer vs. wild-type or heterozygous genotypes with high folate [OR, 2.39 (1.18-4.85) and 3.19 (1.43-7.13)]. Low vitamin B12 and the MTHFR 677 C > T variant also were associated with a higher risk for CIN 2/3 and cervical cancers [OR, 2.52 (1.17-5.42) and 2.40 (1-5.73)] vs. wild-type or heterozygous status with high vitamin levels.
CONCLUSION: Serum folate concentration is inversely associated with the risk of cervical cancer, and the MTHFR variant genotype may increase CIN and cervical cancer risk in women with low folate or vitamin B12 status
Role of SUMO-1 modification in transcriptional activation
No full textIn unstimulated cells, the transcription factor NF-κB is held in the
cytoplasm in an inactive state by IκB inhibitor proteins. Activation of NF--KB is
mediated by signal induced degradation of IκBα via the ubiquitin proteasome-dependent
pathway. Targeting the proteins for ubiquitin-mediated proteolysis is an
irrevocable decision, and as such, the process needs to be highly specific and tightly
regulated. This task is achieved by conjugation and deconjugation enzymes that act
in a dynamic and coordinated mechanism.
In a yeast two hybrid screen designed to identify proteins involved in IκBα
signalling Ubch9 was found to interact with the N-terminal regulatory region of
IκBα. Although Ubch9 is an enzyme homologous to E2 ubiquitin conjugating
enzymes we have shown that is unable to form a thioester with ubiquitin but it is
capable to form a thioester with the small ubiquitin-like protein SUMO- 1. To fully
characterise the SUMO-1 modification reaction we have purified the proteins and
cloned the genes encoding the SUMO-1 activating enzyme (SAEl/SAE2) and
shown that it is homologous to enzymes involved in the activation of ubiquitin,
Smt3p, the yeast SUMO-1 homologue, and Rublp/Nedd8, another ubiquitin-like
protein. SUMO-1 is conjugated to target proteins by a pathway that is distinct from,
but analogous to, ubiquitin conjugation.
SUMO-1 was efficiently conjugated, both in vivo and in vitro, to IκBα on
lysine 21, which is also utilised for ubiquitin modification. Thus, by blocking
ubiquitination SUMO-1 modification acts antagonistically to generate a pool of
IκBα resistant to proteasome-mediated degradation which consequently inhibits
NF-κB dependent transcription activation.
In view of several lines of similarity between NF-kB and p53, the
involvement of SUMO-1 modification in the metabolism of the tumour supressor
p53 was investigated. We have shown that p53 is modified by SUMO-1 at a single
site, lysine 386 in the C-terminus of p53. Although p53 is regulated by
ubiquitination, SUMO-1 and ubiquitin modification do not compete for the same
lysine in p53. However, overexpression of SUMO-1 activates the transcriptional
activity of wild type p53, but not K386R p53 where the SUMO-1 acceptor site has
been mutated.
A consensus sequence was obtained by comparison of the sequences
surrounding the SUMO-1 acceptor lysine in proteins that have been shown to be
modified by SUMO-1 and revealed a possible recognition site for SUMO-1
conjugation machinery.
Tagging of proteins with SUMO-1 regulates transcriptional activation, either
by interfering with subcellular location or with the ubiquitination pathway. The
pathway may represent a novel target for drug development
The number of positive and negative pixels for each chromosome and the ratios between negative and positive at resolutions of 10 kb and 5 kb.
No full textThe range of genomic distances we cared about is from 2 to 200 bins for 10 kb and from 2 to 400 for 5 kb, that is, 20 kb to 2 Mb. The ChIA-PET data are from CTCF of GM12878. (TIFF)</p
Hyojun dai toa bunzu. 18 , Hawai shoto hen /
No full textMap of Hawaii published in Japan in 1943.; Also available in an electronic version via the internet at: http://nla.gov.au/nla.map-vn6451628. 880-04 Inset: Shinjuwan oyobi Honoruru fukin -- Hawai shoto fukin (Sandoicchi shoto). Scale 1:9,000,000.880-04 Inset: 1-MO!KB'IC!5#i%[i%Ni%ki%k!0o
No full text(A) Overlap in ground-truth ChIA-PET interactions between GM12878 and HeLa. (B) The boxplots of APs and ROC-AUCs for all testing chromosomes (chr.1-X) at 10-kb resolution (mean values are added above each boxplot) on all HeLa loops and HeLa-specific loops. (C) The average CTCF coverage surrounding anchors from ground truth and our predicted top-N pixels. (D) ChIA-PET interactions between promoters and enhancers. (E) The APs and ROC-AUCs for chromosomes 1–5 at 5-kb resolution. Error bars show standard deviation (SD).</p
Overall performance of DeepChIA-PET for predicting CTCF ChIA-PET interactions on all testing chromosomes in GM12878 at 10-kb and 5-kb resolution.
No full text(A) The boxplots of APs and ROC-AUCs for all testing chromosomes at 10-kb resolution (mean values are added above each boxplot) with three input types: all (real input), shuffleChIP-seq (shuffling 1D ChIP-seq vector before converting to two 2D matrices), and shuffleHiC (shuffling the 2D Hi-C matrix). (B) The average CTCF coverage surrounding anchors from ground truth and our predicted top-N pixels. (C) CTCF motif orientation analysis at anchors from ground truth and our predicted top-N pixels. (D) ChIA-PET interactions between promoters and enhancers. (E) The APs and ROC-AUCs for chromosomes 1–5 at 5-kb resolution. Error bars show standard deviation (SD).</p
- …
