GenboreeKB: Latest projectshttp://genboree.org/genboreeKB2022-03-29T16:27:33ZGenboreeKB
Redmine areg64-test - Project: areg64-testhttp://genboree.org/genboreeKB/projects/areg64-test2022-03-29T16:27:33Z
<p>UI to test the CAR64 instance on ar-64-prd (10.15.55.211:16004)</p> XDec Deconvolution - Project: XDec Deconvolutionhttp://genboree.org/genboreeKB/projects/xdec-web-deconvolution2021-04-06T21:08:11Z
<p>This project is the web GUI XDec web deconvolution for the paper titled <em>A histoepigenetic map of breast cancer derived using the XDec computational deconvolution method</em>.</p>
<p>The deconvolution tool can be found here <br /><a href="https://vpetrosyan.shinyapps.io/XDec_web_application/" class="external">Online XDec Deconvolution Tool</a> and <a href="https://genboree.org/genboreeKB/projects/xdec-web-deconvolution/wiki" class="external">Example Data</a></p>
<p>The Pancreatic Ductal Adenocarcinoma deconvolution tool can be found here<br /><strong>COMING SOON</strong><br /><a href="https://emilylaplante.shinyapps.io/XDec_web_application_PDAC/" class="external">Online XDec PDAC Deconvolution Tool</a></p>
<p>Tools relating to the publication <em>Cell type specific expression in pancreatic ductal adenocarcinoma reveals subtypes have different mechanisms of expression for PD-L1 and therapeutic targets in human patients</em> are found below.</p>
<p>PDAC Sliding Window Deconvolution tool can be found here<br /><strong>COMING SOON</strong><br /><a href="https://emilylaplante.shinyapps.io/XDec_SlindingWindow_applications/" class="external">Online PDAC Sliding Window Deconvolution Tool</a></p>
<p>BRCA Sliding Window Deconvolution tool can be found here<br /><strong>COMING SOON</strong><br /><a href="https://emilylaplante.shinyapps.io/BRCA_SlidingWindow_app/" class="external">Online BRCA Sliding Window Deconvolution Tool</a></p>
<p>Head and Neck (HPV positive and negative) Sliding Window Deconvolution tool can be found here<br /><strong>COMING SOON</strong><br /><a href="https://emilylaplante.shinyapps.io/HNSC_spectrum/" class="external">Online Head and Neck Sliding Window Deconvolution Tool</a></p>
<p>Glioblastoma and Glioma Sliding Window Deconvolution tool can be found here<br /><strong>COMING SOON</strong><br /><a href="https://emilylaplante.shinyapps.io/GBM_spectrum/" class="external">Online Glioma/Glioblastoma Sliding Window Deconvolution Tool</a></p> Metabolomics Data Portal - Project: Metabolomics Data Portalhttp://genboree.org/genboreeKB/projects/metabolomics-data-portal2021-04-06T01:07:03Z
<a name="The-Metabolomics-Data-Portal"></a>
<h2 >The Metabolomics Data Portal<a href="#The-Metabolomics-Data-Portal" class="wiki-anchor">¶</a></h2>
<p>The Metabolomics Data Portal is a diagnostics tool for untargeted metabolomics data. This application visualizes individuals’ metabolomics data and implements the network-assisted diagnostic functionalities featured in this paper.</p>
<p>You can <strong>access the metabolomics data portal here</strong> <a href="https://lrthistlethwaite.shinyapps.io/metabolomics-data-portal/" class="external">Metabolomics Data Portal</a>.</p>
<a name="References"></a>
<h2 >References<a href="#References" class="wiki-anchor">¶</a></h2>
<p>Thistlethwaite L.R., Li X., Burrage L.C., Riehle K., Hacia J.G., Braverman N., Wangler M.F., Miller M.J., Elsea S.H., Milosavljevic A. (2021). Clinical Diagnosis of Metabolic Disorders Using Untargeted Metabolomic Profiling and Disease-Specific Networks Learned from Profiling Data.</p> Metabolomics Data Portal - Project: Metabolomics Data Portalhttp://genboree.org/genboreeKB/projects/clinical-diagnosis-with-ctd2021-04-05T23:45:12Z
