The documents on this page are the final versions from the tranSMART Foundation 17.1 Project.
These deliverables have been provided by the vendor, the Hyve, and accepted by the Technical Steering Committee for the 17.1 Project.
Use Case Documents LINK
| Approval Date | Document Name | Version |
|---|---|---|
| 17.1 Project Introduction Presentation | ||
| 4/7/2016 | 17.1 Project Requirement Analysis and Use Cases | 1.0 |
| 8/11/2016 | 17.1 Requirements Document | 1.1 |
| 9/13/2016 | 17.1 Design Document | 1.2 |
| 7/10/2016 | 17.1 Project Plan | 1.2 |
4/20/2016 | 17.1 Project Timeline | 1.2 |
| 8/9/2016 | 17.1 Release Plan | 1.0 |
| Third Party and Open Source Components for the 17.1 Project | 1.1 | |
| BACKGROUND DOCUMENTS | ||
| 17.1 Requirements and Priorities from Sponsors | ||
| Use Case Descriptions |
Project Introduction: tranSMART Pro project proposal.pdf
17.1 Project Requirements Analysis and Use Cases: TranSMART17.1BusinessAnalysisSummary.pdf
Requirements: REQ - TMP (17.1) Requirements - Approved - V1.1 - 11-08-2016.pdf
Design: DES - TMP (17.1) Design Document - Approved - V1.2 - 13-09-2016.pdf
Project Plan: PRE - TMP (17.1) Project Plan - Approved - V1.2 (TSF 10.07.16)(5).pdf
17.1 Project Timeline: Transmart Pro Timeline v1.2.pdf
17.1 Release Plan: 17.1 Release Plan
Third Party Components: CLO - Third party materials and Open Source components in 17.1 - V1.1.pdf
17.1 Requirements and Priorities: 17.1 Requirements and Priorities Final.xlsx
| Topic | Average | U.Mich. | Sanofi | Pfizer | Roche | IOI | Takeda | AbbVie | The Hyve | Perkin Elmer | Thompson Reuters | Boehringer | Rancho Biosciences | Average | |||||||||||||||||
| Clinical Data | |||||||||||||||||||||||||||||||
| Platform robustness and performance. | 3.75 | 4 | 4 | 4 | 3 | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 2 | 3.75 | |||||||||||||||||
| Longitudinal data support | 3.17 | 4 | 4 | 4 | 4 | 1 | 1 | 4 | 4 | 1 | 4 | 3 | 4 | 3.17 | |||||||||||||||||
| Upgrade path | 2.92 | 3 | 3 | 4 | 1 | 1 | 4 | 4 | 4 | 1 | 4 | 2 | 4 | 2.92 | |||||||||||||||||
| Continuation of SmartR or SmartR like type of plugin visual analytic interface such as Spotfire and others. | 3.00 | 4 | 4 | 4 | 1 | 1 | 2 | 4 | 4 | 4 | 4 | 3 | 1 | 3.00 | |||||||||||||||||
| Cross Study Support | 2.92 | 4 | 4 | 1 | 4 | 1 | 4 | 4 | 4 | 1 | 1 | 3 | 4 | 2.92 | |||||||||||||||||
| Enable meta analysis, eg virtual cohort normalization | 2.08 | 3 | 2 | 1 | 3 | 1 | 4 | 1 | 4 | 1 | 1 | 3 | 1 | 2.08 | |||||||||||||||||
| Ability to link files to a specific patient. | 1.92 | 4 | 2 | 1 | 1 | 1 | 3 | 4 | 2 | 1 | 2 | 1 | 1 | 1.92 | |||||||||||||||||
| Genomic Data | |||||||||||||||||||||||||||||||
| Support for high volume variant data | 3.083333333 | 4 | 4 | 1 | 4 | 1 | 3 | 4 | 4 | 1 | 4 | 3 | 4 | 3.08 | |||||||||||||||||
| Support for ARVADOS (Mongo DB or similar platform e.g. iRODS) | 2.333333333 | 1 | 4 | 1 | 4 | 1 | 1 | 4 | 2 | 1 | 1 | 4 | 4 | 2.33 | |||||||||||||||||
