Skip to end of metadata
Go to start of metadata

Latest status (21 May 13:30 UTC)

The server is loaded with data and ready for testing

The server has been copied to a new address, see below. Please resume testing.

Reloaded all public studies to match postgres instance.

Browse tab populated with metadata on Test Studies and selected Public Studies.

Cell-line data for clinical and VCF is loaded.

Known issues

GWAS data to be loaded. Workaround for ETL issues. Updating loader to load SNP metadata. Testing first on the Postgres server.

Cell-line data requires individual datatype and subset downloads: Oracle load scripts for most datatypes only run as make targets. VCF data is loaded. We are working with the Cell-line use case developers on ETL procedures for Oracle.

Server address

http://postgres-ci.transmartfoundation.org/transmart  using a numeric address http://54.85.146.148/transmart  until we can add further names.

TranSMART version 16.3

Database created

1-May-2017

Studies loaded

Top LevelDiseaseStudyDatatypesNotes
Public StudiesAcute Lymphoblastic LeukemiaGSE4698
Expression  
  AsthmaGSE13168Expression  
 Brain CancerGSE4271Expression 
 Breast Cancer GSE4922
Expression  
  GSE5327
Expression  
  GSE1456Expression  
 COPD GSE8581
Expression 
 Melanoma UvealGSE27831Expression  
 PsoriasisGSE11903Expression  
 Pulmonary SarcoidosisGSE19976Expression 
 Rheumatoid ArthritisGSE20690Expression 
 Type 2 DiabetesGSE38642
Expression  
Test Studies V1.3
Test diabetes large
clinical only
  test_mannheim_with_samples
clinical only 
  test_mass_spec_proteomics
MsProteomics  
  test_merged data types
Expression, Metabolomics, MsProteomics 
  test_miRNA microarray
Expression 
  

test_qPCR_miRNA_GSE37425

miRNA-qPCR 

 Dictionaries loaded - standard set for 16.3

DictionaryReleaseNotes
Entrez Gene Feb 2017Standard in transmart-data
Gene OntologySep 2015Where is this used in tranSMART 1.2.5?
HMDBAug 2014Human metabolite database , standard in transmart-data 16.2
KEGGJan 2011Last pre-subscription release
MeSH2017Medline subject headings, diseases, standard in transmart-data 16.2
MiRBase

Release 21

Aug 2015

MicroRNA database, standard in transmart-data 16.2
UniProt/SwissProt Feb 2017Human and mouse entries only, standard in transmart-data 16.2
Observation-Diabetes record for MAGIC GWAS sets
VCFdbSNP 146SNP data for GWAS MAGIC datasets
  • No labels