<a name="The-Metabolomics-Data-Portal"></a>
<h2 >The Metabolomics Data Portal<a href="#The-Metabolomics-Data-Portal" class="wiki-anchor">¶</a></h2>
<p>The Metabolomics Data Portal is a diagnostics tool for untargeted metabolomics data. This application visualizes individuals’ metabolomics data and implements the network-assisted diagnostic functionalities featured in this paper.</p>
<p>You can <strong>access the metabolomics data portal here</strong> <a href="https://lrthistlethwaite.shinyapps.io/metabolomics-data-portal/" class="external">the Metabolomics Data Portal</a>.</p>
<a name="References"></a>
<h2 >References<a href="#References" class="wiki-anchor">¶</a></h2>
<p>Thistlethwaite L.R., Li X., Burrage L.C., Riehle K., Hacia J.G., Braverman N., Wangler M.F., Miller M.J., Elsea S.H., Milosavljevic A. (2021). Clinical Diagnosis of Metabolic Disorders Using Untargeted Metabolomic Profiling and Disease-Specific Networks Learned from Profiling Data.</p> AR-test - Project: AR-testhttp://genboree.org/genboreeKB/projects/ar-test2019-08-08T19:56:24Zbrl-raw - Project: brl-rawhttp://genboree.org/genboreeKB/projects/brl-raw2018-12-28T18:33:13ZMerged Ac Release - Project: Merged Ac Releasehttp://genboree.org/genboreeKB/projects/merged-ac-release2018-11-20T22:22:07ZVariant Prioritization Tool Data Hosting (Test) - Project: Variant Prioritization Tool Data Hosti...http://genboree.org/genboreeKB/projects/vpt-ldh-test2018-11-20T15:31:06ZVariant Prioritization Tool Data Hosting - Project: Variant Prioritization Tool Data Hostinghttp://genboree.org/genboreeKB/projects/vpt-ldh2018-11-20T15:23:52ZExtracellular RNA Atlas - Public Holding Area - Project: Extracellular RNA Atlas - Public Holding...http://genboree.org/genboreeKB/projects/extracellular-rna-atlas-public-holding-area2018-10-08T16:42:47Z
<p>This project (and the associated GenboreeKB) is meant for temporarily storing metadata before it is placed into the public Atlas. This helps keep the actual public Atlas KB clean (no partial or broken submissions, for example).</p> Pediatric Actionability Release - Project: Pediatric Actionability Releasehttp://genboree.org/genboreeKB/projects/ped-ac-release2018-09-24T16:12:47ZActionability Release - Project: Actionability Releasehttp://genboree.org/genboreeKB/projects/adult-ac-release2018-09-24T16:05:35ZEvidence Repository - Project: Evidence Repositoryhttp://genboree.org/genboreeKB/projects/evidence-repository2018-08-23T20:13:42Z
<ul class="toc"><li><a href="#A-Redmine-project-links-to-all-the-servers-are-listed-here">A. Redmine project links to all the servers are listed here:</a><ul><li><a href="#A1-Dev">A.1 Dev</a></li><li><a href="#A2-Stage">A.2 Stage</a></li><li><a href="#A3-genboreeorg">A.3 genboree.org</a></li><li><a href="#A4-cgbuilder">A.4 cgbuilder</a></li><li><a href="#A5-RSP-test">A.5 RSP test</a></li><li><a href="#A6-RSP-production">A.6 RSP production</a></li></ul>
</li><li><a href="#B-Links-to-Erepo-collection-models-are-listed-here">B. Links to Erepo collection models are listed here:</a><ul><li><a href="#B1-Affiliations">B.1 Affiliations</a></li><li><a href="#B2-Alleles">B.2 Alleles</a></li><li><a href="#B2-Guidelines">B.2 Guidelines</a></li></ul></li></ul>
