Semantic Infrastructure Services |
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Semantic Infrastructure Domain User Story 6:
Discover and orchestrate services to achieve LS research goals; e.g. start with a hypothesis, identify relevant services that provides the necessary analysis and data, create the worklow/pipeline, report findings.
Domain Description Revised From ICRi Use Cases
A scientist is trying to identify a new genetic biomarker for HER2/neu negative stage I breast cancer patients. The scientist queries for HER2/neu negative tissue specimens of Stage I breast cancer patients using services at his/her cancer center 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 he 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.
Technical Description
The scientist in this case is trying to develop a workflow that will assist biomarker discovery research. S/he first needs to discover the services that provide biospecimen information with the phenotype s/he is looking for (e.g. HER2/neu negative stage I breast cancer) and then the microarray experiment information. Then he needs to create a workflow (orchestrate services) where the input is a phenotype for biospecimens and output is a set of gene of interest. These steps require the support for standard terminologies (and services) and syntaxes to best describe the services' behavior and static data. Furthermore they require inference engines that relates the semantic and syntactic metadata for the inputs/outputs of the services to "assist" scientist to identify what service can be part of the workflow.
Cross Reference
Support development of workflows:
Forum Request
Requirements Input
Requirements Input
