Search Rhea using chemical classes (ChEBI)

You can search for Rhea reactions using chemical classes from the CHEBI dictionary of small molecules.

Content:

Search ChEBI classification by name

For instance, without any prior knowledge, the simplest way to retrieve Rhea reactions involving lipids is to enter the term lipid in the text field and click the Search button.

The Rhea search engine screens the whole ChEBI ontology and returns not only those reactions where participants directly match the query but also reactions where participants have a parent compound class that matches the query.
Hence, searching for 'lipid' allows retrieving all reactions with participants that are specific forms of the compound class 'lipid' (CHEBI:18059) even when this ChEBI entity has no structure representation and is not directly used as a reaction participant.
For instance, 'a fatty acid' is a 'lipid', hence, when searching for 'lipid', Rhea also retrieves reactions with 'a fatty acid' (CHEBI:28868), a lipid class directly used as reaction participant as well as its more specific forms like 'hexadecanoate' (CHEBI:7896) or '(8R)-hydroperoxy-(5Z,9E,11Z,14Z)-eicosatetraenoate' (CHEBI:57447).

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The result for lipid search is a list of Rhea reactions presented as a table.
You can refine your search, filter the results by reaction types or enzyme classification, customize the result table and download it.

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If you want to browse the resulting list of ChEBI entities that match your query, in our example those ChEBIs matching 'lipid', and refine your search, click Choose molecule for lipids in the menu that appears on the left side of the result page. A pop-up window will appear and will display the list of ChEBI entities (reaction participants or classes of molecules) that have a name or a synonym matching 'lipid'.

The first item in the results table is 'lipid'. By clicking the number of associated Rhea reactions next to the ChEBI identifier, you will be redirected to a new results page. The search field now displays chebi:"lipid [18059]" and you will notice that the Refine search option in the menu disappears since you are now performing a search by a CHEBI identifier.

Use the back button of your browser to retrieve the results table containing the ChEBI compounds matching 'lipid' again. If you want to restrict this list to the ChEBI entities that are reaction participants, i.e. the ChEBI entities directly used in a Rhea reaction, you can select the box at the top of the results list to Exclude those classes that are not themselves reaction participants. You will observe that the number of results is reduced.
Next, let's consider the first molecule in the reduced list; 'a hydroperoxy-polyunsaturated fatty acid [CHEBI:61051]'. By clicking the number of associated Rhea reactions you will be redirected to a new results page corresponding to the search chebi:"a hydroperoxy-polyunsaturated fatty acid [61051]"]".

Next to the text search field, you can click the link "Advanced search" to access the advanced text search which, by default, is pre-filled with your current search, which is "a hydroperoxy-polyunsaturated fatty acid [61051]" in our current example. You can then select the box exact ChEBI search and click the 'Search' button. The query changes to chebi_exact:"a hydroperoxy-polyunsaturated fatty acid [61051]" and the number of results is reduced to only one reaction (as of Rhea release 114). This means that ChEBI:61051 is a compound class that is directly used in one reaction, and it has more specific forms (i.e. it has child compounds according to the ChEBI hierarchy) that are reaction participants too.

Term suggestions in the advanced text search

You can use the advanced text search to refine your search by using specific topics. Click the red All box to display the list of available topics.
For instance, select the topic ChEBI and enter 'fatty' in the search box, and you will see a list of suggested terms as shown in the following figure. Note that only ChEBI compounds that are used in Rhea are suggested.

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