Create Root-Level Specimen - A cancer patient volunteers to participate in a clinical trial. When the patient is accepted to the trial, a registered nurse registers the patient. The system automatically requests a new identifier from the specimen identifier service and assigns the grid-unique identifier to identify the patient in the study on the grid. This identifier is stored as a root-level identifier (the identifier has no parent specimen). The root is available to be associated with children any time a specimen is collected from the patient.
Create Child-Level Specimen - New Specimen from a Study Participant: A cancer patient is scheduled for a treatment regimen that involves specimen collection. The researcher schedules a specimen collection through a grid calendar. A grid-unique identifier is automatically created for each sample that is scheduled for collection (with "expected" as a qualifier) and is added to the traceability tree as a child of the patient's grid-unique identifier. The morning of the scheduled collection, a red-top tube and yellow-top tube are created with the specimen identifiers printed along with the associated bar code directly on the vial. When the patient arrives for the scheduled blood collection, the lab technician collects the specimens in the marked tubes. The technician records the storage conditions of the specimen, which will be associated with the specimen identifier. The technician also changes the status of the specimen from "expected" to "existing."
Create Child-Level Specimen - Shipping to a New Institution: A lab researcher reads a paper published in a peer-reviewed journal and is interested in the results. He designs a study and uses the paper as a reference to the biobank from which he can obtain the required tissue samples. Following institution procedures, the biobank personnel checks with the tissue-use committee to see if the samples can be shipped. Upon approval, the biobank technologist updates the inventory record in the grid-enabled specimen management system, indicating the specimen is removed from storage for shipment. The system automatically generates a new identifier for the specimen, making it a child of the old specimen. The technician then replaces the old identifier on the tube with the new identifier before shipping the specimen.
Create Child-Level Specimen - Modifying the Specimen: A patient with leukemia is registered in a clinical trial has donated a blood sample that has a unique identifier associated with it at the time of the draw. A researcher is interested in a particular gene sequence in cancer patients and has received an aliquot of the blood sample appropriately from a biobank. The researcher logs into caArray and indicates she is creating a DNA extract from the sample. The system automatically generates a grid-unique identifier for the DNA and associates it as a child of the blood specimen. The researcher then adds details of storage conditions for the DNA.
Culling a Specimen - A biobank receives a collection of tumor blocks from a breast cancer study. Several slices of the blocks are distributed for research studies, each slice with a unique identifier. After several years, the biobank decides to cull its collection, and the tumor block collection is marked for culling in the specimen management system. The physical specimen is destroyed, and the identifier is marked as "unavailable," but the traceability tree is maintained.
Search History of Specimen - A researcher reads an article and identifies a specimen of interest for an experiment related to her area of research. The data from the study has been published and is made available on the grid. She orders the specimen from the author of the article, but is unable to repeat the experimental results. Suspecting the specimen has not been carefully handled, the researcher searches the history of the specimen and orders a new sample from the originator. With this sample, she is able to duplicate results.
Acquire Source Annotation from External Source - The general ability to acquire tissue annotation from an external source is desired. Whether through navigation of caTissue directly in caArray or The minimum set of annotation to support MIAME will be exposed so that the data pulled in will conform to the standard and allow for expedient searching of caArray as a portion of the data will be moved. Non-caTissue repositories that contain the information could also be used - though their integration is not directly supported by caArray through the user interface.