Docs04 Ontology Term Search

⚠️ This wiki is deprecated, look here for the new wiki: https://nfdi4plants.github.io/Swate-docs/docs/UserDocs/Docs04-Ontology-Term-Search.html

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.

1. General
2. Term Insert
3. Relationship-Directed Search
   1. Theory
   2. Usage

General

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

Features:

• Access to the SwateDB with a list of established, external ontologies deemed fit for use in plant science. In addition we feature our very own ontology nfdi4pso, which we extend with missing but necessary terms.
  • External ontologies are taken from the obofoundry and updated regularly.
  • 👀 You can always ask us to add existing terms/ontologies or even new terms to our database. If you wish to do so, you can fill out an issue here.
• Search through database with autocomplete search on term names.
• If you already know what you are searching for, you can also type in the term unique identifier (example: MS:1000031).
  • To trigger this search the input must match the Swate Regex pattern for term accessions.
• To execute the search query on any search text again after closing the dropdown with the search results double click into the search field.
• You can also use the advanced term search for a more refined search approach. Just click on the blue link close to the related search field.

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.

• Type in the search field to trigger the auto-complete function and find terms. Select the term you want or follow the information under General for more information.
• You can now insert the chosen term anywhere in Excel, not only inside of a Swate annotation table.

  • Terms will be added to all selected rows in the format:

    | term name | term source ontology | purl.obolibrary.org link for term |

    This always done for the next three Excel columns including the selected column.

• You can also click on the Copy to Clipboard-button next to the insert-term-button. This will copy the term information (name, source ontology, purl link) to your clipboard and you can paste it into Excel with Ctrl + V. This will enable you to paste the information spread over three rows instead of columns. This works only for a single column.

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

If a user wants to fill in Parameter [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 (Parameter, Characteristic, Factor) 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.