| FASTQ, SAM/BAM file store | 2.166666667 | 1 | 1 | 1 | 4 | 1 | 1 | 4 | 2 | 1 | 2 | 4 | 4 | 2.17 | |||||||||||||||||
| GWAS analysis results | 1.916666667 | 1 | 1 | 1 | 1 | 1 | 4 | 1 | 2 | 1 | 4 | 2 | 4 | 1.92 | |||||||||||||||||
| Imputed data | 1.583333333 | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 4 | 1 | 2 | 1 | 1 | 1.58 | |||||||||||||||||
| Variant Functional Annotation | 2.25 | 1 | 1 | 1 | 3 | 1 | 4 | 1 | 4 | 1 | 3 | 3 | 4 | 2.25 | |||||||||||||||||
| ADAM stack | 1.666666667 | 3 | 1 | 1 | 4 | 1 | 1 | 1 | 4 | 1 | 1 | 1 | 1 | 1.67 | |||||||||||||||||
| Support for somatic and germline variants | 1.916666667 | 2 | 2 | 1 | 3 | 1 | 4 | 1 | 1 | 1 | 4 | 2 | 1 | 1.92 | |||||||||||||||||
| Support for GA4GH API | 2.333333333 | 4 | 2 | 1 | 4 | 1 | 1 | 1 | 4 | 1 | 2 | 3 | 4 | 2.33 | |||||||||||||||||
| Make expression data easy to normalize (e.g. in a cross-study analysis) | 1.75 | 2 | 1 | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 2 | 3 | 4 | 1.75 | |||||||||||||||||
| Ability to rerun mutation calling pipelines to update the data stored in tranSMART | 1.25 | 1 | 1 | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1.25 | |||||||||||||||||
| Ability to further process data belonging to chromosomal loci and store into RDBMS (eg Oracle) | 1.5 | 1 | 1 | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 2 | 4 | 1 | 1.50 | |||||||||||||||||
| Historization of data, access to updated data without data reload. | 1.666666667 | 1 | 1 | 1 | 3 | 1 | 2 | 2 | 1 | 1 | 2 | 1 | 4 | 1.67 | |||||||||||||||||
| Integrated graf based database, be able to call up a single gene within one graph (NEO4J) Lightning | 1.416666667 | 1 | 1 | 1 | 3 | 1 | 1 | 3 | 1 | 1 | 1 | 2 | 1 | 1.42 | |||||||||||||||||
| Support for Epigenomics | 1.75 | 4 | 1 | 1 | 1 | 1 | 1 | 3 | 3 | 1 | 1 | 3 | 1 | 1.75 | |||||||||||||||||
| interoperability with biobanking/LIMS systems | 1.833333333 | 4 | 1 | 1 | 1 | 1 | 1 | 4 | 3 | 1 | 3 | 1 | 1 | 1.83 | |||||||||||||||||
| Ontology | |||||||||||||||||||||||||||||||
| Support use of standard and internal proprietary ontologies | 2.75 | 4 | 2 | 1 | 4 | 1 | 4 | 4 | 4 | 1 | 3 | 4 | 1 | 2.75 | |||||||||||||||||
| ETL | |||||||||||||||||||||||||||||||
| Better support for robust ETL | 2.333333333 | 1 | 4 | 1 | 3 | 4 | 4 | 1 | 4 | 1 | 1 | 3 | 1 | 2.33 | |||||||||||||||||
| Security | |||||||||||||||||||||||||||||||
| Finer grained access control | 2.583333333 | 4 | 1 | 1 | 4 | 1 | 1 | 4 | 4 | 1 | 3 | 3 | 4 | 2.58 | |||||||||||||||||
| Integration with LDAP/ADS | 1.916666667 | 1 | 4 | 1 | 1 | 1 | 1 | 4 | 1 | 1 | 1 | 3 | 4 | 1.92 | |||||||||||||||||
| Access control integrated with informed consent | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.00 | |||||||||||||||||
| Data | |||||||||||||||||||||||||||||||
| More preloaded/api to trial and genomic data | 1.916666667 | 1 | 1 | 1 | 4 | 1 | 1 | 1 | 4 | 1 | 1 | 3 | 4 | 1.92 | |||||||||||||||||
