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Ontology Term Search

last updated at 2022-09-19

Altough i will mostly talk about the Ontology term search on this page, it will also feature useful information about term search related to the Building Blocks page. Such general applicable information will be listed under General.

Ontologies are controlled vocabularies of Terms. Most of these Terms feature a name, a unique identifier and a description. We use these Ontology Terms for workflow description to utilize the benefits of a unified language in terms of machine-readability and reproducibility, following FAIR principles.

General

You can find ontology term search fields on the Building Blocks and on the Terms tab in the navbar.

Features:


Term Insert

You can find this function on the Terms tab in the navbar. Use this function to insert terms in an ISA-Tab conform way, for example for Swate building blocks.


Relationship-Directed Search Relationship-Directed Search Theory

Ontology terms contain different types of relationships between each other. For example is_a, part_of, xref relationships. Swate and the SwateDB utilize these relationships to provide the user with a predefined set of terms as most likely search requests.

Let's look at this with an example:

Source Name Component [instrument model] Term Source REF (MS:1000031) Term Accession Number (MS:1000031) Sample Name

If a user wants to fill in Component [instrument model] then they are most likely looking for the instrument model used in their experimental workflow. Here for example the instrument model series and the exact instrument models are connected to instrument model (MS:1000031) via is_a relationships.


Relationship-Directed Search Usage
  1. Choose any descriptive building block (all building blocks with 3 or more columns work, e.g. Protocol Type) and select any number of rows in the main column.
  2. Click in the ontology term search field under the Terms tab in the navbar.
    • This will create an additional field in front of the search field with the column header term inside.
    • For the example table under theory one would click in any row below Parameter [instrument model] and then after clicking into the searchfield, one should see instrument model. In this case we call instrument model the parent term and all related terms child terms.
  3. While the slider next to Use related term directed search is turned on, you will now ONLY search through related terms.
    • 👀 You can also explore all available child terms, by double clicking into the empty search field.
  4. You can turn this feature off with the slider next to Use related term directed search.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
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