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- High change semantic environment where novel concepts which have not been previously characterized need to be described
- Computational or analytical workflow compositions processing raw data to derive knowledge
- Description of statistical processes related to computational processes to achieve the above
- Working with the platform, enabling semantic description of raw data potentially of large volume (for example next-gen sequencing, imaging data)
- Support of provenance to trace data acquisition and data ownership and also to achieve reproducibility of analytical results
As a starting point, the requirements gathering effort will be informed by past and current related efforts in caBIG®, such as:
- The recent Semantic Infrastructure Requirements Elicitation effort
- The caBIO ECCF service specification project on molecular and pathway annotation services from the Integrated Cancer Research (ICR) Workspace
- Annotation and Image Markup (AIM) from the In-Vivo Imaging (IMAG) Workspace for both radiological and pathologic images
- Work on "Dynamic Extensions" from the Tissue Banks and Pathology Tools (TBPT) Workspace
Nevertheless, further input from community feedback based on this roadmap document is anticipated, as well as further input from the life sciences workgroup within the Semantic Infrastructure 2.0 Inception effort. This effort will involve both requirements gathering and prototype tool building.
This section highlights some key use cases that depend on data semantics. These use cases provide a representative set to capture the requirements of the life sciences domain. A comprehensive set of all life sciences use-cases can be found at on the ICRi WG GForge wiki. This section includes the following:
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This section highlights some key use cases that depend on data semantics. These use cases provide a representative set to capture the requirements of the life sciences domain. A comprehensive set of all life sciences use-cases can be found at on the ICRi WG GForge wiki. This section includes the following:
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However, part of the Infrastructure Inception activities include Prototyping Orchestrations and/or Choreographies (including Life Science workflows) as well as outreach to community to address other major use cases and requirements. The life sciences communities are engaged with the Roadmap inception efforts now. Lymphoma "workflow" use cases and requirements The use cases and requirements gathering described above being outlined and written in draft at links above and will be migrated to relevant sections in the Roadmaps when mature. |
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Discovering a biomarker
A scientist is trying to identify a new genetic biomarker for HER2/neu negative stage I breast cancer patients. Using a caGrid-aware client, the scientist queries for HER2/neu negative tissue specimens of Stage I breast cancer patients at LCCC (University of North Carolina Lineberger Comprehensive Cancer Center-NC Cancer Hospital) that also have corresponding microarray experiments. Analysis of the microarray experiments identify genes that are significantly over-expressed and under-expressed in a number of cases. The scientist decides that these results are significant, and related literature suggest a hypothesis that gene A may serve as a biomarker in HER2/neu negative Stage I breast cancer. To validate this hypothesis in a significant number of cases the scientist needs a larger data set, so the scientist queries for all the HER2/neu negative specimens of Stage I breast cancer patients with corresponding microarray data and also for appropriate control data from other cancer centers. After retrieving the microarray experiments the scientist analyzes the data for over-expression of genes A.
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