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Search Overview
searching:overviewThe The search and browse functions in caIntegrator allow you to search for subject annotation data, genomic data or imaging data that were uploaded into the application as part of a study. When gene expression and imaging data are uploaded into a caIntegrator study, mapping files that correlate sample IDs in those files to subject IDs (patient IDs) in the subject annotation data file must also be uploaded. When you launch a search, caIntegrator finds and integrates the subject annotation, genomic and imaging data based on the mapping files and the criteria that you define in the search query.
In a search query, you can specify criteria for just one of the data types, or configure complex search criteria that join two or three data types. The available criteria for the query were defined when the study was deployed.
The basic workflow for a study search follows these steps:
- Select the study to be searched.
- Select one data type:
Wiki Markup *\[Annotations\]* – Annotation data can be labeled 'default' or given the annotation 'group' name when annotation groups are specified by the manager, for example, chronologic, therapy, diagnosis, patient, or other annotation group types. This selection searches one or more uploaded CSV files for data identifiers or annotations (column headers) specified during study creation.
Wiki Markup *\[Genomic\]* – Genomic data can be gene expression or copy number data. This selection searches caArray experiments samples uploaded in the study for gene expression or copy number data by gene name, reporter ID, chromosome number, chromosome coordinates and/or segmentation values representing amplification or deletion.
- Image Data – Searches NBIA imaging files uploaded in the study for image annotations or links to images, identified by subject identifiers or image series IDs.
- Define criteria for the search in the selected data type and run the search.
- For a more complex search, select multiple criteria from more than one data type.
- Specify whether you want subject/imaging annotations to display or genomic data to display.
- Review search results.
- Configure results column and sorting display settings. You can do this before or after you run a search. If you choose to do it after, you must re-run the search.
- Download annotation search results as a CSV file. The CSV file contains only the data you specified in the annotation and display configurations.
- Follow links to NBIA in the search results to view or download images located in the search.
Searching a Study
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To initiate a search of all annotations and/or other data in a study, follow these steps:
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