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 Level | Disease | Study | Datatypes | Notes |
|---|---|---|---|---|
| Public Studies | Acute Lymphoblastic Leukemia | GSE4698 | Expression | |
| Asthma | GSE13168 | Expression | ||
| Brain Cancer | GSE4271 | Expression | ||
| Breast Cancer | GSE4922 | Expression | ||
| GSE5327 | Expression | |||
| GSE1456 | Expression | |||
| COPD | GSE8581 | Expression | ||
| Melanoma Uveal | GSE27831 | Expression | ||
| Psoriasis | GSE11903 | Expression | ||
| Pulmonary Sarcoidosis | GSE19976 | Expression | ||
| Rheumatoid Arthritis | GSE20690 | Expression | ||
| Type 2 Diabetes | GSE38642 | 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
| Dictionary | Release | Notes |
|---|---|---|
| Entrez Gene | Feb 2017 | Standard in transmart-data |
| Gene Ontology | Sep 2015 | Where is this used in tranSMART 1.2.5? |
| HMDB | Aug 2014 | Human metabolite database , standard in transmart-data 16.2 |
| KEGG | Jan 2011 | Last pre-subscription release |
| MeSH | 2017 | Medline 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 2017 | Human and mouse entries only, standard in transmart-data 16.2 |
| Observation | - | Diabetes record for MAGIC GWAS sets |
| VCF | dbSNP 146 | SNP data for GWAS MAGIC datasets |
