Skip to end of metadata
Go to start of metadata

Latest status (4 September 2019 - 16:00 UTC)

The server is loaded with data and ready for testing.

We have loaded a set of basic studies and the latest 19.0 war file.

Data Loaded. Details below:

  • Cell-line use case data is loaded as public data (see table for details) including variant data for VCF and RNAseq
  • Additional data loaded for eTRIKS Asthma and Rheumatoid Arthritis studies to test studies at lower levels in the tree.

Data in preparation. Details below:

  • Browse tab data is to be loaded for selected studies using new transmart-data targets. Suggestions on values for "Not applicable" fields - either true values, or useful values for testing filter functionallity - are welcome.
  • GWAS data is in preparation loaded for 5 magic analysis files. SNP data is being loaded for all SNPs in the loaded MAGIC datasets. Gene names have been added where available for each analysis.
  • VCF  data

Features and Testing Protocols

A list of features is in preparation, with links to prevously used testing protocols.

See tranSMART 19.0 Full Feature List

Known Issues

See JIRA

Server address

http://postgres-test.transmartfoundation.org/transmart 

TranSMART version

Release 19.0 (built September 2019)

Database created

July 2019 - using release 19.0 version of transmart-data

Studies loaded

GWAS data loading is in preparation

Top LevelDiseaseStudyDatatypesNotes
 Across Trials



eTRIKS Studies AsthmaGSE23611Expression

 Rheumatoid arthritisGSE10024Expression


GSE10500Expression
Public StudiesAcute Lymphoblastic LeukemiaGSE4698Expression 

AsthmaGSE34466 clinical only 


GSE13168Expression 


GSE31773 clinical only 

Brain CancerGSE4271Expression

Breast Cancer GSE4922 Expression 


GSE5327 Expression 


GSE1456 Expression 


GSE4382Expression

COPD GSE8581Expression

Melanoma UvealGSE27831Expression 

PsoriasisGSE11903Expression 

Pulmonary SarcoidosisGSE19976Expression

Rheumatoid ArthritisGSE20690 Expression

TraIT Cell-lineCell-line

ACGH

expression

MicroRNA

proteomics

RNAseq

VCF

ACGH data under "High-throughput molecular profiling \ Copy number aberrations"

Expression data under "High-throughput molecular profiling \ Expression (mRNA)" ("...array")

MicroRNA data under "High-throughput molecular profiling \ Expression (miRNA)"

Proteomics under "High-throughput molecular profiling \ Expression (protein)"

RNAseq under "High-throughput molecular profiling \ Expression (mRNA)" ("Illumina... RNAseq")

VCF under "High-throughput molecular profiling \ Small Variants (DNA)" and "... (RNA)"


Type 2 DiabetesGSE38642 Expression 
TCGA StudiesBreast CancerBRCAExpression

Lung AdenocarcinomaLUADExpression

Ovarian CancerOVExpression
Test Studies V1.3
Test diabetes largeclinical only


Test mannheim with samples clinical only


test mass spec proteomics MsProteomics 


test merged data typesExpression Metabolomics MsProteomics


test mRNA microarrayExpression


test_qPCR_miRNA_GSE37425miRNA-qPCR

 Dictionaries loaded

DictionaryReleaseNotes
Entrez geneNov 2016Updates to data loaded with transmart-data
Gene ontologyNov 2016Where is this used in tranSMART 16.2?

HMDB

Aug 2015Human metabolite database
KEGGJan 2011Last pre-subscription release
MeSH2016Medline subject headings, diseases
MiRBase

Release 21

Aug 2015

MicroRNA database
UniProt/SwissProt Nov 2016Human entries only 
Observation-Diabetes entry for GWAS
VCFdbSNP 146SNP data for GWAS MAGIC datasets
  • No labels