<a name="A-Redmine-project-links-to-all-the-servers-are-listed-here"></a>
<h2 >A. Redmine project links to all the servers are listed here:<a href="#A-Redmine-project-links-to-all-the-servers-are-listed-here" class="wiki-anchor">¶</a></h2>
<a name="A1-Dev"></a>
<h3 >A.1 Dev<a href="#A1-Dev" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="https://10.15.55.128/genboreeKB_dev/projects/evidence-repo">https://10.15.55.128/genboreeKB_dev/projects/evidence-repo</a></li>
<li>Application - <a class="external" href="https://10.15.55.128/genboreeKB_dev/projects/evidence-repo/pcer/ui/entry">https://10.15.55.128/genboreeKB_dev/projects/evidence-repo/pcer/ui/entry</a></li>
<li>Application direct - <a class="external" href="https://10.15.55.128/evrepo/">https://10.15.55.128/evrepo/</a></li>
</ul>
<a name="A2-Stage"></a>
<h3 >A.2 Stage<a href="#A2-Stage" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="https://10.15.55.128/genboreeKB_stage/projects/evidence-repository">https://10.15.55.128/genboreeKB_stage/projects/evidence-repository</a></li>
<li>Application - <a class="external" href="https://10.15.55.128/genboreeKB_stage/projects/evidence-repository/pcer/ui/entry">https://10.15.55.128/genboreeKB_stage/projects/evidence-repository/pcer/ui/entry</a></li>
<li>Application direct - <a class="external" href="https://10.15.55.128/evrepo-stg/">https://10.15.55.128/evrepo-stg/</a></li>
</ul>
<a name="A3-genboreeorg"></a>
<h3 >A.3 genboree.org<a href="#A3-genboreeorg" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="https://genboree.org/genboreeKB/projects/evidence-repository">https://genboree.org/genboreeKB/projects/evidence-repository</a></li>
<li>Application - <a class="external" href="https://genboree.org/genboreeKB/projects/evidence-repository/pcer/ui/entry">https://genboree.org/genboreeKB/projects/evidence-repository/pcer/ui/entry</a></li>
<li>Application direct - <a class="external" href="https://genboree.org/evrepo/">https://genboree.org/evrepo/</a></li>
</ul>
<a name="A4-cgbuilder"></a>
<h3 >A.4 cgbuilder<a href="#A4-cgbuilder" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="http://10.15.53.110/redmine/projects/evrepo">http://10.15.53.110/redmine/projects/evrepo</a></li>
<li>Application - <a class="external" href="http://10.15.53.110/redmine/projects/evrepo/pcer/ui/entry">http://10.15.53.110/redmine/projects/evrepo/pcer/ui/entry</a></li>
<li>Application Direct - <a class="external" href="http://10.15.53.110/evrepo/ui/entry">http://10.15.53.110/evrepo/ui/entry</a></li>
</ul>
<a name="A5-RSP-test"></a>
<h3 >A.5 RSP test<a href="#A5-RSP-test" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="https://erepo.test.genome.network/redmine/projects/evrepo">https://erepo.test.genome.network/redmine/projects/evrepo</a></li>
<li>Application - <a class="external" href="https://erepo.test.genome.network/redmine/projects/evrepo/pcer/ui/entry">https://erepo.test.genome.network/redmine/projects/evrepo/pcer/ui/entry</a></li>
<li>Application Direct - <a class="external" href="https://erepo.test.genome.network/evrepo/ui/entry">https://erepo.test.genome.network/evrepo/ui/entry</a></li>
</ul>
<a name="A6-RSP-production"></a>
<h3 >A.6 RSP production<a href="#A6-RSP-production" class="wiki-anchor">¶</a></h3>
<ul>
<li>Redmine project - <a class="external" href="https://erepo.clinicalgenome.org/redmine/projects/evrepo/">https://erepo.clinicalgenome.org/redmine/projects/evrepo/</a></li>
