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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.
Wiki Markup \[PatrickBaris\] This is use acase is repeatoverlapping ofwith "Search for all "pre-cancerous" biospecimens.." thatand are"Automatically availablediscover foranalytical sharingsteps at Washington University, Thomas Jefferson University, and Fox Chase Cancer Center."?for Illumina.." examples above
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_Domain Description \[ |
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Domain Description: Forms provide a convenient paper-like electronic mechanism to capture data in a structured way. For example, when a patient is placed on a clinical trial, data about the patient's demographics and eligibility for the trial need to be captured. The trial investigator sits with the forms curator to generate this case report form. The forms curator searches for existing demographics forms and form modules, and the investigator reviews them. They identify an appropriate set of questions, and include them in the case report form. They then move onto the eligibility checklist. The investigator drafted the checklist, and it has been approved by the IRB. The forms curator begins keying in the questions, some of which are identified as existing questions and reused, others of which are created completely new. The form is marked complete and is available by the clinical research staff for gathering and enrolling new patients.
Technical Description: Forms are a collection of data elements annotated and grouped within the metadata repository. The forms curator can search for existing forms and form modules (portions of a form) by question text, annotations, etc. These can be reused by reference, or imported and modified. When new data elements are being curated, the form curator can search the federated set of all metadata repositories to identify data elements for reuse. This can happen automatically within the curation tooling or explicitly through the metadata web interface. The final CRF is saved and annotated within the local metadata repository.
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: Support development of workflows:
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