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.

Resources

• Documentation:

  • Search

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

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.

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. This should narrow down your search and find less results compared with the previous case.

9. Click on the Browse link in one search result line of the last image (in the right-hand part of the centre pane) to navigate back to the main webclient.

Advanced search

The Advanced search in OMERO.web gives the opportunity to construct queries with Lucene syntax. These queries will be sent into the OMERO search (which is based on Lucene) unparsed. The possibilities include using logical operators (AND, OR, NOT, see workflow below) or fuzzy search (see Search Examples below).

1. Still on the search results page, click on the Advanced tab in the upper part of the left-hand side pane.

   

2. 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.

3. 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.

Note

Spaces, stars, question marks and ^ characters are to be avoided in the Keys. If you already have these characters in Keys in your OMERO server, then try to replace them with underscores if you want to use the Search functionality on them. Spaces, stars, question marks and ^ characters in Values are acceptable, but should be avoided if possible, see Search Examples below.

Search examples

Considering the following setup of 13 separate images:

Images with Key-Value pairs

Image ID	Image Name	Key	Value
1	Aurora1	GFP H2B	2 uM
2	Aurora2	GFP^H2B	2 uM
3	Aurora3	H2B	2
4	Aurora4	H2B	4
5	Aurora5	GFP-H2B	2-uM
6	Aurora6	GFP-H2B	2 uM
7	Aurora7	GFP_H2B	2_uM
8	Aurora8	GFP^H2B	2^uM
9	GFP	none	none
10	uM	none	none
11	H2B	none	none
12	2	none	none
13	Aurora13	H2B	2 uM

Basic Search tab:

• GFP H2B:2 uM finds images 1,2,3,5,6,7,8,9,10. In that case, the query is interpreted as GFP OR H2B:2 OR uM.

• "GFP H2B":2 uM throws an error. Do not use quotes around Keys!

• GFP H2B:"2 uM" finds images 1,2,5,6,7,8,9. In that case, the query is interpreted as GFP OR H2B:2 uM which prevents finding of image 3 with Value 2.

• GFP^H2B:2 uM finds images 1,2,3,5,6,7,8,9,10. In that case, the query is interpreted as GFP OR H2B:2 OR uM.

• H2B:2 finds image 3.

• H2B:4 finds image 4.

• GFP-H2B:2 uM finds images 1,2,5,6,7,8,10.

• GFP-H2B:2-uM finds images 5,6.

• GFP-H2B:"2-uM" finds images 5,6.

• GFP-H2B:"2 uM" finds images 5,6.

• GFP-H2B:"2_uM" finds images 5,6.

• GFP_H2B:2_uM finds image 7.

• GFP^H2B:2^uM finds images 1,2,3,5,6,7,8,9,10.

• GFP finds images 1,2,5,6,7,8,9.

• GFP with checkbox Name under Restricted by Field section checked finds image 9.

• uM with checkbox Name under Restricted by Field section checked finds image 10.

• H2B with checkbox Name under Restricted by Field section checked finds image 11.

• 2 with checkbox Name under Restricted by Field section checked finds image 12.

• GFP*:2 uM throws an error. Do not use wildcards in Keys!

• H2B:* finds images 3,4,13. The wildcard can be used in Values.

• H2B:2* finds images 3,13.

Advanced tab:

• GFP^H2B:2^uM and GFP^H2B:2 uM throw an error in Advanced tab. This is due to the different interpretation of the ^ character between the basic Search and Advanced tabs.

• As there is no Name checkbox in the Advanced tab, use name:GFP instead, which finds image 9.

• Aurora2~0.85 finds 1,2,3,4,5,6,7,8. The ~ denotes a fuzzy search, which is possible only in Advanced tab. The number behind the ~ indicates the precision with which the result must match the query.

• Aurora2~0.86 finds image 2.

The behaviour for the rest of the query examples in Advanced tab is the same as listed above for the basic Search tab.