Search for Data

In this section, we present the server-wide search in OMERO. This is an additional option for data management, which complements filtering, mining and using annotations to organize your data, which are described elsewhere in Annotate Data and Filter using Annotations.

Description

We will show:

  • How to start a search in OMERO.web.
  • How to search for objects annotated with a specific Key-Value Pair.
  • How to use Advanced Search.
    • How to search for terms in specific fields e.g. “name”.
    • How to combine search terms using AND.
    • How to combine search terms using AND NOT.

Setup

  • The data used are from the siRNAi-HeLa folder.
  • The Key-Value Pairs were added to the images in the siRNAi-HeLa Dataset for all users using the script key_value_pairs.py.

Step-by-Step

  1. Open a browser and enter the provided URL
  2. Connect using the provided credentials
  3. Enter mitomycin-A into the search box in the top right corner of the webclient image1
  4. Press Enter.
  5. The search results will show any objects e.g. Images or Datasets, which have anywhere the string mitomycin-A.
  6. Several images should be found, from two different datasets.
  7. Refine the search now for only Key-Value Pairs which have the key mitomycin-A and value 0mM by entering mitomycin-A:0mM into the search box and pressing Enter.
  8. Now you should find only 21 images.
  9. Click on the Advanced search tab in the search results.
  10. Enter mitomycin-A:0mM AND name:VRAQ which will narrow down your previous search for mitomycin-A:0mM to objects which also have VRAQ in their name.
  11. You should see 5 results now.
  12. Enter mitomycin-A:0mM AND NOT name:VRAQ which will reject all objects which have VRAQ in their name and find only the ones which are named differently.
  13. You should see 16 results now.
  14. Click on the Browse link image2in one search result line of the last image (in the right-hand part of the centre pane) to navigate back to the main webclient.