<li>Application - <a class="external" href="https://erepo.clinicalgenome.org/redmine/projects/evrepo/pcer/ui/entry">https://erepo.clinicalgenome.org/redmine/projects/evrepo/pcer/ui/entry</a></li>
<li>Application direct - <a class="external" href="https://erepo.clinicalgenome.org/evrepo/">https://erepo.clinicalgenome.org/evrepo/</a></li>
</ul>
<a name="B-Links-to-Erepo-collection-models-are-listed-here"></a>
<h2 >B. Links to Erepo collection models are listed here:<a href="#B-Links-to-Erepo-collection-models-are-listed-here" class="wiki-anchor">¶</a></h2>
<a name="B1-Affiliations"></a>
<h3 >B.1 Affiliations<a href="#B1-Affiliations" class="wiki-anchor">¶</a></h3>
<ul>
<li>GenboreeKB UI - <a class="external" href="http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Affiliations">http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Affiliations</a></li>
<li>Google spreadsheet - <a class="external" href="https://docs.google.com/spreadsheets/d/15H1BYkmKnr2UztfbBHC-SIOX-5EYWJwRMqvAXlfGfks/edit?skip_itp2_check=true#gid=5364704">https://docs.google.com/spreadsheets/d/15H1BYkmKnr2UztfbBHC-SIOX-5EYWJwRMqvAXlfGfks/edit?skip_itp2_check=true#gid=5364704</a></li>
</ul>
<a name="B2-Alleles"></a>
<h3 >B.2 Alleles<a href="#B2-Alleles" class="wiki-anchor">¶</a></h3>
<ul>
<li>GenboreeKB UI - <a class="external" href="http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Alleles">http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Alleles</a></li>
</ul>
<a name="B2-Guidelines"></a>
<h3 >B.2 Guidelines<a href="#B2-Guidelines" class="wiki-anchor">¶</a></h3>
<ul>
<li>GenboreeKB UI - <a class="external" href="http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Guidelines">http://genboree.org/genboreeKB/genboree_kbs?project_id=evidence-repository&showModelTree=true&coll=Guidelines</a></li>
</ul> pcer - Project: pcerhttp://genboree.org/genboreeKB/projects/pcer2018-05-08T16:41:45ZExtracellular RNA Atlas V4P1 - Project: Extracellular RNA Atlas V4P1http://genboree.org/genboreeKB/projects/extracellular-rna-atlas-v4p12018-04-18T18:04:01Z
<p>This project contains a GenboreeKB that is associated with the "ExRNA Atlas analysis reveals distinct extracellular RNA cargo types present across human biofluids" paper (under revision).</p> Files4U - Project: Files4Uhttp://genboree.org/genboreeKB/projects/files4u2018-01-24T16:04:43ZEVB Hub - Project: EVB Hubhttp://genboree.org/genboreeKB/projects/evb-non-proto2017-03-20T19:04:58Z
<p>Hub UI project for demo purposes</p> Allelic Epigenome Project - Project: Allelic Epigenome Projecthttp://genboree.org/genboreeKB/projects/allelic-epigenome2017-01-03T16:25:06Z
<p>Data sharing of the allelic imbalance dataset generated from the Allelic Epigenome Project.</p>
<p>In the GenboreeKB tab, you can explore the data through our UI. Data is separated by chromosome number. If you are interested in downloading the data in bulk, you can download it from our FTP server at: <a class="external" href="ftp://ftp.genboree.org/allelic-epigenome/">ftp://ftp.genboree.org/allelic-epigenome/</a>.</p> Customer Feedback - Project: Customer Feedbackhttp://genboree.org/genboreeKB/projects/customer-feedback2016-12-02T02:19:05Z
<p>Customer support is a public feedback forum to provide the experience they faced while taking the service of particular company or organization.</p> Extracellular RNA Atlas v4 - Project: Extracellular RNA Atlas v4http://genboree.org/genboreeKB/projects/extracellular-rna-atlas-v42016-10-23T21:15:55Z
<p>Project backing exrna-atlas.org as of 2016/10/25. This project has the latest Redmine plugin for the public exRNA Atlas. The models are updated as of October 2016. (<em>Not actually in use for <a class="external" href="https://exrna-atlas.org">https://exrna-atlas.org</a> as of 2020-10-16. Possibly was being prepped but was rejected.</em> )</p> actionability_application_release - Project: actionability_application_releasehttp://genboree.org/genboreeKB/projects/actionability_application_release2016-07-15T15:25:04ZExtracellular RNA Atlas - Project: Extracellular RNA Atlashttp://genboree.org/genboreeKB/projects/extracellular-rna-atlas-v22016-07-07T15:13:23Z
<p>Project backing exrna-atlas.org as of 2016/10/18. This project has the latest Redmine plugin for the public exRNA Atlas. The models are updated as of late June 2016.</p> Extracellular RNA Atlas v1 - Project: Extracellular RNA Atlas v1http://genboree.org/genboreeKB/projects/extracellular-rna-atlas2015-12-22T16:28:35Z
<p>Project for the public version of the extracellular RNA atlas. Public exrna-atlas.org backed by sub-project of this.</p> V2.0 - Project: V2.0http://genboree.org/genboreeKB/projects/v2-02015-09-28T18:40:47Zpawlicze_testKb - Project: pawlicze_testKbhttp://genboree.org/genboreeKB/projects/pawlicze_testkb2015-09-14T18:16:57ZV1.5 - Project: V1.5http://genboree.org/genboreeKB/projects/v1-52015-07-08T18:38:17Z
<p>Pathogenicity Calculator V1.5 related KB and collections.</p>
<p>This version has the following upgrades and can be accessed via <a class="external" href="http://genboree.org/java-bin/clingenV1.5.jsp">http://genboree.org/java-bin/clingenV1.5.jsp</a></p>
<ul>
<li>MODEL AND GENBOREE KB DOCUMENT CHANGES
<ul>
<li>Simple Allele - Model follows the one that is given here: <a class="external" href="http://genboree.org/genboreeKB/genboree_kbs?project_id=allelemodels&showModelTree=true&coll=SimpleAllele_0.4&modelVersion=">http://genboree.org/genboreeKB/genboree_kbs?project_id=allelemodels&showModelTree=true&coll=SimpleAllele_0.4&modelVersion=</a></li>
<li>Canonical Allele - Model follows the one that is given here: <a class="external" href="http://genboree.org/genboreeKB/genboree_kbs?project_id=allelemodels&showModelTree=true&coll=CanonicalAllele_0.4&modelVersion=">http://genboree.org/genboreeKB/genboree_kbs?project_id=allelemodels&showModelTree=true&coll=CanonicalAllele_0.4&modelVersion=</a></li>
<li>PathCalConfigurations - changed to have properties for Canonical Allele information</li>
</ul></li>
</ul>
<ul>
<li>FEATURES
<ul>
<li>Manage links to the tag - a edit window to add/delete and save links to the tag (evidence document)</li>
<li>Provide link summary - summarises links for each tag</li>
<li>Search canonical document to match the subject of the canonical collection</li>
</ul></li>
</ul> alleleModels - Project: alleleModelshttp://genboree.org/genboreeKB/projects/allelemodels2015-04-15T19:19:55ZGenboreeKB Introduction - Project: GenboreeKB Introductionhttp://genboree.org/genboreeKB/projects/genboreekb-introduction2014-12-09T17:09:07Z
This project contains resources to introduce GenboreeKB to new users.<br />Resources available in this project:
<ul>
<li>A test GenboreeKB with example collections and documents </li>
<li><a href="http://genboree.org/genboreeKB/projects/genboreekb-introduction/wiki" class="wiki-page">Wiki pages</a> describing features of GenboreeKB</li>
</ul>